fix(server): log skip-embedding count and table-not-found swallow path

Addresses review feedback on PR #823:
- Log count of already-embedded nodes when skipNodeIds is populated
  (aids debugging if Kuzu driver row shape changes).
- Log when the 'table does not exist' swallow path fires so ops can
  catch it if Kuzu ever changes error wording.
- Document the {} config positional argument with an inline comment
  referencing the runEmbeddingPipeline signature.

.cursor/.gitignore

@@ -1 +0,0 @@
-plans/

.dockerignore

@@ -1,19 +0,0 @@
-.git
-.gitignore
-.DS_Store
-
-node_modules
-**/node_modules
-
-dist
-**/dist
-coverage
-**/coverage
-
-.env
-.env.local
-.env.*.local
-
-.gitnexus
-gitnexus-web/playwright-report
-gitnexus-web/test-results

.env.example

@@ -1,15 +0,0 @@
-# Images (signed Cosign keyless on every push from main / vX.Y.Z tags)
-SERVER_IMAGE=ghcr.io/abhigyanpatwari/gitnexus:latest
-WEB_IMAGE=ghcr.io/abhigyanpatwari/gitnexus-web:latest
-
-# Container names
-SERVER_CONTAINER_NAME=gitnexus-server
-WEB_CONTAINER_NAME=gitnexus-web
-
-# Host ports — the web UI expects the server on http://localhost:4747 by default.
-SERVER_HOST_PORT=4747
-WEB_HOST_PORT=4173
-
-# Optional read-only mount, exposed to the server as /workspace.
-# Override with the directory that contains the repos you want to index.
-WORKSPACE_DIR=./

.github/dependabot.yml

@@ -1,75 +0,0 @@
-version: 2
-updates:
-  # Keep third-party Actions SHA pins current. See CONTRIBUTING.md — when
-  # reviewing these bumps, verify the SHA corresponds to the claimed tag by
-  # running `gh api repos/<owner>/<action>/git/refs/tags/<tag>` before merge.
-  - package-ecosystem: github-actions
-    directory: /
-    schedule:
-      interval: weekly
-    open-pull-requests-limit: 5
-    commit-message:
-      prefix: chore
-      include: scope
-    labels:
-      - dependencies
-      - ci
-
-  # Gitnexus npm deps — tree-sitter grammars checked daily so we catch
-  # new releases that unblock the tree-sitter 0.25 upgrade ASAP. Grammars
-  # are grouped so lockstep bumps produce a single PR. The tree-sitter
-  # RUNTIME is pinned — upgrade deliberately via the drift check workflow.
-  # See .github/scripts/check-tree-sitter-upgrade-readiness.py for
-  # the upgrade readiness tracker.
-  - package-ecosystem: npm
-    directory: /gitnexus
-    schedule:
-      interval: daily
-    open-pull-requests-limit: 10
-    commit-message:
-      prefix: chore(deps)
-      include: scope
-    labels:
-      - dependencies
-    groups:
-      tree-sitter-grammars:
-        patterns:
-          - tree-sitter-*
-        exclude-patterns:
-          - tree-sitter
-          - tree-sitter-cli
-    ignore:
-      # Pin the tree-sitter runtime at 0.21.x until the drift check
-      # reports all grammars are peer-dep compatible with 0.25.
-      - dependency-name: tree-sitter
-        update-types:
-          - version-update:semver-major
-          - version-update:semver-minor
-      # tree-sitter-cli follows the runtime's version cadence. Bump when
-      # regenerating vendor/tree-sitter-proto/src/parser.c, not on a schedule.
-      - dependency-name: tree-sitter-cli
-
-  # gitnexus-web (thin frontend client).
-  - package-ecosystem: npm
-    directory: /gitnexus-web
-    schedule:
-      interval: weekly
-    open-pull-requests-limit: 5
-    commit-message:
-      prefix: chore(deps)
-      include: scope
-    labels:
-      - dependencies
-      - frontend
-
-  # Shared types package.
-  - package-ecosystem: npm
-    directory: /gitnexus-shared
-    schedule:
-      interval: weekly
-    open-pull-requests-limit: 5
-    commit-message:
-      prefix: chore(deps)
-      include: scope
-    labels:
-      - dependencies

.github/release-drafter.yml

@@ -1,53 +0,0 @@
-# release-drafter config — used only for PR autolabeling by
-# `.github/workflows/pr-labeler.yml` (the workflow passes `disable-releaser: true`,
-# so the draft-release side of release-drafter never runs).
-#
-# The labels applied here are the same ones `.github/release.yml` maps to
-# categorized release-notes sections.
-#
-# `sync-labels: true` removes managed autolabels that no longer match the PR —
-# critical for the breaking-change case: if a PR title drops the `!` or the body
-# drops `BREAKING CHANGE:`, the `breaking` label is pulled off automatically.
-
-# Required by release-drafter; not used because releaser is disabled.
-name-template: 'unused'
-tag-template: 'unused'
-template: |
-  $CHANGES
-
-sync-labels: true
-
-autolabeler:
-  - label: enhancement
-    title:
-      - '/^feat(\([^)]+\))?!?:/i'
-  - label: bug
-    title:
-      - '/^fix(\([^)]+\))?!?:/i'
-  - label: performance
-    title:
-      - '/^perf(\([^)]+\))?!?:/i'
-  - label: refactor
-    title:
-      - '/^refactor(\([^)]+\))?!?:/i'
-  - label: documentation
-    title:
-      - '/^docs(\([^)]+\))?!?:/i'
-  - label: test
-    title:
-      - '/^test(\([^)]+\))?!?:/i'
-  - label: ci
-    title:
-      - '/^ci(\([^)]+\))?!?:/i'
-  - label: dependencies
-    title:
-      - '/^(build|deps)(\([^)]+\))?!?:/i'
-  - label: chore
-    title:
-      - '/^(chore|revert)(\([^)]+\))?!?:/i'
-  # Breaking-change marker: either `!` in the type prefix or `BREAKING CHANGE:` in body.
-  - label: breaking
-    title:
-      - '/^[a-z]+(\([^)]+\))?!:/i'
-    body:
-      - '/BREAKING[ -]CHANGE:/i'

.github/scripts/check-tree-sitter-upgrade-readiness.py

@@ -1,358 +0,0 @@
-#!/usr/bin/env python3
-"""Monitor tree-sitter 0.25 upgrade readiness.
-
-Tracks two things Dependabot cannot see:
-
-  1. Peer-dep compatibility. Each tree-sitter-* grammar declares a peer
-     dependency on the tree-sitter runtime. We want to know when every
-     grammar's *latest npm release* satisfies tree-sitter@0.25.0 so we
-     can upgrade without --legacy-peer-deps.
-
-  2. Vendored upstream drift. vendor/tree-sitter-proto/ is a snapshot of
-     coder3101/tree-sitter-proto's parser.c. When upstream moves, we want
-     to know whether we can pick it up.
-
-Invoked from .github/workflows/tree-sitter-upgrade-readiness.yml daily.
-Runs locally too:
-
-    python3 .github/scripts/check-tree-sitter-upgrade-readiness.py
-
-Outputs Markdown to stdout. Exit 0 when every grammar is upgrade-ready
-and the vendored proto is in sync. Exit 1 when blockers remain (the
-workflow uses this to open or update a tracking issue).
-
-No external deps -- stdlib only, so it runs on any vanilla runner.
-"""
-
-from __future__ import annotations
-
-import json
-import os
-import pathlib
-import re
-import sys
-import urllib.error
-import urllib.request
-
-REPO_ROOT = pathlib.Path(__file__).resolve().parents[2]
-GITNEXUS_DIR = REPO_ROOT / "gitnexus"
-VENDOR_PROTO_DIR = GITNEXUS_DIR / "vendor" / "tree-sitter-proto"
-
-# ── Upgrade target ──────────────────────────────────────────────────────
-# The runtime version we want to upgrade TO. Update this when the goal
-# changes (e.g. once 0.25 lands and we target 0.26).
-TARGET_RUNTIME = "0.25.0"
-TARGET_RUNTIME_MAJOR_MINOR = ".".join(TARGET_RUNTIME.split(".")[:2])
-
-# Tree-sitter runtime -> (min_abi, max_abi) it can load. Only the current
-# and target entries matter; extend when changing TARGET_RUNTIME.
-RUNTIME_ABI_RANGES: dict[str, tuple[int, int]] = {
-    "0.21": (13, 14),
-    "0.25": (13, 15),
-}
-
-assert TARGET_RUNTIME_MAJOR_MINOR in RUNTIME_ABI_RANGES, (
-    f"RUNTIME_ABI_RANGES has no entry for {TARGET_RUNTIME_MAJOR_MINOR!r}. "
-    f"Add the ABI range after auditing the upstream release notes."
-)
-
-# Grammars we use. Values are the upstream GitHub repos to check for
-# unreleased ABI bumps (owner/repo, branch, parser.c path).
-GRAMMARS: dict[str, tuple[str, str, str]] = {
-    "tree-sitter-c":          ("tree-sitter/tree-sitter-c",          "master", "src/parser.c"),
-    "tree-sitter-c-sharp":    ("tree-sitter/tree-sitter-c-sharp",    "master", "src/parser.c"),
-    "tree-sitter-cpp":        ("tree-sitter/tree-sitter-cpp",        "master", "src/parser.c"),
-    "tree-sitter-dart":       ("UserNobody14/tree-sitter-dart",      "master", "src/parser.c"),
-    "tree-sitter-go":         ("tree-sitter/tree-sitter-go",         "master", "src/parser.c"),
-    "tree-sitter-java":       ("tree-sitter/tree-sitter-java",       "master", "src/parser.c"),
-    "tree-sitter-javascript": ("tree-sitter/tree-sitter-javascript", "master", "src/parser.c"),
-    "tree-sitter-kotlin":     ("fwcd/tree-sitter-kotlin",            "main",   "src/parser.c"),
-    "tree-sitter-php":        ("tree-sitter/tree-sitter-php",        "master", "php/src/parser.c"),
-    "tree-sitter-python":     ("tree-sitter/tree-sitter-python",     "master", "src/parser.c"),
-    "tree-sitter-ruby":       ("tree-sitter/tree-sitter-ruby",       "master", "src/parser.c"),
-    "tree-sitter-rust":       ("tree-sitter/tree-sitter-rust",       "master", "src/parser.c"),
-    "tree-sitter-swift":      ("alex-pinkus/tree-sitter-swift",      "main",   "src/parser.c"),
-    "tree-sitter-typescript": ("tree-sitter/tree-sitter-typescript", "master",  "typescript/src/parser.c"),
-}
-
-UPSTREAM_PROTO_OWNER = "coder3101"
-UPSTREAM_PROTO_REPO = "tree-sitter-proto"
-UPSTREAM_PROTO_BRANCH = "main"
-
-
-# ── Helpers ─────────────────────────────────────────────────────────────
-
-def read_current_runtime() -> str:
-    """Return the tree-sitter runtime version pinned in package.json (e.g. '0.21')."""
-    pkg = json.loads((GITNEXUS_DIR / "package.json").read_text())
-    raw = pkg["dependencies"]["tree-sitter"]
-    match = re.search(r"(\d+)\.(\d+)", raw)
-    if not match:
-        raise SystemExit(f"could not parse tree-sitter version: {raw!r}")
-    return f"{match.group(1)}.{match.group(2)}"
-
-
-def npm_view_json(pkg: str) -> dict | None:
-    """Fetch package metadata from the npm registry via HTTPS.
-
-    Uses the registry API directly so we don't depend on the npm CLI
-    being available (it's a batch file on Windows which complicates
-    subprocess calls).
-    """
-    url = f"https://registry.npmjs.org/{pkg}/latest"
-    try:
-        req = urllib.request.Request(url, headers={"Accept": "application/json"})
-        with urllib.request.urlopen(req, timeout=8) as resp:
-            return json.loads(resp.read().decode("utf-8"))
-    except (urllib.error.URLError, urllib.error.HTTPError, json.JSONDecodeError):
-        return None
-
-
-def satisfies_target(peer_range: str | None, target: str) -> bool:
-    """Check if a semver range like '^0.22.4' or '^0.25.0' satisfies the target.
-
-    Simple heuristic: extract the minimum version from the range and check
-    if target >= min. For caret ranges (^X.Y.Z), the upper bound is the
-    next major (for X>0) or next minor (for X==0). We check both bounds.
-    """
-    if peer_range is None:
-        # No peer dep declared = no constraint = compatible.
-        return True
-    match = re.search(r"(\d+)\.(\d+)\.(\d+)", peer_range)
-    if not match:
-        return False
-    min_major, min_minor, min_patch = int(match.group(1)), int(match.group(2)), int(match.group(3))
-
-    t_match = re.search(r"(\d+)\.(\d+)\.(\d+)", target)
-    if not t_match:
-        return False
-    t_major, t_minor, t_patch = int(t_match.group(1)), int(t_match.group(2)), int(t_match.group(3))
-
-    # Target must be >= minimum.
-    target_tuple = (t_major, t_minor, t_patch)
-    min_tuple = (min_major, min_minor, min_patch)
-    if target_tuple < min_tuple:
-        return False
-
-    # For caret ranges with major 0: ^0.X.Y allows [0.X.Y, 0.(X+1).0).
-    if peer_range.startswith("^") and min_major == 0:
-        if t_major != 0 or t_minor >= min_minor + 1:
-            return False
-    # For caret ranges with major >0: ^X.Y.Z allows [X.Y.Z, (X+1).0.0).
-    elif peer_range.startswith("^") and min_major > 0:
-        if t_major >= min_major + 1:
-            return False
-
-    return True
-
-
-_GITHUB_TOKEN = os.environ.get("GITHUB_TOKEN")
-
-
-def fetch_text(url: str, timeout: int = 8) -> str | None:
-    """Fetch a URL and return its text, or None on failure.
-
-    Adds an Authorization header for github.com URLs when GITHUB_TOKEN is
-    set (raises the rate limit from 60 to 5 000 requests/hour).
-    """
-    headers: dict[str, str] = {}
-    if _GITHUB_TOKEN and ("github.com" in url or "githubusercontent.com" in url):
-        headers["Authorization"] = f"Bearer {_GITHUB_TOKEN}"
-    try:
-        req = urllib.request.Request(url, headers=headers)
-        with urllib.request.urlopen(req, timeout=timeout) as resp:
-            return resp.read().decode("utf-8", errors="ignore")
-    except (urllib.error.URLError, urllib.error.HTTPError):
-        return None
-
-
-def extract_abi_from_text(text: str) -> int | None:
-    """Extract LANGUAGE_VERSION from parser.c text."""
-    match = re.search(r"#define\s+LANGUAGE_VERSION\s+(\d+)", text[:4096])
-    return int(match.group(1)) if match else None
-
-
-def extract_language_version(parser_c: pathlib.Path) -> int | None:
-    """Return the LANGUAGE_VERSION defined in a parser.c, or None if absent."""
-    if not parser_c.is_file():
-        return None
-    with parser_c.open("r", encoding="utf-8", errors="ignore") as fh:
-        head = fh.read(4096)
-    return extract_abi_from_text(head)
-
-
-def md_h(text: str, level: int = 2) -> str:
-    return f"{'#' * level} {text}\n"
-
-
-# ── Main ────────────────────────────────────────────────────────────────
-
-def main() -> int:
-    blockers: dict[str, str] = {}
-    lines: list[str] = []
-    lines.append(md_h("Tree-sitter 0.25 upgrade readiness", 1))
-    lines.append("")
-
-    current_runtime = read_current_runtime()
-    current_abi_range = RUNTIME_ABI_RANGES.get(current_runtime, (0, 0))
-    target_abi_range = RUNTIME_ABI_RANGES.get(TARGET_RUNTIME_MAJOR_MINOR, (0, 0))
-
-    lines.append(f"- Current runtime: `tree-sitter@{current_runtime}.x` (ABI {current_abi_range[0]}..{current_abi_range[1]})")
-    lines.append(f"- Target runtime: `tree-sitter@{TARGET_RUNTIME}` (ABI {target_abi_range[0]}..{target_abi_range[1]})")
-    lines.append("")
-
-    # ── Grammar peer-dep compatibility ───────────────────────────────
-    lines.append(md_h("Grammar compatibility", 2))
-    lines.append("| Grammar | npm latest | Peer dep | Satisfies 0.25? | ABI | Upstream ABI | Status |")
-    lines.append("|---|---|---|---|---|---|---|")
-
-    ready_count = 0
-    total_count = len(GRAMMARS)
-
-    for name, (upstream_repo, upstream_branch, parser_path) in sorted(GRAMMARS.items()):
-        # Fetch latest npm metadata.
-        info = npm_view_json(name)
-        fetch_failed = info is None
-        npm_version = "?"
-        peer_range = None
-        peer_optional = True
-        if info:
-            npm_version = info.get("version", "?")
-            peers = info.get("peerDependencies") or {}
-            peer_range = peers.get("tree-sitter")
-            meta = info.get("peerDependenciesMeta") or {}
-            ts_meta = meta.get("tree-sitter") or {}
-            peer_optional = ts_meta.get("optional", False) if peer_range else True
-
-        if fetch_failed:
-            peer_display = "? (fetch failed)"
-            compatible = False
-        else:
-            peer_display = peer_range or "none"
-            if peer_range and not peer_optional:
-                peer_display += " (required)"
-            compatible = satisfies_target(peer_range, TARGET_RUNTIME)
-
-        # Check installed ABI using the same parser_path from GRAMMARS.
-        installed_parser = GITNEXUS_DIR / "node_modules" / name / parser_path
-        if not installed_parser.is_file():
-            # Fallback to default location.
-            installed_parser = GITNEXUS_DIR / "node_modules" / name / "src" / "parser.c"
-        installed_abi = extract_language_version(installed_parser)
-        abi_display = str(installed_abi) if installed_abi else "?"
-
-        # Check upstream (main/master branch) ABI for unreleased work.
-        upstream_url = (
-            f"https://raw.githubusercontent.com/{upstream_repo}/"
-            f"{upstream_branch}/{parser_path}"
-        )
-        upstream_text = fetch_text(upstream_url)
-        upstream_abi = extract_abi_from_text(upstream_text) if upstream_text else None
-        upstream_abi_display = str(upstream_abi) if upstream_abi else "?"
-
-        # Determine status.
-        if fetch_failed:
-            status = "Unknown (fetch failed)"
-            blockers[name] = f"`{name}`: npm registry fetch failed — could not verify peer dep"
-        elif compatible:
-            status = "Ready"
-            ready_count += 1
-        elif upstream_abi and upstream_abi >= 15:
-            status = "Unreleased (ABI 15 on main)"
-            blockers[name] = f"`{name}`: ABI 15 on `{upstream_repo}` main but not published to npm"
-        else:
-            status = "Blocking"
-            blockers[name] = f"`{name}@{npm_version}`: peer `{peer_display}` incompatible with 0.25"
-
-        # Also check upstream package.json for relaxed peer dep.
-        if not compatible and not fetch_failed:
-            upstream_pkg_url = (
-                f"https://raw.githubusercontent.com/{upstream_repo}/"
-                f"{upstream_branch}/package.json"
-            )
-            upstream_pkg_text = fetch_text(upstream_pkg_url)
-            if upstream_pkg_text:
-                try:
-                    upstream_pkg = json.loads(upstream_pkg_text)
-                    upstream_peer = (upstream_pkg.get("peerDependencies") or {}).get("tree-sitter")
-                    if upstream_peer and satisfies_target(upstream_peer, TARGET_RUNTIME):
-                        status = "Unreleased (peer relaxed on main)"
-                        blockers[name] = f"`{name}`: peer dep relaxed on `{upstream_repo}` main but not published to npm"
-                except json.JSONDecodeError:
-                    pass
-
-        compat_icon = "Yes" if compatible else "**No**"
-        lines.append(
-            f"| `{name}` | {npm_version} | {peer_display} | {compat_icon} | {abi_display} | {upstream_abi_display} | {status} |"
-        )
-
-    lines.append("")
-    lines.append(f"**{ready_count}/{total_count}** grammars ready for `tree-sitter@{TARGET_RUNTIME}`.")
-    lines.append("")
-
-    # ── Vendored proto drift ─────────────────────────────────────────
-    lines.append(md_h("Vendored tree-sitter-proto", 2))
-    vendored_abi = extract_language_version(VENDOR_PROTO_DIR / "src" / "parser.c")
-
-    upstream_proto_url = (
-        f"https://raw.githubusercontent.com/{UPSTREAM_PROTO_OWNER}/"
-        f"{UPSTREAM_PROTO_REPO}/{UPSTREAM_PROTO_BRANCH}/src/parser.c"
-    )
-    upstream_proto_text = fetch_text(upstream_proto_url)
-    upstream_proto_abi = extract_abi_from_text(upstream_proto_text) if upstream_proto_text else None
-
-    sha_url = (
-        f"https://api.github.com/repos/{UPSTREAM_PROTO_OWNER}/"
-        f"{UPSTREAM_PROTO_REPO}/commits/{UPSTREAM_PROTO_BRANCH}"
-    )
-    sha_text = fetch_text(sha_url)
-    upstream_sha = "?"
-    if sha_text:
-        try:
-            upstream_sha = json.loads(sha_text).get("sha", "?")[:12]
-        except json.JSONDecodeError:
-            pass
-
-    local_proto_path = VENDOR_PROTO_DIR / "src" / "parser.c"
-    local_proto_text = local_proto_path.read_text(encoding="utf-8", errors="ignore") if local_proto_path.is_file() else ""
-    in_sync = bool(
-        upstream_proto_text
-        and local_proto_text.replace("\r\n", "\n")
-        == upstream_proto_text.replace("\r\n", "\n")
-    )
-
-    lines.append(f"- Upstream: `{UPSTREAM_PROTO_OWNER}/{UPSTREAM_PROTO_REPO}@{UPSTREAM_PROTO_BRANCH}` (HEAD `{upstream_sha}`)")
-    lines.append(f"- Upstream ABI: **{upstream_proto_abi}**")
-    lines.append(f"- Vendored ABI: **{vendored_abi}**")
-    lines.append(f"- In sync: {'yes' if in_sync else 'no — upstream has diverged'}")
-
-    if upstream_proto_abi and vendored_abi and upstream_proto_abi > vendored_abi:
-        can_upgrade = upstream_proto_abi <= target_abi_range[1]
-        lines.append(f"- Upstream ABI {upstream_proto_abi} {'is' if can_upgrade else 'is NOT'} within target runtime range ({target_abi_range[0]}..{target_abi_range[1]})")
-        if can_upgrade:
-            lines.append(f"- **Action:** after upgrading to tree-sitter@{TARGET_RUNTIME}, regenerate vendored parser.c from upstream `{upstream_sha}`")
-        else:
-            lines.append(f"- **Action:** wait for runtime upgrade beyond {TARGET_RUNTIME} that supports ABI {upstream_proto_abi}")
-            blockers["vendored-proto-abi"] = f"vendored tree-sitter-proto: upstream ABI {upstream_proto_abi} outside target range"
-    elif not in_sync:
-        lines.append("- **Action:** review upstream changes; vendored copy may need updating")
-        blockers["vendored-proto-sync"] = "vendored tree-sitter-proto: out of sync with upstream"
-
-    # ── Summary ──────────────────────────────────────────────────────
-    lines.append("")
-    lines.append(md_h("Summary", 2))
-    if blockers:
-        lines.append(f"**{len(blockers)} blocker(s) remaining:**\n")
-        for b in blockers.values():
-            lines.append(f"- {b}")
-        lines.append("")
-        lines.append("Upgrade to `tree-sitter@0.25` is **blocked**.")
-    else:
-        lines.append("All grammars are compatible. Upgrade to `tree-sitter@0.25` is **ready**.")
-
-    print("\n".join(lines))
-    return 1 if blockers else 0
-
-
-if __name__ == "__main__":
-    sys.exit(main())

.github/scripts/check-workflow-concurrency.py

@@ -1,173 +0,0 @@
-#!/usr/bin/env python3
-"""Enforce the GitHub Actions concurrency convention.
-
-See CONTRIBUTING.md -> "GitHub Actions — Concurrency Convention" for the rules.
-
-Invoked from .github/workflows/ci-quality.yml. Runs locally too:
-    python3 .github/scripts/check-workflow-concurrency.py .github/workflows
-
-Rules:
-  1. Every entry-point (non-reusable) workflow declares a top-level
-     `concurrency:` block.
-  2. Reusable workflows (on: workflow_call ONLY) do NOT declare one.
-  3. The `concurrency.group` expression MUST reference either
-     `${{ github.workflow }}` or a literal `CI-` prefix (the documented
-     ci.yml reusable-workflow-safe exception). This is checked by substring
-     containment rather than prefix match because ci.yml's group is a
-     conditional expression that resolves to a `CI-…` literal at runtime.
-
-We deliberately do not use a YAML library — keeps the script dependency-free
-on any vanilla runner. `on:` block parsing is line-based and handles both the
-flat (`on: workflow_call`) and mapping (`on:\n  workflow_call:`) forms.
-"""
-
-from __future__ import annotations
-
-import pathlib
-import re
-import sys
-
-
-REQUIRED_TOKENS = ("${{ github.workflow }}", "CI-")
-
-
-def is_reusable(lines: list[str]) -> bool:
-    """Return True iff the workflow's `on:` block names only `workflow_call`."""
-    in_on = False
-    on_indent: int | None = None
-    keys: list[str] = []
-
-    for raw in lines:
-        # Skip blank lines and comments
-        stripped = raw.strip()
-        if not stripped or stripped.startswith("#"):
-            continue
-
-        indent = len(raw) - len(raw.lstrip(" "))
-
-        if not in_on:
-            if raw.startswith("on:"):
-                remainder = raw[len("on:"):].strip()
-                if not remainder:
-                    # `on:` followed by indented mapping on next lines
-                    in_on = True
-                    on_indent = indent
-                    continue
-                if remainder.startswith("[") and remainder.endswith("]"):
-                    # Flow-style list: on: [workflow_call]
-                    items = [
-                        item.strip() for item in remainder.strip("[]").split(",")
-                    ]
-                    return items == ["workflow_call"]
-                # Scalar form: on: workflow_call  (or a single other event)
-                return remainder == "workflow_call"
-            continue
-
-        # Inside the `on:` block; stop when indentation returns to <= on_indent
-        if on_indent is not None and indent <= on_indent:
-            break
-
-        # Only consider keys at on_indent + indentation step (anything deeper
-        # is nested config like `types:`)
-        if ":" not in stripped:
-            continue
-        # Heuristic: first-level event keys are those with indent == on_indent + 2
-        # (the canonical step for a 2-space YAML doc). We collect all first-level
-        # keys by tracking the smallest indent seen inside the block.
-        keys.append((indent, stripped.split(":", 1)[0].strip()))
-
-    if not keys:
-        return False
-
-    # Take only the outermost-indented keys as the event list
-    min_indent = min(i for i, _ in keys)
-    events = [name for i, name in keys if i == min_indent]
-    return events == ["workflow_call"]
-
-
-CONCURRENCY_RE = re.compile(r"^concurrency:\s*$")
-GROUP_RE = re.compile(r"^\s+group:\s*(.+?)\s*$")
-
-
-def extract_group_key(lines: list[str]) -> str | None:
-    """Return the `group:` value of the top-level `concurrency:` block, or None."""
-    for idx, raw in enumerate(lines):
-        if CONCURRENCY_RE.match(raw):
-            # Scan forward until we leave the concurrency block (next top-level key
-            # is at column 0 and ends with `:`).
-            for follow in lines[idx + 1:]:
-                if follow and not follow.startswith(" ") and follow.rstrip().endswith(":"):
-                    break
-                m = GROUP_RE.match(follow)
-                if m:
-                    return m.group(1).strip().strip("'").strip('"')
-            break
-    return None
-
-
-def has_top_level_concurrency(lines: list[str]) -> bool:
-    return any(CONCURRENCY_RE.match(raw) for raw in lines)
-
-
-def check(workflows_dir: pathlib.Path) -> int:
-    fail = 0
-    files = sorted(
-        list(workflows_dir.glob("*.yml")) + list(workflows_dir.glob("*.yaml"))
-    )
-    for path in files:
-        lines = path.read_text(encoding="utf-8").splitlines()
-        reusable = is_reusable(lines)
-        has_conc = has_top_level_concurrency(lines)
-
-        if reusable:
-            if has_conc:
-                print(
-                    f"::error file={path}::Reusable workflow (on: workflow_call) "
-                    "must NOT declare its own concurrency block — it inherits "
-                    "from the caller. See CONTRIBUTING.md -> GitHub Actions — "
-                    "Concurrency Convention."
-                )
-                fail = 1
-            continue
-
-        if not has_conc:
-            print(
-                f"::error file={path}::Missing top-level concurrency block. "
-                "See CONTRIBUTING.md -> GitHub Actions — Concurrency Convention."
-            )
-            fail = 1
-            continue
-
-        group = extract_group_key(lines)
-        if group is None:
-            print(
-                f"::error file={path}::concurrency block is missing a "
-                "`group:` key."
-            )
-            fail = 1
-            continue
-
-        if not any(token in group for token in REQUIRED_TOKENS):
-            print(
-                f"::error file={path}::concurrency.group `{group}` must "
-                f"reference one of {REQUIRED_TOKENS}. See CONTRIBUTING.md -> "
-                "GitHub Actions — Concurrency Convention."
-            )
-            fail = 1
-
-    return fail
-
-
-def main(argv: list[str]) -> int:
-    if len(argv) != 2:
-        print(f"usage: {argv[0]} <workflows-dir>", file=sys.stderr)
-        return 2
-    workflows_dir = pathlib.Path(argv[1])
-    if not workflows_dir.is_dir():
-        print(f"not a directory: {workflows_dir}", file=sys.stderr)
-        return 2
-    return check(workflows_dir)
-
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))

.github/workflows/ci-e2e.yml

@@ -11,8 +11,8 @@ jobs:
     outputs:
       web_changed: ${{ steps.filter.outputs.web }}
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v3
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
         id: filter
         with:
           filters: |
@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
 
       - uses: ./.github/actions/setup-gitnexus-web
 
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: e2e-results
           path: |

.github/workflows/ci-quality.yml

@@ -8,8 +8,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
         with:
           node-version: 20
           cache: npm
@@ -21,8 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
         with:
           node-version: 20
           cache: npm
@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
       - uses: ./.github/actions/setup-gitnexus
       - run: npx tsc --noEmit
         working-directory: gitnexus
@@ -43,30 +43,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
       - uses: ./.github/actions/setup-gitnexus-web
       - run: npx tsc -b --noEmit
         working-directory: gitnexus-web
-
-  # Enforces the convention documented in CONTRIBUTING.md → "GitHub Actions —
-  # Concurrency Convention":
-  #   1. Every entry-point (non-reusable) workflow declares a top-level
-  #      `concurrency:` block.
-  #   2. Reusable workflows (`on: workflow_call` only) do NOT declare one —
-  #      they inherit concurrency from the caller.
-  #   3. The concurrency group key starts with `${{ github.workflow }}` or
-  #      the literal `CI-` prefix (the documented ci.yml exception for
-  #      reusable-workflow-safe grouping).
-  # Reusability is detected by parsing each workflow's `on:` block, not an
-  # allowlist, so new reusable workflows never produce false positives.
-  workflow-convention:
-    name: Workflow concurrency convention
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - name: Validate workflow concurrency convention
-        shell: bash
-        run: |
-          set -euo pipefail
-          python3 .github/scripts/check-workflow-concurrency.py .github/workflows

.github/workflows/ci-report.yml

@@ -14,16 +14,6 @@ permissions:
   contents: read # needed for sparse checkout of vitest.config.ts
   pull-requests: write # needed to post sticky PR comment
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Serialize sticky-comment writes per PR so two rapid CI completions don't race.
-# Internal PRs surface in `pull_requests[0].number`. Fork PRs leave that array empty,
-# so we fall back to `<head-repo-full-name>/<head-branch>`, which is stable across
-# reruns and subsequent pushes for the same fork PR (unlike `workflow_run.id` which
-# is unique per run and therefore does not serialize anything).
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.workflow_run.pull_requests[0].number || format('{0}/{1}', github.event.workflow_run.head_repository.full_name, github.event.workflow_run.head_branch) }}
-  cancel-in-progress: false
-
 jobs:
   pr-report:
     name: PR Report
@@ -36,7 +26,7 @@ jobs:
     steps:
       # ── Download artifacts from the CI run ────────────────────────
       - name: Download artifacts
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v7
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         with:
           script: |
             const fs = require('fs');
@@ -123,7 +113,7 @@ jobs:
 
       - name: Checkout (for vitest config)
         if: steps.meta.outputs.skip != 'true'
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
         with:
           sparse-checkout: gitnexus/vitest.config.ts
           sparse-checkout-cone-mode: false
@@ -132,7 +122,7 @@ jobs:
       - name: Fetch base branch coverage
         if: steps.meta.outputs.skip != 'true'
         id: base-coverage
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v7
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         with:
           script: |
             const fs = require('fs');
@@ -416,7 +406,7 @@ jobs:
 
       - name: Comment on PR
         if: steps.meta.outputs.skip != 'true'
-        uses: marocchino/sticky-pull-request-comment@0ea0beb66eb9baf113663a64ec522f60e49231c0 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           header: ci-report
           number: ${{ steps.meta.outputs.pr_number }}

.github/workflows/ci-tests.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 25
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
       - uses: ./.github/actions/setup-gitnexus
         with:
           build: 'true'
@@ -41,12 +41,9 @@ jobs:
           --outputFile=web-test-results.json
         working-directory: gitnexus-web
 
-      - name: Run docker-server integration tests
-        run: node --test docker-server.test.mjs
-
       - name: Upload test reports
         if: always()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: test-reports
           path: |
@@ -66,7 +63,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 25
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
       - uses: ./.github/actions/setup-gitnexus
         with:
           build: 'true'

.github/workflows/ci.yml

@@ -9,20 +9,9 @@ on:
     paths-ignore: ['**.md', 'docs/**', 'LICENSE']
   workflow_call:
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Hardcoded `CI-` prefix (not `${{ github.workflow }}`) because this workflow is
-# invoked as a reusable workflow from publish.yml and release-candidate.yml. In
-# called-workflow context `github.workflow` evaluation is ambiguous across GitHub
-# Actions versions, and a prefix that could resolve to the caller's name would
-# share a concurrency group with the caller → deadlock. A literal prefix is
-# immune. Direct `push`/`pull_request` invocations use `CI-<ref>`; invocations
-# from a reusable-workflow caller fall into a per-run-unique group that never
-# serializes with the caller.
-# cancel-in-progress is event-aware: cancel superseded PR runs, queue every other
-# event (push to main, workflow_call from publish.yml, etc.).
 concurrency:
-  group: ${{ (github.event_name == 'pull_request' || github.event_name == 'push') && format('CI-{0}', github.ref) || format('CI-nested-{0}', github.run_id) }}
-  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
 
 # ── Reusable workflow orchestration ─────────────────────────────────
 # Each concern lives in its own workflow file for maintainability:
@@ -85,7 +74,7 @@ jobs:
           cp pr-meta/e2e_result      pr-meta/e2e-result
 
       - name: Upload PR metadata
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: pr-meta
           path: pr-meta/
@@ -107,9 +96,9 @@ jobs:
           TESTS: ${{ needs.tests.result }}
           E2E: ${{ needs.e2e.result }}
         run: |
-          echo "Quality:        $QUALITY"
-          echo "Tests:          $TESTS"
-          echo "E2E:            $E2E"
+          echo "Quality:     $QUALITY"
+          echo "Tests:       $TESTS"
+          echo "E2E:         $E2E"
           if [[ "$QUALITY" != "success" ]] ||
              [[ "$TESTS" != "success" ]]; then
             echo "::error::Quality or test jobs failed"

.github/workflows/claude-code-review.yml

@@ -16,10 +16,9 @@ on:
   issue_comment:
     types: [created]
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Serialize per-PR to avoid racing review comments.
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number || github.event.pull_request.number }}
+  group: claude-review-${{ github.event.issue.number || github.event.pull_request.number }}
   cancel-in-progress: false
 
 jobs:
@@ -57,7 +56,7 @@ jobs:
       # For issue_comment triggers, resolve the PR number, head SHA, and fork repo
       - name: Resolve PR context
         id: pr
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v7
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         with:
           script: |
             let pr;
@@ -77,7 +76,7 @@ jobs:
             core.setOutput('branch', pr.head.ref);
 
       - name: Checkout PR head
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
         with:
           repository: ${{ steps.pr.outputs.repo }}
           ref: ${{ steps.pr.outputs.sha }}

.github/workflows/claude.yml

@@ -10,10 +10,9 @@ on:
   pull_request_review:
     types: [submitted]
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Serialize per-PR/issue to avoid racing comments.
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.issue.number || github.event.pull_request.number || github.event.issue.id }}
+  group: claude-code-${{ github.event.issue.number || github.event.pull_request.number || github.event.issue.id }}
   cancel-in-progress: false
 
 jobs:
@@ -59,7 +58,7 @@ jobs:
       # For PR-related triggers, resolve the fork repo so we can checkout correctly.
       - name: Resolve PR context
         id: pr
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v7
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         with:
           script: |
             // Determine if this event is PR-related
@@ -91,7 +90,7 @@ jobs:
             core.setOutput('branch', pr.head.ref);
 
       - name: Checkout repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
         with:
           repository: ${{ steps.pr.outputs.is_pr == 'true' && steps.pr.outputs.repo || github.repository }}
           ref: ${{ steps.pr.outputs.is_pr == 'true' && steps.pr.outputs.sha || '' }}

.github/workflows/docker.yml

@@ -1,155 +0,0 @@
-name: Docker Build & Push
-
-on:
-  push:
-    tags:
-      - 'v*'
-  # No workflow_dispatch: publishing is exclusively tag-driven so that every
-  # signed image corresponds 1:1 to a published `gitnexus@X.Y.Z` on npm. A
-  # manual run from a branch ref would fail the version check below anyway.
-
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Tag refs are unique per release, so distinct tags run in parallel.
-# Re-pushes of the same tag serialize. cancel-in-progress: false — never cancel a publish mid-flight.
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: false
-
-jobs:
-  build-push:
-    name: Build & Push ${{ matrix.image.name }}
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
-    permissions:
-      contents: read
-      packages: write
-      # Required for Cosign keyless signing via the OIDC token exchange,
-      # and for build provenance / SBOM attestations.
-      id-token: write
-      attestations: write
-
-    strategy:
-      fail-fast: false
-      matrix:
-        image:
-          # Static UI bundle. Small, fast image. Drop-in replacement for the
-          # legacy single-image setup at the same `gitnexus` repository slug
-          # is intentionally avoided — the UI now lives at `gitnexus-web` and
-          # the CLI/server takes the canonical `gitnexus` slug below.
-          - name: gitnexus-web
-            dockerfile: Dockerfile.web
-            slug: gitnexus-web
-          # CLI / `gitnexus serve` backend. Heavy native deps (tree-sitter,
-          # onnxruntime-node) live only in this image.
-          - name: gitnexus
-            dockerfile: Dockerfile.cli
-            slug: gitnexus
-
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-
-      # ── Lock the docker image version to the npm package version ──────────
-      # Mirrors the check in publish.yml: refuse to build unless the git tag
-      # exactly matches `gitnexus/package.json`'s version. This guarantees
-      # `ghcr.io/<owner>/gitnexus:X.Y.Z` always corresponds to the same
-      # `gitnexus@X.Y.Z` published to npm — no drift, no surprises.
-      - name: Verify tag matches gitnexus/package.json version
-        id: version
-        shell: bash
-        run: |
-          TAG_VERSION="${GITHUB_REF#refs/tags/v}"
-          if ! [[ "$TAG_VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$ ]]; then
-            echo "::error::Tag does not follow semver: v$TAG_VERSION"
-            exit 1
-          fi
-          PKG_VERSION=$(node -p "require('./gitnexus/package.json').version")
-          if [ "$TAG_VERSION" != "$PKG_VERSION" ]; then
-            echo "::error::Tag version (v$TAG_VERSION) does not match gitnexus/package.json version ($PKG_VERSION)"
-            exit 1
-          fi
-          echo "version=$PKG_VERSION" >> "$GITHUB_OUTPUT"
-          echo "Version verified: $PKG_VERSION"
-
-      # Required for multi-platform (linux/arm64) emulation.
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4.0.0
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0
-
-      - name: Install Cosign
-        uses: sigstore/cosign-installer@cad07c2e89fa2edd6e2d7bab4c1aa38e53f76003 # v4.1.1
-
-      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4.1.0
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Computes image tags and labels from the verified semver tag:
-      #   v1.2.3        → :1.2.3, :1.2, :1, :latest (auto, only for non-prerelease)
-      #   v1.2.3-rc.1   → :1.2.3-rc.1 only (prereleases never become :latest)
-      # `:latest` is only emitted for tag pushes thanks to `flavor: latest=auto`,
-      # ensuring it always points at a real npm-published version.
-      - name: Extract Docker metadata
-        id: meta
-        uses: docker/metadata-action@030e881283bb7a6894de51c315a6bfe6a94e05cf # v6.0.0
-        with:
-          images: ghcr.io/${{ github.repository_owner }}/${{ matrix.image.slug }}
-          flavor: latest=auto
-          tags: |
-            type=semver,pattern={{version}}
-            type=semver,pattern={{major}}.{{minor}}
-            type=semver,pattern={{major}}
-
-      - name: Build and push
-        id: build
-        uses: docker/build-push-action@bcafcacb16a39f128d818304e6c9c0c18556b85f # v7.1.0
-        with:
-          context: .
-          file: ${{ matrix.image.dockerfile }}
-          platforms: linux/amd64,linux/arm64
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha,scope=${{ matrix.image.slug }}
-          cache-to: type=gha,mode=max,scope=${{ matrix.image.slug }}
-          provenance: mode=max
-          sbom: true
-
-      # Cosign keyless signing. Each pushed tag is signed by the workflow's
-      # OIDC identity, so consumers can verify the image with the strict,
-      # fully-anchored identity regex (kept in sync with README.md and
-      # deploy/kubernetes/cluster-image-policy.yaml — update all three together).
-      # NOTE: `${...}` expression syntax is NOT evaluated inside YAML comments, so
-      # the example below uses literal `<owner>/<repo>` placeholders that consumers
-      # substitute themselves; the canonical, fully-rendered command lives in README.md.
-      #   cosign verify ghcr.io/<owner>/<slug>:<tag> \
-      #     --certificate-identity-regexp '^https://github\.com/<owner>/<repo>/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
-      #     --certificate-oidc-issuer https://token.actions.githubusercontent.com
-      # Do NOT relax to `@.*` — that accepts signatures from any ref, including
-      # unprotected branches and PRs, and defeats the supply-chain guarantee.
-      - name: Sign image with Cosign (keyless)
-        env:
-          # Cosign v2 (installed by sigstore/cosign-installer above) makes
-          # keyless the default. COSIGN_EXPERIMENTAL is a v1-only opt-in flag
-          # that is now deprecated/no-op, so it is intentionally omitted.
-          DIGEST: ${{ steps.build.outputs.digest }}
-          TAGS: ${{ steps.meta.outputs.tags }}
-        run: |
-          # Sign every tag at the same digest so consumers can verify by tag or by digest.
-          # Use `while read` instead of `for $TAGS` to be robust against tags that
-          # could ever contain whitespace (the metadata-action output is newline-
-          # separated, not space-separated).
-          while IFS= read -r tag; do
-            [[ -n "$tag" ]] && cosign sign --yes "${tag}@${DIGEST}"
-          done <<< "$TAGS"
-
-      # Attach the SBOM produced by buildx as a verifiable attestation on the digest.
-      - name: Generate build provenance attestation
-        uses: actions/attest-build-provenance@a2bbfa25375fe432b6a289bc6b6cd05ecd0c4c32 # v4.1.0
-        with:
-          subject-name: ghcr.io/${{ github.repository_owner }}/${{ matrix.image.slug }}
-          subject-digest: ${{ steps.build.outputs.digest }}
-          push-to-registry: true

.github/workflows/pr-description-check.yml

@@ -8,9 +8,8 @@ on:
 permissions:
   pull-requests: write
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
+  group: pr-desc-${{ github.event.pull_request.number }}
   cancel-in-progress: true
 
 jobs:
@@ -19,7 +18,7 @@ jobs:
     timeout-minutes: 5
     steps:
       - name: Check PR description quality
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
         with:
           script: |
             const MIN_BODY_LENGTH = 50;

.github/workflows/pr-labeler.yml

@@ -1,113 +0,0 @@
-name: PR Conventional Labeler
-
-# Two workflows in one file with different triggers, matched to the minimum
-# privilege each needs:
-#
-#   validate-title (on: pull_request)
-#     Fork-safe. Runs with the PR-head's read-only GITHUB_TOKEN. Uses
-#     `amannn/action-semantic-pull-request` to fail the check when the PR
-#     title doesn't follow the conventional-commit format. Because the
-#     action only reads the event payload, no fork-controlled code runs.
-#
-#   autolabel (on: pull_request_target)
-#     Needs `pull-requests: write` to apply labels, so must be
-#     pull_request_target. Uses `release-drafter/release-drafter` with
-#     `dry-run: true` to only run the autolabeler against the
-#     `.github/release-drafter.yml` config from the BASE ref (release-
-#     drafter reads the config from the repository's default branch, NOT
-#     the PR head — verify with `gh api repos/release-drafter/release-drafter/contents/...`
-#     or a fork-test PR before merging if the repo is high-value).
-#     `sync-labels: true` in the config removes managed autolabels that no
-#     longer match (e.g. when `!` or `BREAKING CHANGE:` is dropped).
-#
-# Title format: <type>[(scope)][!]: <subject>
-#   Allowed types: feat, fix, perf, refactor, docs, test, ci, build, chore, revert, deps
-#   Trailing `!` on the type marks a breaking change.
-# See CONTRIBUTING.md → "Pull request titles".
-
-on:
-  pull_request:
-    # Title-only changes fire `edited`. `opened` and `reopened` cover creation.
-    # `synchronize` (push to the PR branch) is intentionally excluded — titles
-    # don't change on push, so it only wastes CI minutes and broadens the
-    # privileged-token exposure window on the autolabel job.
-    types: [opened, edited, reopened]
-  pull_request_target:
-    types: [opened, edited, reopened]
-
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Include `github.event_name` so `pull_request` (validate-title) and
-# `pull_request_target` (autolabel) runs for the same PR do NOT share a slot
-# and therefore cannot cancel each other — a cancelled required-check would
-# permanently block merge until the next title edit.
-# Within each trigger the latest title edit still supersedes the prior run.
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
-jobs:
-  validate-title:
-    # Fork-safe job — only runs on `pull_request` (not `pull_request_target`).
-    # Token is read-only; writes a commit status that branch protection can
-    # require before merge.
-    name: Validate PR title
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    permissions:
-      pull-requests: read
-    steps:
-      # Pinned to v6.1.1. Verify SHA via:
-      #   gh api repos/amannn/action-semantic-pull-request/git/refs/tags/v6.1.1
-      - uses: amannn/action-semantic-pull-request@48f256284bd46cdaab1048c3721360e808335d50 # v6.1.1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          types: |
-            feat
-            fix
-            perf
-            refactor
-            docs
-            test
-            ci
-            build
-            chore
-            revert
-            deps
-          requireScope: false
-          # Subject must be non-empty. We DO allow capitalized proper nouns
-          # (MCP, GitHub, API, etc.) — the old `^(?![A-Z]).+$` pattern
-          # rejected legitimate titles like `fix: MCP tool schema`.
-          subjectPattern: ^\S.{2,}$
-          subjectPatternError: |
-            The subject "{subject}" in PR title "{title}" is invalid.
-            Subjects must be at least 3 characters and must not start with whitespace.
-          wip: false
-
-  autolabel:
-    # Privileged job — runs only on `pull_request_target` so it can write labels.
-    # Never checks out fork code, never executes fork-controlled input; only
-    # reads the PR metadata (title, body, labels) and calls the GitHub API.
-    name: Apply conventional label
-    if: github.event_name == 'pull_request_target'
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    permissions:
-      # `contents: read` is required — release-drafter's context.config() reads
-      # `.github/release-drafter.yml` from the repo's default branch via the
-      # repo-contents API. Without it the job silently 403s and no labels are
-      # applied. Job-level permissions nullify all unlisted scopes, so an
-      # explicit grant is necessary here.
-      contents: read
-      pull-requests: write
-    steps:
-      # Pinned to v7.2.0. Verify SHA via:
-      #   gh api repos/release-drafter/release-drafter/git/refs/tags/v7.2.0
-      # v7 removed `disable-releaser`; use `dry-run: true` to only autolabel.
-      - uses: release-drafter/release-drafter@5de93583980a40bd78603b6dfdcda5b4df377b32 # v7.2.0
-        with:
-          config-name: release-drafter.yml
-          dry-run: true
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -7,22 +7,13 @@ on:
 
 # No workflow-level permissions — scoped per job below.
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Tag refs are unique per release, so distinct tags run in parallel. Re-pushes of the
-# same tag serialize. cancel-in-progress: false — never cancel a publish mid-flight.
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: false
-
 jobs:
   ci:
     uses: ./.github/workflows/ci.yml
     permissions:
       contents: read
       actions: read
-      # No pull-requests:write — `ci.yml`'s save-pr-meta job is gated on
-      # `github.event_name == 'pull_request'`, so it never runs during a
-      # tag-triggered publish. Least-privilege for release-critical paths.
+      pull-requests: write
 
   publish:
     needs: ci
@@ -32,8 +23,8 @@ jobs:
       contents: write
       id-token: write
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
         with:
           node-version: 20
           registry-url: https://registry.npmjs.org
@@ -91,7 +82,7 @@ jobs:
           fi
 
       - name: Create GitHub Release
-        uses: softprops/action-gh-release@b4309332981a82ec1c5618f44dd2e27cc8bfbfda # v2
+        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2
         with:
           body_path: ${{ steps.changelog.outputs.fallback == 'false' && '/tmp/release-notes.md' || '' }}
           generate_release_notes: ${{ steps.changelog.outputs.fallback == 'true' }}

.github/workflows/release-candidate.yml

@@ -1,366 +0,0 @@
-name: Release Candidate
-
-on:
-  # Publish a release-candidate build whenever a merge/commit lands on main.
-  # Docs/README-only changes are filtered out so prose updates don't
-  # cut a release.
-  push:
-    branches: [main]
-    paths-ignore:
-      - '**.md'
-      - 'docs/**'
-      - 'LICENSE'
-  workflow_dispatch:
-    inputs:
-      bump:
-        description: >-
-          Cycle policy. 'auto' (default) continues the active rc cycle on
-          this branch if there is one, otherwise bumps patch from latest.
-          Choose 'patch' / 'minor' / 'major' to explicitly start or reset
-          an rc cycle.
-        required: false
-        default: 'auto'
-        type: choice
-        options:
-          - auto
-          - patch
-          - minor
-          - major
-      force:
-        description: 'Publish even when HEAD already has an rc marker'
-        required: false
-        default: 'false'
-        type: choice
-        options:
-          - 'false'
-          - 'true'
-
-# No workflow-level permissions — scoped per job below.
-permissions: {}
-
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Serialize all runs on the same ref (push + workflow_dispatch) to prevent two publishes
-# racing on the rc counter. cancel-in-progress: false — the earlier merge publishes first.
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: false
-
-jobs:
-  # ── Skip when HEAD already has an rc marker (retry / duplicate dispatch) ──
-  # The marker is a lightweight tag `rc/<HEAD_SHA>` pushed *before* `npm
-  # publish`, so a failed publish leaves the marker in place and the guard
-  # refuses to re-publish. Recovery path after a partial failure:
-  #   git push --delete origin rc/<HEAD_SHA> v<RC_VERSION>
-  # then redispatch with force=true.
-  guard:
-    name: Check if release candidate should run
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    permissions:
-      contents: read
-    outputs:
-      should_run: ${{ steps.decide.outputs.should_run }}
-      head_sha: ${{ steps.decide.outputs.head_sha }}
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-        with:
-          fetch-depth: 0
-          fetch-tags: true
-
-      - name: Decide
-        id: decide
-        shell: bash
-        env:
-          FORCE: ${{ inputs.force }}
-          BUMP_INPUT: ${{ inputs.bump }}
-          EVENT_NAME: ${{ github.event_name }}
-        run: |
-          set -euo pipefail
-          HEAD_SHA=$(git rev-parse HEAD)
-          echo "head_sha=$HEAD_SHA" >> "$GITHUB_OUTPUT"
-
-          if [ "$FORCE" = "true" ]; then
-            echo "Force flag set — running regardless of marker tag."
-            echo "should_run=true" >> "$GITHUB_OUTPUT"
-            exit 0
-          fi
-
-          # An explicit cycle reset on dispatch (bump != auto) also bypasses
-          # the dedup guard — the maintainer is deliberately asking for a
-          # new rc from the same commit.
-          if [ "$EVENT_NAME" = "workflow_dispatch" ] \
-             && [ -n "${BUMP_INPUT:-}" ] \
-             && [ "${BUMP_INPUT:-auto}" != "auto" ]; then
-            echo "Explicit bump=$BUMP_INPUT — bypassing marker dedup."
-            echo "should_run=true" >> "$GITHUB_OUTPUT"
-            exit 0
-          fi
-
-          # Dedup: is there already an rc/<HEAD_SHA> marker pointing at HEAD?
-          MARKER="rc/${HEAD_SHA}"
-          if git rev-parse "refs/tags/$MARKER" >/dev/null 2>&1; then
-            echo "HEAD already has marker $MARKER — skipping."
-            echo "should_run=false" >> "$GITHUB_OUTPUT"
-          else
-            echo "No marker on HEAD — proceeding."
-            echo "should_run=true" >> "$GITHUB_OUTPUT"
-          fi
-
-  # ── Reuse the stable CI workflow ─────────────────────────────────────
-  ci:
-    needs: guard
-    if: needs.guard.outputs.should_run == 'true'
-    uses: ./.github/workflows/ci.yml
-    permissions:
-      contents: read
-    secrets: inherit
-
-  # ── Publish the rc build to npm + create GitHub prerelease ───────────
-  publish:
-    name: Publish release candidate to npm
-    needs: [guard, ci]
-    if: needs.guard.outputs.should_run == 'true'
-    runs-on: ubuntu-latest
-    timeout-minutes: 20
-    permissions:
-      contents: write # push rc tag + marker
-      id-token: write # npm provenance
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-        with:
-          fetch-depth: 0
-          fetch-tags: true
-
-      - uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
-        with:
-          node-version: 20
-          registry-url: https://registry.npmjs.org
-          cache: npm
-          cache-dependency-path: gitnexus/package-lock.json
-
-      - name: Build gitnexus-shared
-        run: npm install && npm run build
-        working-directory: gitnexus-shared
-
-      - name: Install gitnexus dependencies
-        run: npm ci
-        working-directory: gitnexus
-
-      - name: Resolve rc version
-        id: version
-        shell: bash
-        working-directory: gitnexus
-        env:
-          BUMP_INPUT: ${{ inputs.bump }}
-          EVENT_NAME: ${{ github.event_name }}
-          PKG_NAME: gitnexus
-        run: |
-          set -euo pipefail
-
-          # 1. Current published `latest` — the floor for any new rc base.
-          #    Only E404 ("never published") falls back to package.json; any
-          #    other error (network, auth, malformed response) fails fast.
-          NPM_STDERR_LATEST="$(mktemp)"
-          if CURRENT_LATEST="$(npm view "$PKG_NAME" version 2>"$NPM_STDERR_LATEST")"; then
-            :
-          else
-            if grep -q 'E404' "$NPM_STDERR_LATEST"; then
-              CURRENT_LATEST="$(node -p "require('./package.json').version")"
-              echo "Package not on registry (E404) — seeding from package.json: $CURRENT_LATEST"
-            else
-              echo "::error::npm registry unreachable for 'view version':" >&2
-              cat "$NPM_STDERR_LATEST" >&2
-              rm -f "$NPM_STDERR_LATEST"
-              exit 1
-            fi
-          fi
-          rm -f "$NPM_STDERR_LATEST"
-          CURRENT_LATEST_CLEAN="${CURRENT_LATEST%%-*}"
-
-          # 2. Full version list — needed for the counter and for active-cycle
-          #    inference. Same E404-only fallback.
-          NPM_STDERR_VERSIONS="$(mktemp)"
-          if VERSIONS_JSON="$(npm view "$PKG_NAME" versions --json 2>"$NPM_STDERR_VERSIONS")"; then
-            :
-          else
-            if grep -q 'E404' "$NPM_STDERR_VERSIONS"; then
-              VERSIONS_JSON='[]'
-              echo "No published versions for $PKG_NAME yet (E404)."
-            else
-              echo "::error::npm registry unreachable for 'view versions':" >&2
-              cat "$NPM_STDERR_VERSIONS" >&2
-              rm -f "$NPM_STDERR_VERSIONS"
-              exit 1
-            fi
-          fi
-          rm -f "$NPM_STDERR_VERSIONS"
-
-          # 3. Base selection.
-          #    - workflow_dispatch + bump ∈ {patch,minor,major} → explicit cycle
-          #      reset from latest.
-          #    - Everything else (push, or dispatch with bump=auto) → continue
-          #      the highest active rc base > latest if one exists; else
-          #      default to patch from latest.
-          if [ "$EVENT_NAME" = "workflow_dispatch" ] \
-             && [ -n "${BUMP_INPUT:-}" ] \
-             && [ "${BUMP_INPUT:-auto}" != "auto" ]; then
-            BASE="$(npx --yes -p semver@7 semver -i "$BUMP_INPUT" "$CURRENT_LATEST_CLEAN")"
-            echo "Explicit bump=$BUMP_INPUT → BASE=$BASE"
-          else
-            cat > /tmp/active_base.mjs <<'NODESCRIPT'
-          const latest = process.env.LATEST;
-          let v;
-          try { v = JSON.parse(process.env.VERSIONS_JSON); } catch { v = []; }
-          if (!Array.isArray(v)) v = [v];
-          const parse = s => s.split(".").map(n => parseInt(n, 10));
-          const gt = (a, b) => {
-            const [A, B] = [parse(a), parse(b)];
-            for (let i = 0; i < 3; i++) if (A[i] !== B[i]) return A[i] > B[i];
-            return false;
-          };
-          const bases = new Set();
-          for (const s of v) {
-            const m = /^(\d+\.\d+\.\d+)-rc\.\d+$/.exec(s);
-            if (m && gt(m[1], latest)) bases.add(m[1]);
-          }
-          if (!bases.size) { process.stdout.write(""); process.exit(0); }
-          const sorted = [...bases].sort((a, b) => gt(a, b) ? 1 : -1);
-          process.stdout.write(sorted[sorted.length - 1]);
-          NODESCRIPT
-            ACTIVE_BASE="$(LATEST="$CURRENT_LATEST_CLEAN" VERSIONS_JSON="$VERSIONS_JSON" node /tmp/active_base.mjs)"
-            if [ -n "$ACTIVE_BASE" ]; then
-              BASE="$ACTIVE_BASE"
-              echo "Continuing active rc cycle → BASE=$BASE"
-            else
-              BASE="$(npx --yes -p semver@7 semver -i patch "$CURRENT_LATEST_CLEAN")"
-              echo "No active rc cycle → patch bump from latest → BASE=$BASE"
-            fi
-          fi
-
-          # 4. Counter: 1 + max existing N for `${BASE}-rc.*`, else 1.
-          cat > /tmp/next_rc.mjs <<'NODESCRIPT'
-          const base = process.env.BASE;
-          const prefix = base + "-rc.";
-          let v;
-          try { v = JSON.parse(process.env.VERSIONS_JSON); } catch { v = []; }
-          if (!Array.isArray(v)) v = [v];
-          const ns = v
-            .filter(s => typeof s === "string" && s.startsWith(prefix))
-            .map(s => parseInt(s.slice(prefix.length), 10))
-            .filter(n => Number.isInteger(n) && n >= 0);
-          process.stdout.write(String(ns.length ? Math.max(...ns) + 1 : 1));
-          NODESCRIPT
-          NEXT_N="$(BASE="$BASE" VERSIONS_JSON="$VERSIONS_JSON" node /tmp/next_rc.mjs)"
-          RC_VERSION="${BASE}-rc.${NEXT_N}"
-          echo "Computed rc: $RC_VERSION"
-
-          # 5. Defensive: if the exact version already exists on the registry
-          #    (e.g., race with another run), abort before re-publishing.
-          #    Same E404-only pattern used above — a transient network
-          #    failure must fail loudly, not pretend the version is missing.
-          NPM_STDERR_EXISTS="$(mktemp)"
-          if npm view "$PKG_NAME@$RC_VERSION" version 2>"$NPM_STDERR_EXISTS" >/dev/null; then
-            rm -f "$NPM_STDERR_EXISTS"
-            echo "::error::Version $RC_VERSION already exists on npm — aborting."
-            exit 1
-          else
-            if grep -qiE 'E404|not found' "$NPM_STDERR_EXISTS"; then
-              rm -f "$NPM_STDERR_EXISTS"
-              # Version doesn't exist — safe to proceed.
-            else
-              echo "::error::npm registry unreachable for existence check:" >&2
-              cat "$NPM_STDERR_EXISTS" >&2
-              rm -f "$NPM_STDERR_EXISTS"
-              exit 1
-            fi
-          fi
-
-          echo "base=$BASE"             >> "$GITHUB_OUTPUT"
-          echo "rc_n=$NEXT_N"           >> "$GITHUB_OUTPUT"
-          echo "rc_version=$RC_VERSION" >> "$GITHUB_OUTPUT"
-
-      - name: Apply rc version in-CI
-        shell: bash
-        working-directory: gitnexus
-        run: |
-          set -euo pipefail
-          npm version "${{ steps.version.outputs.rc_version }}" \
-            --no-git-tag-version --allow-same-version
-
-      - name: Build gitnexus
-        run: npm run build
-        working-directory: gitnexus
-
-      - name: Dry-run publish
-        run: npm publish --dry-run --tag rc
-        working-directory: gitnexus
-
-      # ── Acquire the "rc lock" BEFORE publishing (fixes idempotency) ─────
-      # We create two tags and push them atomically:
-      #   v<RC_VERSION>      → annotated tag on a detached release commit
-      #                        whose tree contains the rewritten package.json
-      #                        (so the tag's source matches the npm tarball)
-      #   rc/<HEAD_SHA>      → lightweight tag on HEAD; the guard's dedup key
-      # If this push fails, nothing is published — safe.
-      # If this push succeeds but npm publish fails, the marker stays on
-      # the remote and blocks retries until an operator manually cleans up.
-      - name: Create and push rc tags
-        id: reltag
-        shell: bash
-        working-directory: gitnexus
-        env:
-          RC_VERSION: ${{ steps.version.outputs.rc_version }}
-          HEAD_SHA: ${{ needs.guard.outputs.head_sha }}
-        run: |
-          set -euo pipefail
-          VTAG="v${RC_VERSION}"
-          MARKER="rc/${HEAD_SHA}"
-          git config user.name  'github-actions[bot]'
-          git config user.email '41898282+github-actions[bot]@users.noreply.github.com'
-
-          # Detached release commit with the version bump — keeps `main`
-          # pristine but gives the v-tag a tree that matches the published
-          # package contents exactly (fixes release-integrity gap).
-          git add package.json package-lock.json 2>/dev/null || git add package.json
-          git commit -m "release: ${VTAG}" --allow-empty
-          RELEASE_SHA="$(git rev-parse HEAD)"
-          echo "Detached release commit: $RELEASE_SHA"
-
-          # Annotated release tag on the release commit.
-          git tag -a "$VTAG" "$RELEASE_SHA" -m "$VTAG"
-          # Lightweight marker on the user-visible HEAD for the guard.
-          git tag "$MARKER" "$HEAD_SHA"
-
-          # Atomic push of both refs. If either would clobber an existing
-          # remote ref, the push fails and we stop before npm publish.
-          git push --atomic origin "refs/tags/$VTAG" "refs/tags/$MARKER"
-
-          echo "vtag=$VTAG"     >> "$GITHUB_OUTPUT"
-          echo "marker=$MARKER" >> "$GITHUB_OUTPUT"
-          echo "release_sha=$RELEASE_SHA" >> "$GITHUB_OUTPUT"
-
-      - name: Publish to npm (rc dist-tag)
-        run: npm publish --provenance --access public --tag rc
-        working-directory: gitnexus
-        env:
-          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
-
-      - name: Create GitHub prerelease
-        uses: softprops/action-gh-release@b4309332981a82ec1c5618f44dd2e27cc8bfbfda # v2
-        with:
-          tag_name: ${{ steps.reltag.outputs.vtag }}
-          name: Release Candidate ${{ steps.reltag.outputs.vtag }}
-          prerelease: true
-          make_latest: 'false'
-          generate_release_notes: true
-          body: |
-            Automated release candidate build from `main`.
-
-            **npm:** `npm install gitnexus@rc`
-            **Version:** `${{ steps.version.outputs.rc_version }}`
-            **Target base:** `${{ steps.version.outputs.base }}` (rc #${{ steps.version.outputs.rc_n }})
-            **Source commit (main):** ${{ needs.guard.outputs.head_sha }}
-            **Release commit (versioned tree):** ${{ steps.reltag.outputs.release_sha }}
-
-            Release candidates are pre-stable builds intended for early testing.
-            Stable releases remain on the `latest` dist-tag.

.github/workflows/tree-sitter-upgrade-readiness.yml

@@ -1,185 +0,0 @@
-name: Tree-sitter Upgrade Readiness
-
-# Monitors readiness for upgrading tree-sitter to 0.25.x. Tracks:
-#   1. Peer-dep compatibility — can each grammar install cleanly with
-#      tree-sitter@0.25.0 without --legacy-peer-deps?
-#   2. Vendored proto drift — has coder3101/tree-sitter-proto moved
-#      ahead of our vendored snapshot?
-# See .github/scripts/check-tree-sitter-upgrade-readiness.py for the logic.
-#
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-
-on:
-  schedule:
-    # Daily at 09:00 UTC. Matches Dependabot's daily cadence so drift
-    # and dep PRs surface together.
-    - cron: '0 9 * * *'
-  workflow_dispatch:
-  pull_request:
-    paths:
-      - '.github/scripts/check-tree-sitter-upgrade-readiness.py'
-      - '.github/workflows/tree-sitter-upgrade-readiness.yml'
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
-
-permissions:
-  contents: read
-
-jobs:
-  readiness:
-    name: Check upgrade readiness
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    permissions:
-      contents: read
-      # Needed to open/update the tracking issue on scheduled runs.
-      issues: write
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-
-      - uses: ./.github/actions/setup-gitnexus
-        with:
-          build: 'false'
-
-      - name: Run upgrade readiness check
-        id: readiness
-        shell: bash
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          set +e
-          python3 .github/scripts/check-tree-sitter-upgrade-readiness.py > drift-report.md
-          code=$?
-          set -e
-          echo "exit_code=$code" >> "$GITHUB_OUTPUT"
-          {
-            echo 'report<<DRIFT_EOF'
-            cat drift-report.md
-            echo 'DRIFT_EOF'
-          } >> "$GITHUB_OUTPUT"
-          echo "=== Report ==="
-          cat drift-report.md
-
-      # On PR runs, the script validates that it runs correctly. Blockers
-      # are informational — the scheduled run opens a tracking issue.
-      - name: Annotate PR with readiness status
-        if: github.event_name == 'pull_request' && steps.readiness.outputs.exit_code != '0'
-        run: |
-          echo "::warning::Tree-sitter 0.25 upgrade has blockers. See job output for the full readiness report."
-
-      - name: Upsert tracking issue on scheduled runs
-        if: >
-          github.event_name == 'schedule' &&
-          steps.readiness.outputs.exit_code != '0'
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0
-        env:
-          REPORT: ${{ steps.readiness.outputs.report }}
-        with:
-          script: |
-            const title = 'Tree-sitter 0.25 upgrade readiness';
-            const report = process.env.REPORT;
-            const body = report + '\n\n' +
-              '<sub>Generated daily by `.github/workflows/tree-sitter-upgrade-readiness.yml`. ' +
-              'Closes automatically when all blockers are resolved.</sub>';
-            const { data: open } = await github.rest.issues.listForRepo({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              state: 'open',
-              labels: 'tree-sitter-drift',
-              per_page: 10,
-            });
-            const existing = open.find(i => i.title === title);
-            if (existing) {
-              // Extract ready/total count for the changelog comment.
-              const readyMatch = report.match(/\*\*(\d+)\/(\d+)\*\* grammars ready/);
-              const blockerMatch = report.match(/\*\*(\d+) blocker/);
-              const ready = readyMatch ? readyMatch[1] : '?';
-              const total = readyMatch ? readyMatch[2] : '?';
-              const blockers = blockerMatch ? blockerMatch[1] : '?';
-
-              // Find grammars whose status changed by diffing the old and
-              // new table rows.  Each row looks like:
-              //   | `tree-sitter-foo` | ... | Ready |
-              //   | `tree-sitter-foo` | ... | Blocking |
-              const parseRows = (md) => {
-                const map = {};
-                for (const m of md.matchAll(/\| `(tree-sitter-[^`]+)` \|.*?\| (\S+(?:\s\S+)*?) \|$/gm)) {
-                  map[m[1]] = m[2].trim();
-                }
-                return map;
-              };
-              const oldRows = parseRows(existing.body || '');
-              const newRows = parseRows(report);
-              const changes = [];
-              for (const [name, newStatus] of Object.entries(newRows)) {
-                const oldStatus = oldRows[name];
-                if (oldStatus && oldStatus !== newStatus) {
-                  changes.push(`\`${name}\`: ${oldStatus} → ${newStatus}`);
-                }
-              }
-
-              const today = new Date().toISOString().slice(0, 10);
-              let comment = `**${today}:** ${ready}/${total} ready. ${blockers} blocker(s) remaining.`;
-              if (changes.length > 0) {
-                comment += '\n\nChanges:\n' + changes.map(c => `- ${c}`).join('\n');
-              } else {
-                comment += ' No changes from previous run.';
-              }
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: existing.number,
-                body: comment,
-              });
-
-              await github.rest.issues.update({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: existing.number,
-                body,
-              });
-              core.info(`Updated existing issue #${existing.number}`);
-            } else {
-              const { data: created } = await github.rest.issues.create({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                title,
-                body,
-                labels: ['tree-sitter-drift', 'dependencies'],
-              });
-              core.info(`Opened issue #${created.number}`);
-            }
-
-      - name: Close tracking issue on clean scheduled runs
-        if: >
-          github.event_name == 'schedule' &&
-          steps.readiness.outputs.exit_code == '0'
-        uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0
-        with:
-          script: |
-            const title = 'Tree-sitter 0.25 upgrade readiness';
-            const { data: open } = await github.rest.issues.listForRepo({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              state: 'open',
-              labels: 'tree-sitter-drift',
-              per_page: 10,
-            });
-            const existing = open.find(i => i.title === title);
-            if (existing) {
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: existing.number,
-                body: 'All grammars are now compatible with tree-sitter@0.25. Upgrade is ready! Closing automatically.',
-              });
-              await github.rest.issues.update({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: existing.number,
-                state: 'closed',
-              });
-              core.info(`Closed issue #${existing.number}`);
-            }

.github/workflows/triage-sweep.yml

@@ -47,10 +47,8 @@ permissions:
   issues: write
   pull-requests: write
 
-# Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-# Single global slot — newest manual dispatch supersedes any in-flight run.
 concurrency:
-  group: ${{ github.workflow }}
+  group: triage-sweep
   cancel-in-progress: true
 
 jobs:
@@ -76,7 +74,7 @@ jobs:
         run: pip install -r .github/scripts/triage/requirements.txt
 
       - name: Cache FastEmbed model weights
-        uses: actions/cache@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5
+        uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5
         with:
           path: ${{ github.workspace }}/.fastembed_cache
           key: fastembed-bge-small-en-v1.5

.gitignore

@@ -23,7 +23,6 @@ Thumbs.db
 .env
 .env.local
 .env.*.local
-docker/.env
 
 # Logs
 *.log
@@ -82,11 +81,6 @@ GitNexus.sln
 # Git worktrees
 .worktrees/
 
-# Vendored tree-sitter grammar build artifacts (created at install time,
-# never committed). See docs/plans/2026-04-15-002-fix-tree-sitter-proto-vendor-deps-plan.md
-gitnexus/vendor/**/build/
-gitnexus/vendor/**/node_modules/
-
 /github/scripts/triage/__pycache__/
 
 .claude-flow/
@@ -101,5 +95,4 @@ gitnexus/vendor/**/node_modules/
 
 .swarm/
 
-local_docs/
-
+local_docs/

AGENTS.md

@@ -1,122 +1,117 @@
-<!-- version: 1.4.0 -->
-<!-- Last updated: 2026-04-16 -->
+<!-- version: 1.3.0 -->
+<!--
+  Metadata: version, last reviewed, scope, model policy, reference docs, changelog.
+  Last updated: 2026-03-22
+-->
 
-Last reviewed: 2026-04-16
+Last reviewed: 2026-04-13
 
 **Project:** GitNexus · **Environment:** dev · **Maintainer:** repository maintainers (see GitHub)
 
+This file uses a standard agent header (version, scope, model policy, reference docs, changelog), adapted for this **TypeScript/JavaScript monorepo**.
+
 ## Scope
 
-| Boundary | Rule |
-|----------|------|
-| **Reads** | `gitnexus/`, `gitnexus-web/`, `eval/`, plugin packages, `.github/`, `.gitnexus/`, docs. |
-| **Writes** | Only paths required for the change; keep diffs minimal. Update lockfiles when deps change. |
-| **Executes** | `npm`, `npx`, `node` under `gitnexus/` and `gitnexus-web/`; `uv run` for Python under `eval/`; documented CI/dev workflows. |
-| **Off-limits** | Real `.env` / secrets, production credentials, unrelated repos, destructive git ops without confirmation. |
+| | |
+|--|--|
+| **Reads** | Repository tree as needed for the task: `gitnexus/`, `gitnexus-web/`, `eval/`, plugin packages, `.github/`, `.gitnexus/` when present, and docs. |
+| **Writes** | Only paths required for the requested change; keep diffs minimal. Update lockfiles when dependencies change. |
+| **Executes** | `npm`, `npx`, `node` under `gitnexus/` and `gitnexus-web/`; `uv run` for Python under `eval/` when applicable; shell utilities for documented CI/dev workflows. |
+| **Off-limits** | User secrets (e.g. real `.env`), production deployment credentials, unrelated repositories, destructive git history operations without explicit human confirmation. |
 
 ## Model Configuration
 
-- **Primary:** Use a named model (e.g. Claude Sonnet 4.x). Avoid `Auto` or unversioned `latest` when reproducibility matters.
-- **Notes:** The GitNexus CLI indexer does not call an LLM.
+- **Primary:** Pin in **Cursor** (Settings → model). Use a **named** model (e.g. GPT-5.2, Claude Sonnet 4.x). Avoid relying on **Auto** when reproducibility or audit trail matters.
+- **Fallback:** As configured in Cursor or your organization (do not encode `latest` or wildcards in automation configs).
+- **Notes:** The open-source GitNexus CLI indexer does not call an LLM. Optional Nexus AI in the web UI uses end-user provider keys and models.
 
 ## Execution Sequence (complex tasks)
 
-For multi-step work, state up front:
-1. Which rules in this file and **[GUARDRAILS.md](GUARDRAILS.md)** apply (and any relevant Signs).
-2. Current **Scope** boundaries.
-3. Which **validation commands** you will run (`cd gitnexus && npm test`, `npx tsc --noEmit`).
+Long sessions dilute instructions. For **multi-step** work, state up front:
 
-On long threads, *"Remember: apply all AGENTS.md rules"* re-weights these instructions against context dilution.
+1. Which rules in this file and **[GUARDRAILS.md](GUARDRAILS.md)** apply (and any relevant Signs).
+2. Current **Scope** boundaries (Reads / Writes / Off-limits).
+3. Which **validation commands** you will run (e.g. `cd gitnexus && npm test`, `npx tsc --noEmit`).
+
+On very long threads, the human may add *“Remember: apply all AGENTS.md rules”* to re-weight rule tokens against context dilution.
 
 ## Claude Code hooks
 
-**PreToolUse** hooks can block tools (e.g. `git_commit`) until checks pass. Adapt to this repo: `cd gitnexus && npm test` before commit.
+Hooks enforce gates that prompts cannot. In **Claude Code**, **PreToolUse** hooks can block tools such as `git_commit` until checks pass. Adapt to this repo: e.g. `cd gitnexus && npm test` before commit.
 
-## Context budget
+## Context budget (Cursor / standards)
 
-Commands and gotchas live under **Repo reference** below and in **[CONTRIBUTING.md](CONTRIBUTING.md)**. If always-on rules grow, split into **`.cursor/rules/*.mdc`** (globs). **Cursor:** project-wide rules in `.cursor/index.mdc`. **Claude Code:** load `STANDARDS.md` only when needed.
+Generic “core standards” playbooks are often long and stack-specific. For this monorepo, commands and gotchas live under **Cursor Cloud specific instructions** below and in **[CONTRIBUTING.md](CONTRIBUTING.md)**. If always-on rules grow, split domain rules into **`.cursor/rules/*.mdc`** (globs). **Cursor:** project-wide rules live in **`.cursor/index.mdc`** (YAML frontmatter with `alwaysApply: true`). **Claude Code:** optionally load a **`STANDARDS.md`** only when needed (e.g. *“When writing new code, read STANDARDS.md”*) to save context.
 
-## Reference docs
+## Reference Documentation
 
-- **[ARCHITECTURE.md](ARCHITECTURE.md)**, **[CONTRIBUTING.md](CONTRIBUTING.md)**, **[GUARDRAILS.md](GUARDRAILS.md)**
-- **Call-resolution DAG:** See ARCHITECTURE.md § Call-Resolution DAG. Typed 6-stage DAG inside the `parse` phase; language-specific behavior behind `inferImplicitReceiver` / `selectDispatch` hooks on `LanguageProvider`. Shared code in `gitnexus/src/core/ingestion/` must not name languages. Types: `gitnexus/src/core/ingestion/call-types.ts`.
-- **Cursor:** `.cursor/index.mdc` (always-on); `.cursor/rules/*.mdc` (glob-scoped). Legacy `.cursorrules` deprecated.
-- **GitNexus:** skills in `.claude/skills/gitnexus/`; MCP rules in `gitnexus:start` block below.
+- **This repository:** **[ARCHITECTURE.md](ARCHITECTURE.md)**, **[CONTRIBUTING.md](CONTRIBUTING.md)**, **[GUARDRAILS.md](GUARDRAILS.md)**.
+- **Cursor:** `.cursor/index.mdc` (always-on rules); optional `.cursor/rules/*.mdc` (glob-scoped). Legacy `.cursorrules` is deprecated — see `.cursor/index.mdc`.
+- **Optional local files:** `NOTES.md` (short vendor-neutral project snapshot). For handoffs, keep notes local (e.g., a scratch file outside the repo) rather than committing `HANDOFF.md`.
+- **GitNexus:** skills under `.claude/skills/gitnexus/`; machine-oriented rules in the `gitnexus:start` … `gitnexus:end` block below.
 
 ## Changelog
 
 | Date | Version | Change |
 |------|---------|--------|
-| 2026-04-16 | 1.4.0 | Fixed: web UI description, pre-commit behavior, MCP tools (7->16), added gitnexus-shared, removed stale vite-plugin-wasm gotcha. |
 | 2026-04-13 | 1.3.0 | Updated GitNexus index stats after DAG refactor. |
-| 2026-03-24 | 1.2.0 | Fixed gitnexus:start block duplication. |
-| 2026-03-23 | 1.1.0 | Updated agent instructions, references, Cursor layout. |
-| 2026-03-22 | 1.0.0 | Initial structured header and changelog. |
+| 2026-03-24 | 1.2.0 | Fixed gitnexus:start block duplication (was inlined in Reference Docs bullet). |
+| 2026-03-23 | 1.1.0 | Updated agent instructions (sections, references, Cursor layout). |
+| 2026-03-22 | 1.0.0 | Added structured agent header and changelog. |
 
 ---
 
 <!-- gitnexus:start -->
 # GitNexus — Code Intelligence
 
-Indexed as **GitNexus** (4325 symbols, 10556 relationships, 300 execution flows). Use MCP tools to understand code, assess impact, and navigate safely.
+This project is indexed by GitNexus as **GitNexus** (4325 symbols, 10556 relationships, 300 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
 
-> If any tool warns the index is stale, run `npx gitnexus analyze` first.
+> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
 
 ## Always Do
 
-- **MUST run impact analysis before editing any symbol.** `gitnexus_impact({target: "symbolName", direction: "upstream"})` — report blast radius to the user.
-- **MUST run `gitnexus_detect_changes()` before committing** — verify only expected symbols and flows are affected.
-- **MUST warn the user** if impact returns HIGH or CRITICAL risk.
-- Explore unfamiliar code with `gitnexus_query({query: "concept"})` (process-grouped, ranked) instead of grepping.
-- Full context on a symbol: `gitnexus_context({name: "symbolName"})`.
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
 
 ## When Debugging
 
-1. `gitnexus_query({query: "<error or symptom>"})` — find related execution flows
-2. `gitnexus_context({name: "<suspect function>"})` — callers, callees, process participation
-3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace flow step by step
-4. Regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})`
+1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
+2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
+3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
+4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed
 
 ## When Refactoring
 
-- **Rename:** `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Graph edits are safe; text_search edits need manual review.
-- **Extract/Split:** `gitnexus_context` (incoming/outgoing refs) then `gitnexus_impact` (upstream callers) before moving code.
-- **After any refactor:** `gitnexus_detect_changes({scope: "all"})` to verify scope.
+- **Renaming**: MUST use `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with `dry_run: false`.
+- **Extracting/Splitting**: MUST run `gitnexus_context({name: "target"})` to see all incoming/outgoing refs, then `gitnexus_impact({target: "target", direction: "upstream"})` to find all external callers before moving code.
+- After any refactor: run `gitnexus_detect_changes({scope: "all"})` to verify only expected files changed.
 
 ## Never Do
 
-- Edit a symbol without running `gitnexus_impact` first.
-- Ignore HIGH/CRITICAL risk warnings.
-- Rename with find-and-replace — use `gitnexus_rename`.
-- Commit without `gitnexus_detect_changes()`.
-- Add language-specific behavior to shared ingestion code (`gitnexus/src/core/ingestion/`) — use a `LanguageProvider` hook. Seeing `provider.mroStrategy === 'xxx'` or an import from `languages/xxx.ts` in shared code means stop and add a hook.
+- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
+- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
+- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
 
 ## Tools Quick Reference
 
-| Tool | When to use | Example |
+| Tool | When to use | Command |
 |------|-------------|---------|
-| `list_repos` | Discover indexed repos | `gitnexus_list_repos({})` |
 | `query` | Find code by concept | `gitnexus_query({query: "auth validation"})` |
 | `context` | 360-degree view of one symbol | `gitnexus_context({name: "validateUser"})` |
 | `impact` | Blast radius before editing | `gitnexus_impact({target: "X", direction: "upstream"})` |
 | `detect_changes` | Pre-commit scope check | `gitnexus_detect_changes({scope: "staged"})` |
 | `rename` | Safe multi-file rename | `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` |
 | `cypher` | Custom graph queries | `gitnexus_cypher({query: "MATCH ..."})` |
-| `api_impact` | Pre-change API route impact | `gitnexus_api_impact({route: "/api/users", method: "GET"})` |
-| `route_map` | Route → handler → consumer map | `gitnexus_route_map({})` |
-| `tool_map` | MCP/RPC tool definitions | `gitnexus_tool_map({})` |
-| `shape_check` | Response shape vs consumer access | `gitnexus_shape_check({route: "/api/users"})` |
-| `group_list` | List repo groups | `gitnexus_group_list({})` |
-| `group_query` | Cross-repo search in a group | `gitnexus_group_query({name: "myGroup", query: "auth"})` |
-| `group_sync` | Rebuild group Contract Registry | `gitnexus_group_sync({name: "myGroup"})` |
-| `group_contracts` | Inspect group contracts | `gitnexus_group_contracts({name: "myGroup"})` |
-| `group_status` | Group staleness report | `gitnexus_group_status({name: "myGroup"})` |
 
 ## Impact Risk Levels
 
 | Depth | Meaning | Action |
 |-------|---------|--------|
-| d=1 | WILL BREAK — direct callers/importers | MUST update |
+| d=1 | WILL BREAK — direct callers/importers | MUST update these |
 | d=2 | LIKELY AFFECTED — indirect deps | Should test |
 | d=3 | MAY NEED TESTING — transitive | Test if critical path |
 
@@ -124,80 +119,87 @@ Indexed as **GitNexus** (4325 symbols, 10556 relationships, 300 execution flows)
 
 | Resource | Use for |
 |----------|---------|
-| `gitnexus://repo/GitNexus/context` | Codebase overview, index freshness |
+| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
 | `gitnexus://repo/GitNexus/clusters` | All functional areas |
 | `gitnexus://repo/GitNexus/processes` | All execution flows |
 | `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
 
 ## Self-Check Before Finishing
 
+Before completing any code modification task, verify:
 1. `gitnexus_impact` was run for all modified symbols
-2. No HIGH/CRITICAL warnings were ignored
-3. `gitnexus_detect_changes()` confirms expected scope
-4. All d=1 dependents were updated
+2. No HIGH/CRITICAL risk warnings were ignored
+3. `gitnexus_detect_changes()` confirms changes match expected scope
+4. All d=1 (WILL BREAK) dependents were updated
 
 ## Keeping the Index Fresh
 
+After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
+
 ```bash
-npx gitnexus analyze              # basic refresh
-npx gitnexus analyze --embeddings # preserve embeddings
+npx gitnexus analyze
 ```
 
-Check `.gitnexus/meta.json` `stats.embeddings` (0 = none). Running without `--embeddings` deletes existing vectors.
+If the index previously included embeddings, preserve them by adding `--embeddings`:
 
-> Claude Code: PostToolUse hook handles this after `git commit` and `git merge`.
+```bash
+npx gitnexus analyze --embeddings
+```
 
-## CLI Skills
+To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.embeddings` field shows the count (0 means no embeddings). **Running analyze without `--embeddings` will delete any previously generated embeddings.**
 
-| Task | Skill file |
-|------|-----------|
-| Architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
-| Blast radius / "What breaks?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
-| Debugging / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
-| Refactoring | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
-| Tools/resources/schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
-| CLI commands (index, status, clean, wiki) | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
+> Claude Code users: A PostToolUse hook handles this automatically after `git commit` and `git merge`.
+
+## CLI
+
+| Task | Read this skill file |
+|------|---------------------|
+| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
+| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
+| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
+| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
 
 <!-- gitnexus:end -->
 
-## Repo reference
+## Cursor Cloud specific instructions
 
-### Packages
+### Repository structure
 
-| Package | Path | Purpose |
-|---------|------|---------|
-| **CLI/Core** | `gitnexus/` | TypeScript CLI, indexing pipeline, MCP server. Published to npm. |
-| **Web UI** | `gitnexus-web/` | React/Vite thin client. All queries via `gitnexus serve` HTTP API. |
-| **Shared** | `gitnexus-shared/` | Shared TypeScript types and constants. |
-| Claude Plugin | `gitnexus-claude-plugin/` | Static config for Claude marketplace. |
-| Cursor Integration | `gitnexus-cursor-integration/` | Static config for Cursor editor. |
-| Eval | `eval/` | Python evaluation harness (Docker + LLM API keys). |
+This is a monorepo with two main products and supporting config packages:
+
+| Component | Path | Purpose |
+|-----------|------|---------|
+| **GitNexus CLI/Core** | `gitnexus/` | Main product — TypeScript CLI, indexing pipeline, MCP server. Published to npm. |
+| **GitNexus Web UI** | `gitnexus-web/` | React/Vite browser app — graph explorer + AI chat. Runs entirely in WASM. |
+| Claude Plugin | `gitnexus-claude-plugin/` | Static config for Claude marketplace (no build). |
+| Cursor Integration | `gitnexus-cursor-integration/` | Static config for Cursor editor (no build). |
+| SWE-bench Eval | `eval/` | Python evaluation harness (optional; needs Docker + LLM API keys). |
 
 ### Running services
 
-```bash
-cd gitnexus && npm run dev                 # CLI: tsx watch mode
-cd gitnexus-web && npm run dev             # Web UI: Vite on port 5173
-npx gitnexus serve                         # HTTP API on port 4747 (from any indexed repo)
-```
+- **CLI/Core**: `cd gitnexus && npm run dev` (tsx watch mode) or `npm run build && node dist/cli/index.js <command>`
+- **Web UI**: `cd gitnexus-web && npm run dev` (Vite on port 5173)
+- **Backend mode**: `cd <indexed-repo> && node /workspace/gitnexus/dist/cli/index.js serve` (HTTP API on port 3741 by default)
 
 ### Testing
 
 **CLI / Core (`gitnexus/`)**
-- `npm test` — full vitest suite (~2000 tests)
-- `npm run test:unit` — unit tests only
-- `npm run test:integration` — integration (~1850 tests). LadybugDB file-locking tests may fail in containers (known env issue).
-- `npx tsc --noEmit` — typecheck
+- **Unit tests**: `cd gitnexus && npm test` (vitest, ~2000 tests)
+- **Integration tests**: `cd gitnexus && npm run test:integration` (vitest, ~1850 tests). Two LadybugDB file-locking tests (`lbug-core-adapter`, `search-core`) may fail in containerized environments due to `/tmp` locking limitations — this is a known environment issue, not a code bug.
+- **TypeScript check**: `cd gitnexus && npx tsc --noEmit`
 
 **Web UI (`gitnexus-web/`)**
-- `npm test` — vitest (~200 tests)
-- `npm run test:e2e` — Playwright (7 spec files; requires `gitnexus serve` + `npm run dev`)
-- `npx tsc -b --noEmit` — typecheck
+- **Unit tests**: `cd gitnexus-web && npm test` (vitest, ~200 tests)
+- **E2E tests**: `cd gitnexus-web && E2E=1 npx playwright test` (Playwright, 5 tests — requires `gitnexus serve` + `npm run dev` running)
+- **TypeScript check**: `cd gitnexus-web && npx tsc -b --noEmit`
 
-**Pre-commit hook** (`.husky/pre-commit`): formatting (prettier via lint-staged) + typecheck for staged packages. Tests do **not** run in pre-commit — CI only.
+No separate lint command is configured; TypeScript strict checking serves as the primary static analysis.
 
 ### Gotchas
 
-- `npm install` in `gitnexus/` triggers `prepare` (builds via `tsc`) and `postinstall` (patches tree-sitter-swift, builds tree-sitter-proto). Native bindings need `python3`, `make`, `g++`.
-- `tree-sitter-kotlin` and `tree-sitter-swift` are optional — install warnings expected.
-- ESLint configured via `eslint.config.mjs` (TS, React Hooks, unused-imports). No `npm run lint` script; use `npx eslint .`. Prettier runs via lint-staged. CI checks both in `ci-quality.yml`.
+- `npm install` in `gitnexus/` triggers `prepare` (builds via `tsc`) and `postinstall` (patches tree-sitter-swift). Native tree-sitter bindings require `python3`, `make`, and `g++` to be present.
+- `tree-sitter-kotlin` and `tree-sitter-swift` are optional dependencies — install warnings for these are expected and non-blocking.
+- The Web UI uses `vite-plugin-wasm` and requires `Cross-Origin-Opener-Policy`/`Cross-Origin-Embedder-Policy` headers for `SharedArrayBuffer` (handled automatically by Vite dev server).
+- There is no ESLint/Prettier configuration in this repo.

ARCHITECTURE.md

@@ -1,129 +1,99 @@
 # Architecture — GitNexus
 
-Monorepo: **CLI/MCP** (`gitnexus/`) + **browser UI** (`gitnexus-web/`).
+This repository is a **monorepo** with two main products: the **CLI / MCP package** (`gitnexus/`) and the **browser UI** (`gitnexus-web/`). Supporting folders ship editor integrations and plugins without changing the core graph engine.
 
 ## Repository layout
 
 | Path | Role |
 |------|------|
-| `gitnexus/` | npm package `gitnexus`: CLI, MCP server (stdio), HTTP API, ingestion pipeline, LadybugDB graph, embeddings. |
-| `gitnexus-web/` | Vite + React thin client: graph explorer + AI chat. All queries via `gitnexus serve` HTTP API. |
-| `gitnexus-shared/` | Shared TypeScript types and constants (consumed by CLI and Web). |
-| `.claude/`, `gitnexus-claude-plugin/`, `gitnexus-cursor-integration/` | Agent skills and plugin metadata. |
-| `eval/` | Evaluation harnesses for benchmarking tool usage. |
-| `.github/` | CI workflows + composite actions (`setup-gitnexus/`, `setup-gitnexus-web/`). |
+| `gitnexus/` | Published npm package `gitnexus`: CLI, MCP server (stdio), local HTTP API for bridge mode, ingestion pipeline, LadybugDB graph, embeddings (optional). |
+| `gitnexus-web/` | Vite + React UI: in-browser indexing (WASM), graph visualization, optional connection to `gitnexus serve`. |
+| `.claude/`, `gitnexus-claude-plugin/`, `gitnexus-cursor-integration/` | Packaged **skills** and plugin metadata so agents discover the same workflows as documented in `AGENTS.md`. |
+| `eval/` | Evaluation harnesses and docs for benchmarking tool usage. |
+| `.github/` | CI workflows (quality, unit, integration, E2E) and composite actions. |
 
 ## End-to-end flow: index → graph → tools
 
-1. **Ingestion** — `analyze.ts` → `runFullAnalysis` (`run-analyze.ts`) → `runPipelineFromRepo` (`pipeline.ts`). DAG of 12 phases builds a `KnowledgeGraph` in memory, then loads into LadybugDB under `.gitnexus/`. Repo registered in `~/.gitnexus/registry.json` for MCP discovery.
+1. **Ingestion** (`gitnexus analyze`)  
+   - Entry: `gitnexus/src/cli/analyze.ts` → `runPipelineFromRepo` in `gitnexus/src/core/ingestion/pipeline.ts`.  
+   - The pipeline is structured as a **DAG (Directed Acyclic Graph)** of named phases (see [Pipeline Phase DAG](#pipeline-phase-dag) below).  
+   - Output is loaded into **LadybugDB** under **`.gitnexus/`** at the repo root (`lbug/`, `meta.json`, etc.). Optional **FTS** indexes and **embeddings** attach to the same store.  
+   - The repo is registered in **`~/.gitnexus/registry.json`** so MCP can find it from any working directory.
 
-2. **Persistence** — `repo-manager.ts` (paths, registry, KuzuDB cleanup). `lbug-adapter.ts` (graph load, queries, embedding batches).
+2. **Persistence & metadata**  
+   - `gitnexus/src/storage/repo-manager.ts` — paths, registry, cleanup of legacy Kuzu artifacts.  
+   - `gitnexus/src/core/lbug/lbug-adapter.ts` — graph load, queries, embedding restore batches.
 
-3. **Query layer** — three interfaces to the same backend:
-   - **MCP (stdio):** `mcp.ts` → `LocalBackend` → tools (`tools.ts`) + resources (`resources.ts`)
-   - **HTTP bridge:** `serve.ts` → Express (`api.ts`, `mcp-http.ts`) for web UI
-   - **CLI direct:** `gitnexus query|context|impact|cypher` in `tool.ts`
+3. **Query & agents**  
+   - **MCP (stdio):** `gitnexus/src/cli/mcp.ts` → `startMCPServer` → `LocalBackend` (`gitnexus/src/mcp/local/local-backend.ts`) opens registered repos and serves **tools** from `gitnexus/src/mcp/tools.ts` and **resources** from `gitnexus/src/mcp/resources.ts`.  
+   - **Bridge HTTP:** `gitnexus/src/cli/serve.ts` → Express app in `gitnexus/src/server/api.ts` (CORS-limited) exposes REST + MCP-over-HTTP for the web UI.  
+   - **CLI tools (no MCP):** `gitnexus query`, `context`, `impact`, `cypher` in `gitnexus/src/cli/tool.ts` call the same backend for scripts and CI.
 
-4. **Staleness** — `staleness.ts` compares indexed `lastCommit` to `HEAD`, surfaces hints.
+4. **Staleness**  
+   - `gitnexus/src/mcp/staleness.ts` compares indexed `lastCommit` to `HEAD` and surfaces hints when the graph is behind git.
 
-## MCP tools
+## MCP tools (summary)
 
 | Tool | Purpose |
 |------|---------|
-| `list_repos` | Discover indexed repos |
-| `query` | Hybrid BM25 + vector search over the graph |
-| `cypher` | Ad hoc Cypher against the schema |
-| `context` | Callers, callees, processes for one symbol |
-| `impact` | Blast radius (upstream/downstream) with risk summary |
-| `detect_changes` | Map git diffs to affected symbols and processes |
-| `rename` | Graph-assisted multi-file rename with `dry_run` preview |
-| `api_impact` | Pre-change impact report for an API route handler |
-| `route_map` | API route → handler → consumer mappings |
-| `tool_map` | MCP/RPC tool definitions and handlers |
-| `shape_check` | Response shape vs consumer property access mismatches |
-| `group_list` | List repo groups or details for one group |
-| `group_query` | Cross-repo search in a group (reciprocal rank fusion) |
-| `group_sync` | Rebuild group Contract Registry (`contracts.json`) |
-| `group_contracts` | Inspect group contracts and cross-links |
-| `group_status` | Index and Contract Registry staleness per repo in a group |
+| `list_repos` | Discover indexed repositories when more than one is registered. |
+| `query` | Natural-language / keyword search over the graph (hybrid BM25 + optional vectors). |
+| `cypher` | Ad hoc **Cypher** against the schema (see resource `gitnexus://repo/{name}/schema`). |
+| `context` | Callers, callees, processes for one symbol (with disambiguation). |
+| `impact` | Blast radius (upstream/downstream) with depth and risk summary. |
+| `detect_changes` | Map git diffs to affected symbols and processes. |
+| `rename` | Graph-assisted rename with `dry_run` preview (`graph` vs `text_search` confidence). |
 
 ## Where to change what
 
-| Concern | Start in |
-|---------|----------|
-| CLI commands/flags | `src/cli/` (`index.ts`, per-command modules) |
-| Parsing/graph construction | `src/core/ingestion/pipeline-phases/` + `pipeline.ts` |
-| Graph schema/DB | `src/core/lbug/` (`schema.ts`, `lbug-adapter.ts`) |
-| MCP tools/resources | `src/mcp/server.ts`, `tools.ts`, `resources.ts` |
-| Search ranking | `src/core/search/` (BM25, hybrid fusion) |
-| Embeddings | `src/core/embeddings/` + `src/core/run-analyze.ts` |
-| Wiki generation | `src/core/wiki/` |
-| Language support | `src/core/ingestion/languages/` + `tree-sitter-queries.ts` + `gitnexus-shared/src/languages.ts` |
-| Import resolution | `src/core/ingestion/import-processor.ts` + `import-resolvers/configs/` + `model/resolution-context.ts` |
-| Call resolution/MRO | `src/core/ingestion/call-processor.ts` + `model/resolve.ts` |
-| Type extraction | `src/core/ingestion/type-extractors/` |
-| Worker pool | `src/core/ingestion/workers/` |
-| Web UI | `gitnexus-web/src/` |
-| CI | `.github/workflows/*.yml`, `.github/actions/` |
-
-> Paths above are relative to `gitnexus/` unless they start with `gitnexus-web/` or `.github/`.
-
----
+| If you are changing… | Start in… |
+|----------------------|-----------|
+| CLI commands / flags | `gitnexus/src/cli/` (`index.ts`, per-command modules). |
+| Parsing or graph construction | `gitnexus/src/core/ingestion/pipeline-phases/` (individual phase files), `pipeline.ts` (orchestrator). |
+| Graph schema / DB access | `gitnexus/src/core/lbug/` (`schema.ts`, `lbug-adapter.ts`), `gitnexus/src/mcp/core/lbug-adapter.ts` if MCP-specific. |
+| MCP protocol, tools, resources | `gitnexus/src/mcp/server.ts`, `tools.ts`, `resources.ts`. |
+| Search ranking | `gitnexus/src/core/search/` (BM25, hybrid fusion). |
+| Embeddings | `gitnexus/src/core/embeddings/`, phases in `analyze.ts`. |
+| Wiki generation | `gitnexus/src/core/wiki/`. |
+| Web UI behavior | `gitnexus-web/src/` (components, workers, graph client). |
+| CI | `.github/workflows/*.yml`, `.github/actions/setup-gitnexus/`. |
 
 ## Pipeline Phase DAG
 
-12 phases defined in `gitnexus/src/core/ingestion/pipeline-phases/`, each with explicit `deps` and typed output.
+The ingestion pipeline is a DAG of named phases. Each phase is defined in its own file under `gitnexus/src/core/ingestion/pipeline-phases/` with explicit dependencies, typed inputs, and typed outputs.
 
 ```
 scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
   → crossFile → mro → communities → processes
 ```
 
-| Phase | File | Deps | Output |
-|-------|------|------|--------|
-| `scan` | `scan.ts` | (root) | File paths + sizes |
-| `structure` | `structure.ts` | `scan` | File/Folder nodes, CONTAINS edges, `allPathSet` |
-| `markdown` | `markdown.ts` | `structure` | Section nodes, cross-link edges from .md/.mdx |
-| `cobol` | `cobol.ts` | `structure` | COBOL program/paragraph/section nodes (regex, no tree-sitter) |
-| `parse` | `parse.ts` + `parse-impl.ts` | `structure`, `markdown`, `cobol` | Symbol nodes, IMPORTS/CALLS/EXTENDS edges, extracted routes/tools/ORM queries |
-| `routes` | `routes.ts` | `parse` | Route nodes + HANDLES_ROUTE edges (Next.js, Expo, PHP, decorators) |
-| `tools` | `tools.ts` | `parse` | Tool nodes + HANDLES_TOOL edges |
-| `orm` | `orm.ts` | `parse` | QUERIES edges (Prisma, Supabase) |
-| `crossFile` | `cross-file.ts` + `cross-file-impl.ts` | `parse`, `routes`, `tools`, `orm` | Cross-file type propagation in topological import order |
-| `mro` | `mro.ts` | `crossFile`, `structure` | METHOD_OVERRIDES + METHOD_IMPLEMENTS edges |
-| `communities` | `communities.ts` | `mro`, `structure` | Community nodes + MEMBER_OF edges (Leiden algorithm) |
-| `processes` | `processes.ts` | `communities`, `routes`, `tools`, `structure` | Process nodes + STEP_IN_PROCESS edges |
+### Phase files
 
-**Non-phase files in the same directory:** `parse-impl.ts`, `cross-file-impl.ts` (implementation), `wildcard-synthesis.ts` (whole-module import expansion), `orm-extraction.ts` (sequential ORM fallback), `types.ts`, `runner.ts`, `index.ts`.
-
-### DAG runner
-
-`runner.ts` — static phase graph, no plugins, compile-time type safety.
-
-1. **Validation** — Kahn's topological sort. Rejects on: duplicate names, missing deps, cycles (DFS traces the concrete cycle path, e.g., `A -> B -> C -> A`, plus count of transitively blocked dependents).
-
-2. **Execution** — sequential in topological order. Each phase receives:
-   - `ctx: PipelineContext` — shared mutable `KnowledgeGraph`, `repoPath`, progress callback, options
-   - `deps: ReadonlyMap<string, PhaseResult>` — **declared deps only** (runner filters the results map to prevent hidden coupling)
-
-3. **Error handling** — wraps phase errors with the phase name, emits terminal `error` progress event, swallows progress handler errors to preserve the original cause.
-
-4. **Timing** — per-phase `durationMs` in `PhaseResult`, dev-mode console logging.
-
-**Design patterns:**
-- **Single graph accumulator** — all phases mutate the same `KnowledgeGraph` in `ctx`; the graph is the primary output.
-- **Typed phase access** — `getPhaseOutput<T>(deps, 'name')` for type-safe upstream results.
-- **Binding accumulator lifecycle** — created in `parse`, disposed by `crossFile` (in `finally`). No other phase should take ownership.
-- **Skippable phases** — `skipGraphPhases` omits MRO/communities/processes (faster tests). `skipWorkers` forces sequential parsing.
+| Phase | File | Dependencies | What it does |
+|-------|------|-------------|--------------|
+| `scan` | `scan.ts` | (root) | Walk repo filesystem, collect paths + sizes |
+| `structure` | `structure.ts` | `scan` | Build File/Folder nodes + CONTAINS edges |
+| `markdown` | `markdown.ts` | `structure` | Extract headings and cross-links from .md/.mdx |
+| `cobol` | `cobol.ts` | `structure` | Regex-based COBOL/JCL extraction |
+| `parse` | `parse.ts` + `parse-impl.ts` | `structure`, `markdown`, `cobol` | Chunked tree-sitter parse, import/call/heritage resolution |
+| `routes` | `routes.ts` | `parse` | Route registry (Next.js, Expo, PHP, decorator-based) |
+| `tools` | `tools.ts` | `parse` | MCP/RPC tool detection |
+| `orm` | `orm.ts` | `parse` | Prisma/Supabase ORM query edges |
+| `crossFile` | `cross-file.ts` + `cross-file-impl.ts` | `parse`, `routes`, `tools`, `orm` | Cross-file type propagation in topological order |
+| `mro` | `mro.ts` | `crossFile` | Method Resolution Order, METHOD_OVERRIDES edges |
+| `communities` | `communities.ts` | `mro` | Leiden community detection |
+| `processes` | `processes.ts` | `communities`, `routes`, `tools` | Execution flow detection, Route/Tool → Process links |
 
 ### How to add a new phase
 
-1. Create `pipeline-phases/my-phase.ts` with a `PipelinePhase<MyOutput>` (name, deps, execute)
-2. Export from `pipeline-phases/index.ts`
-3. Add to `buildPhaseList()` in `pipeline.ts`
+1. Create a new file in `pipeline-phases/` (e.g. `my-phase.ts`)
+2. Define a `PipelinePhase<MyOutput>` object with `name`, `deps`, and `execute(ctx, deps)`
+3. Export it from `pipeline-phases/index.ts`
+4. Add it to the `buildPhaseList()` function in `pipeline.ts`
 
 ```typescript
-import type { PipelinePhase, PhaseResult } from './types.js';
+// pipeline-phases/my-phase.ts
+import type { PipelinePhase, PipelineContext, PhaseResult } from './types.js';
 import { getPhaseOutput } from './types.js';
 import type { ParseOutput } from './parse.js';
 
@@ -131,235 +101,81 @@ export interface MyPhaseOutput { /* ... */ }
 
 export const myPhase: PipelinePhase<MyPhaseOutput> = {
   name: 'myPhase',
-  deps: ['parse'],
+  deps: ['parse'],   // runs after parse completes
   async execute(ctx, deps) {
     const { allPaths } = getPhaseOutput<ParseOutput>(deps, 'parse');
-    // ... write to ctx.graph ...
+    // ... do work, write to ctx.graph ...
     return { /* typed output */ };
   },
 };
 ```
 
----
+### DAG runner
 
-## Call-Resolution DAG
-
-Typed 6-stage pipeline in `call-processor.ts` (inside the `parse` phase) that resolves method/function calls and emits CALLS edges. Language behavior plugs in at two `LanguageProvider` hook points (stages 3–4); shared code names no languages. Scope: call resolution only — import resolution, type extraction, heritage, and symbol-table population live in other phases.
-
-### Stages
-
-```
-extract-call ──▶ classify-form ──▶ infer-receiver ──▶ select-dispatch ──▶ resolve-target ──▶ emit-edge
-     (1)              (2)            (3)  [hook]       (4)  [hook]         (5)                 (6)
-```
-
-| Stage | Produces | Location |
-|-------|----------|----------|
-| **extract-call** | `ExtractedCallSite` (name, form, receiver, argCount) | `call-extractors/` (per-language); runs in worker |
-| **classify-form** | callForm (`free`/`member`/`constructor`) + arity | `call-analysis.ts` → `inferCallForm`; shared, runs in worker |
-| **infer-receiver** | `ReceiverEnriched` (receiver type finalized) | `call-processor.ts`; shared default chain, then `inferImplicitReceiver` hook |
-| **select-dispatch** | `DispatchDecision` (primary, fallback, ancestryView) | `selectDispatch` hook, falls back to shared default |
-| **resolve-target** | `TieredCandidates` | `model/resolve.ts` → `lookupMethodByOwnerWithMRO` (MRO walk) |
-| **emit-edge** | CALLS edge in graph | `call-processor.ts`; writes edge with confidence tier |
-
-### Provider hooks
-
-Both hooks are optional on `LanguageProvider`. Ruby is the only current implementer.
-
-**`inferImplicitReceiver`** — called after shared infer-receiver defaults. Returns `ImplicitReceiverOverride | null`.
-
-| | |
-|---|---|
-| Inputs | `calledName`, `callForm`, `receiverName`, `receiverTypeName`, `callNode` (AST), `filePath` |
-| Non-null fields | `callForm`, `receiverName`, `receiverTypeName` (required); `receiverSource: 'implicit-self'` (fixed); `hint?` (opaque, passed to `selectDispatch`) |
-| Null | Keep existing `ReceiverEnriched` state |
-
-**`selectDispatch`** — called after infer-receiver (including hook). Returns `DispatchDecision | null`; null uses shared default (constructor → `primary:'constructor'`; typed receiver → `primary:'owner-scoped'`; else → `primary:'free'`).
-
-| | |
-|---|---|
-| Inputs | `calledName`, `callForm`, `receiverName`, `receiverTypeName`, `receiverSource`, `hint` |
-| Non-null fields | `primary: 'owner-scoped' \| 'free' \| 'constructor'`; `fallback?: 'free-arity-narrowed'`; `ancestryView?: 'instance' \| 'singleton'`; `hint?` |
-
-**`DispatchDecision` field semantics:**
-- `primary: 'owner-scoped'` — MRO walk from receiver's type; used when receiver type is known.
-- `fallback: 'free-arity-narrowed'` — after owner-scoped miss, search free-call candidates by arity only (Ruby uses this for implicit-self calls that miss their owner's MRO).
-- `ancestryView: 'singleton'` — walk singleton/class ancestry instead of instance ancestry (Ruby `def self.foo` bodies, so `extend`-ed methods are found).
-
-### Adding language behavior
-
-1. **Implicit receivers** — implement `inferImplicitReceiver`: return null if call already has a receiver; otherwise use `findEnclosingClassInfo` (`ast-helpers.ts`) to find the enclosing context, return `ImplicitReceiverOverride` with `receiverSource: 'implicit-self'`, and optionally set `hint` for `selectDispatch`.
-2. **Custom dispatch** — implement `selectDispatch`: inspect `receiverSource` and `hint`, return `DispatchDecision` with `primary`, optional `fallback`, optional `ancestryView`; return null to keep shared defaults.
-3. **MRO strategy** — confirm `mroStrategy` is `'first-wins'`, `'c3'`, `'ruby-mixin'`, or `'none'`; consumed by `lookupMethodByOwnerWithMRO`.
-
-**Ruby example** (`languages/ruby.ts` + `utils/ruby-self-call.ts`): `inferImplicitReceiver` rewrites bare-identifier calls to `self.method` and sets `hint` to `'instance'`/`'singleton'`; `selectDispatch` uses hint for `ancestryView` and adds `fallback: 'free-arity-narrowed'` for implicit-self calls.
-
-### Code references
-
-| Module | Purpose |
-|--------|---------|
-| `core/ingestion/call-types.ts` | DAG types: `ReceiverEnriched`, `DispatchDecision`, `ImplicitReceiverOverride` |
-| `core/ingestion/language-provider.ts` | Hook signatures: `inferImplicitReceiver`, `selectDispatch` |
-| `core/ingestion/call-processor.ts` | `processCalls`: stages 3–6 |
-| `core/ingestion/model/resolve.ts` | `lookupMethodByOwnerWithMRO`: stage 5 MRO walk |
-| `core/ingestion/languages/ruby.ts` | Both hooks + `mroStrategy: 'ruby-mixin'` |
-| `core/ingestion/utils/ruby-self-call.ts` | Bare-call rewrite for `inferImplicitReceiver` |
-
----
-
-## Language-agnostic graph feeding
-
-16 languages → single unified graph. Four abstraction layers:
-
-```
- Unified Graph Schema (44 node types, 21 relationship types)
-           ↑
- Unified Resolution (3-tier name lookup + MRO walk)
-           ↑
- Language Providers (import semantics, type config, export checker, MRO strategy)
-           ↑
- Tree-Sitter Queries (per-language S-expressions, unified capture tags)
-```
-
-### Language providers
-
-Each language implements `LanguageProvider` (`language-provider.ts`). Key fields:
-
-| Field | Purpose |
-|-------|---------|
-| `id`, `extensions` | Language identity and file matching |
-| `treeSitterQueries` | S-expression queries for AST extraction |
-| `importSemantics` | `named` / `wildcard-leaf` / `wildcard-transitive` / `namespace` |
-| `importResolver` | Language-specific path → file resolution |
-| `exportChecker` | Public/exported symbol detection |
-| `typeConfig` | Type annotation extraction rules |
-| `mroStrategy` | `first-wins` / `c3` / `none` |
-
-16 providers in `languages/index.ts` via `satisfies Record<SupportedLanguages, LanguageProvider>` — missing a language is a compile error.
-
-### Unified capture tags
-
-Per-language tree-sitter queries use different AST node names but produce the **same semantic capture tags**: `@definition.class`, `@definition.function`, `@call.name`, `@import.source`, `@heritage.extends`. Downstream extraction needs no language branching. Defined in `tree-sitter-queries.ts`.
-
-### Import resolution
-
-Per-language import resolution uses the **configs + factory** pattern (like call/method/class extractors). Each language declares an `ImportResolutionConfig` in `import-resolvers/configs/`, listing an ordered chain of `ImportResolverStrategy` functions. `createImportResolver()` (in `resolver-factory.ts`) composes them: first non-null result wins. Low-level helpers shared across strategies live alongside the configs in `import-resolvers/` (e.g. `go.ts`, `rust.ts`, `python.ts`).
-
-Unified 3-tier algorithm (`model/resolution-context.ts`), per-language `importSemantics` controls which tier activates:
-
-| Tier | Confidence | Mechanism |
-|------|-----------|-----------|
-| 1 — same-file | 0.95 | Symbol table for caller's file |
-| 2 — import-scoped | 0.9 | `NamedImportMap` chains (named) or all files in `importMap` (wildcard) |
-| 3 — global | 0.5 | O(1) index lookups: class, impl, callable. Fallback only |
-
-| Import strategy | Languages | Behavior |
-|----------------|-----------|----------|
-| `named` | TS, JS, Java, C#, Rust, PHP, Kotlin | Only explicitly imported names visible |
-| `wildcard-leaf` | Go, Ruby, Swift, Dart | Whole-package import, no transitive re-exports |
-| `wildcard-transitive` | C, C++ | `#include` closure chains through re-exports |
-| `namespace` | Python | Module aliases resolved at call site |
-
-### Chunked parse-and-resolve
-
-`parse` processes files in ~20 MB byte-budget chunks to bound memory. Per chunk:
-1. Worker pool dispatches files (or sequential fallback via `skipWorkers`)
-2. Each worker: detect language → load grammar → run queries → return unified `ParseWorkerResult`
-3. Synthesize wildcard bindings (`wildcard-synthesis.ts`)
-4. Resolve imports and heritage
-5. Collect `BindingAccumulator` entries for cross-file propagation
-
-Workers: `workers/worker-pool.ts`, `workers/parse-worker.ts`.
-
-### Heritage and MRO
-
-All languages emit unified `ExtractedHeritage` (child, parent, `EXTENDS`/`IMPLEMENTS`). MRO phase walks the heritage graph using per-language strategy:
-- **`first-wins`** — Java, C#, C++, TS, Ruby, Go
-- **`c3`** — Python (C3 linearization)
-- **`none`** — single-inheritance languages
-
-Unified walk: `lookupMethodByOwnerWithMRO()` in `model/resolve.ts`.
-
----
-
-## Full analysis flow
-
-`runFullAnalysis` in `run-analyze.ts` orchestrates everything around the pipeline:
-
-```
-CLI (analyze.ts) → runFullAnalysis(repoPath, options, callbacks)
-  1. Early exit if lastCommit == HEAD (unless --force)     [0%]
-  2. Cache existing embeddings from prior index             [0%]
-  3. runPipelineFromRepo() → KnowledgeGraph                [0-60%]
-  4. Clean up legacy KuzuDB files                          [60%]
-  5. initLbug() → loadGraphToLbug() via CSV streaming      [60-85%]
-  6. Create FTS indexes (File, Function, Class, Method...) [85-90%]
-  7. Restore cached embeddings (batch insert)              [88%]
-  8. Generate new embeddings if --embeddings               [90-98%]
-  9. Save metadata + register repo + update .gitignore     [98-100%]
- 10. Generate AI context files (AGENTS.md, CLAUDE.md)      [100%]
-```
-
-**Options:** `--force` (rebuild regardless), `--embeddings` (opt-in, skipped if >50k nodes), `--skipGit`, `--noStats`.
-
-## Storage
-
-```
-<repo>/.gitnexus/
-  ├── lbug           # LadybugDB database
-  ├── lbug.wal       # Write-ahead log
-  ├── lbug.lock      # Single-writer lock
-  └── meta.json      # lastCommit, indexedAt, stats
-
-~/.gitnexus/
-  └── registry.json  # Global repo registry (MCP discovery)
-```
-
-Managed by `repo-manager.ts`.
-
-## LadybugDB schema
-
-Defined in `lbug/schema.ts`. Separate node tables per type, single `CodeRelation` table.
-
-**Node tables:** File, Folder, Function, Class, Interface, Method, Constructor, CodeElement, Struct, Enum, Macro, Typedef, Union, Namespace, Trait, Impl, TypeAlias, Const, Static, Property, Record, Delegate, Annotation, Template, Module, Community, Process, Route, Tool, Section, Embedding.
-
-**Relation types** (`CodeRelation.type`): CONTAINS, DEFINES, CALLS, IMPORTS, EXTENDS, IMPLEMENTS, HAS_METHOD, HAS_PROPERTY, ACCESSES, METHOD_OVERRIDES, METHOD_IMPLEMENTS, MEMBER_OF, STEP_IN_PROCESS, HANDLES_ROUTE, FETCHES, HANDLES_TOOL, ENTRY_POINT_OF.
-
-## Embeddings and search
-
-**Embeddings** (`src/core/embeddings/`): Snowflake arctic-embed-xs (384D). Embeddable: File, Function, Class, Method, Interface. Incremental via SHA1 content hash. Separate `Embedding` table.
-
-**Search** (`src/core/search/`): Hybrid BM25 + semantic vector, merged via Reciprocal Rank Fusion (K=60).
+The runner (`pipeline-phases/runner.ts`) validates the DAG at startup (detects cycles and missing deps via topological sort), then executes phases in dependency order. Each phase receives:
+- `ctx: PipelineContext` — shared graph, repoPath, progress callback
+- `deps: Map<string, PhaseResult>` — outputs from all upstream phases
 
 ## Known limitations
 
 ### Overloaded method resolution
 
-Node IDs use arity suffix (`#<paramCount>`): `Method:file:Class.method#1` vs `#2`.
+Method and Constructor node IDs include an arity suffix (`#<paramCount>`) to
+disambiguate overloaded methods. Two overloads with different parameter counts
+produce distinct graph nodes: `Method:file:Class.method#1` vs
+`Method:file:Class.method#2`.
 
-**Same-arity disambiguation:** type-hash suffix `~type1,type2` when collision detected and type annotations present. Languages without types (Python, Ruby, JS) use arity-only. TS/JS overload signatures excluded (collapse to implementation body). See #651.
+**Same-arity overload disambiguation:** When two overloads share the same
+parameter count but differ in types (e.g. `save(int)` vs `save(String)`), a
+type-hash suffix `~type1,type2` is appended to produce distinct node IDs:
+`Method:file:Class.save#1~int` vs `Method:file:Class.save#1~String`. The suffix
+is only added when a same-arity collision is detected within a class and all
+parameters have non-null type annotations. Languages without type info (Python,
+Ruby, JS) fall back to arity-only IDs. TypeScript/JavaScript overload signatures
+are intentionally excluded from type-hashing because they are declaration-only
+contracts that should collapse to the implementation body's node ID. See issue
+\#651.
 
-**C++ const-qualified:** `$const` suffix after type-hash when non-const collision exists: `Method:file:Container.begin#0$const`.
+**C++ const-qualified overload disambiguation:** Methods overloaded by const
+qualification (e.g. `begin()` vs `begin() const`) are disambiguated via an
+`isConst` property and a `$const` ID suffix appended to the const-qualified
+variant when a non-const collision exists. The `$const` suffix appears after the
+type-hash suffix: e.g. `Method:file:Container.begin#0$const`.
 
-**Generic/template types:** type-hash uses `rawType` (full AST text including generics): `~vector<int>` vs `~vector<std::string>`.
+**Generic/template type preservation in type-hash:** The type-hash suffix uses
+`rawType` (full AST text including generic/template args) rather than the
+simplified `type` from `extractSimpleTypeName`. This means C++ template overloads
+like `process(vector<int>)` vs `process(vector<string>)` produce distinct IDs:
+`~vector<int>` vs `~vector<std::string>`. Java generic overloads like
+`process(List<String>)` vs `process(List<Integer>)` are a compile error due to
+type erasure, so this gap is theoretical for Java.
 
-**ID stability:** collision-only tags mean IDs change when overloads are added. `save#1` becomes `save#1~int` when `save(String)` is added.
+**ID stability on first overload:** Type and const tags are collision-only. When
+a class has `save(int)` as its only `save` method, the ID is `save#1` (no tag).
+Adding `save(String)` changes the original to `save#1~int`. This is correct for
+fresh analysis but means IDs are not stable across overload additions. Future
+incremental re-analysis should account for this.
 
-**Variadic matching:** confidence 0.7 when one side is variadic and the other has fixed count.
+**Variadic method matching:** When one side is variadic (`parameterCount`
+undefined) and the other has a fixed count, `METHOD_IMPLEMENTS` edges are
+emitted with confidence 0.7 instead of 1.0. Variadic methods like
+`foo(String... args)` may superficially match `foo(String s)` by type but
+are not guaranteed to be interchangeable across all languages (Java/Kotlin
+accept this via varargs sugar; TypeScript, C#, Rust do not).
 
-**METHOD_IMPLEMENTS confidence tiering:**
+**Confidence tiering** for `METHOD_IMPLEMENTS` edges:
 
-| Match quality | Confidence |
-|---|---|
-| Exact parameter types match | 1.0 |
-| Arity match, types unavailable | 1.0 |
-| Variadic vs fixed | 0.7 |
-| Insufficient info | 0.7 |
+| Match quality | Confidence | When |
+|---|---|---|
+| Exact parameter types match | 1.0 | Both sides have `parameterTypes` arrays and they match |
+| Arity (count) matches | 1.0 | Both sides have `parameterCount`, types unavailable |
+| Variadic vs fixed | 0.7 | One side is variadic, other has fixed count |
+| Lenient (insufficient info) | 0.7 | One or both sides lack type and count data |
 
 ## Related docs
 
-- [MIGRATION.md](MIGRATION.md) — breaking changes and migration guidance
-- [RUNBOOK.md](RUNBOOK.md) — operational commands and recovery
-- [GUARDRAILS.md](GUARDRAILS.md) — safety boundaries for humans and agents
-- [TESTING.md](TESTING.md) — how to run tests
-- `AGENTS.md` / `CLAUDE.md` — agent workflows and tool usage
+- [MIGRATION.md](MIGRATION.md) — breaking changes and migration guidance.
+- [RUNBOOK.md](RUNBOOK.md) — operational commands and recovery.  
+- [GUARDRAILS.md](GUARDRAILS.md) — safety boundaries for humans and agents.  
+- [TESTING.md](TESTING.md) — how to run tests.  
+- `AGENTS.md` / `CLAUDE.md` — agent workflows and tool usage expectations for **this** repo when indexed by GitNexus.

CLAUDE.md

@@ -35,7 +35,6 @@ If always-on instructions grow, load deep conventions via conditional reads (e.g
 ## Reference Documentation
 
 - **This repository:** [AGENTS.md](AGENTS.md) (Cursor + monorepo notes), [ARCHITECTURE.md](ARCHITECTURE.md), [CONTRIBUTING.md](CONTRIBUTING.md), [GUARDRAILS.md](GUARDRAILS.md).
-- **Call-resolution DAG:** See ARCHITECTURE.md § Call-Resolution DAG. Shared pipeline code in `gitnexus/src/core/ingestion/` must not name languages — use `LanguageProvider` hooks instead (see AGENTS.md).
 - **GitNexus:** `.claude/skills/gitnexus/`; MCP and indexed-repo rules live only in [AGENTS.md](AGENTS.md) (`gitnexus:start` … `gitnexus:end`). See **GitNexus rules** below.
 
 ## Changelog
@@ -51,4 +50,206 @@ If always-on instructions grow, load deep conventions via conditional reads (e.g
 
 ## GitNexus rules
 
-See the `<!-- gitnexus:start --> … <!-- gitnexus:end -->` block in **[AGENTS.md](AGENTS.md)** for the canonical MCP tools, impact analysis rules, and index instructions.
+GitNexus MCP rules are in the `<!-- gitnexus:start -->
+# GitNexus — Code Intelligence
+
+This project is indexed by GitNexus as **GitNexus** (4325 symbols, 10556 relationships, 300 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+
+> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+
+## Always Do
+
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+
+## When Debugging
+
+1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
+2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
+3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
+4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed
+
+## When Refactoring
+
+- **Renaming**: MUST use `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with `dry_run: false`.
+- **Extracting/Splitting**: MUST run `gitnexus_context({name: "target"})` to see all incoming/outgoing refs, then `gitnexus_impact({target: "target", direction: "upstream"})` to find all external callers before moving code.
+- After any refactor: run `gitnexus_detect_changes({scope: "all"})` to verify only expected files changed.
+
+## Never Do
+
+- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
+- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
+- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+
+## Tools Quick Reference
+
+| Tool | When to use | Command |
+|------|-------------|---------|
+| `query` | Find code by concept | `gitnexus_query({query: "auth validation"})` |
+| `context` | 360-degree view of one symbol | `gitnexus_context({name: "validateUser"})` |
+| `impact` | Blast radius before editing | `gitnexus_impact({target: "X", direction: "upstream"})` |
+| `detect_changes` | Pre-commit scope check | `gitnexus_detect_changes({scope: "staged"})` |
+| `rename` | Safe multi-file rename | `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` |
+| `cypher` | Custom graph queries | `gitnexus_cypher({query: "MATCH ..."})` |
+
+## Impact Risk Levels
+
+| Depth | Meaning | Action |
+|-------|---------|--------|
+| d=1 | WILL BREAK — direct callers/importers | MUST update these |
+| d=2 | LIKELY AFFECTED — indirect deps | Should test |
+| d=3 | MAY NEED TESTING — transitive | Test if critical path |
+
+## Resources
+
+| Resource | Use for |
+|----------|---------|
+| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
+| `gitnexus://repo/GitNexus/clusters` | All functional areas |
+| `gitnexus://repo/GitNexus/processes` | All execution flows |
+| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
+
+## Self-Check Before Finishing
+
+Before completing any code modification task, verify:
+1. `gitnexus_impact` was run for all modified symbols
+2. No HIGH/CRITICAL risk warnings were ignored
+3. `gitnexus_detect_changes()` confirms changes match expected scope
+4. All d=1 (WILL BREAK) dependents were updated
+
+## Keeping the Index Fresh
+
+After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
+
+```bash
+npx gitnexus analyze
+```
+
+If the index previously included embeddings, preserve them by adding `--embeddings`:
+
+```bash
+npx gitnexus analyze --embeddings
+```
+
+To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.embeddings` field shows the count (0 means no embeddings). **Running analyze without `--embeddings` will delete any previously generated embeddings.**
+
+> Claude Code users: A PostToolUse hook handles this automatically after `git commit` and `git merge`.
+
+## CLI
+
+| Task | Read this skill file |
+|------|---------------------|
+| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
+| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
+| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
+| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
+
+<!-- gitnexus:end -->`  block in **[AGENTS.md](AGENTS.md)** — load that section when working with MCP tools or the graph index.
+
+<!-- gitnexus:start -->
+# GitNexus — Code Intelligence
+
+This project is indexed by GitNexus as **GitNexus** (3298 symbols, 7954 relationships, 185 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+
+> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+
+## Always Do
+
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+
+## When Debugging
+
+1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
+2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
+3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
+4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed
+
+## When Refactoring
+
+- **Renaming**: MUST use `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with `dry_run: false`.
+- **Extracting/Splitting**: MUST run `gitnexus_context({name: "target"})` to see all incoming/outgoing refs, then `gitnexus_impact({target: "target", direction: "upstream"})` to find all external callers before moving code.
+- After any refactor: run `gitnexus_detect_changes({scope: "all"})` to verify only expected files changed.
+
+## Never Do
+
+- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
+- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
+- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+
+## Tools Quick Reference
+
+| Tool | When to use | Command |
+|------|-------------|---------|
+| `query` | Find code by concept | `gitnexus_query({query: "auth validation"})` |
+| `context` | 360-degree view of one symbol | `gitnexus_context({name: "validateUser"})` |
+| `impact` | Blast radius before editing | `gitnexus_impact({target: "X", direction: "upstream"})` |
+| `detect_changes` | Pre-commit scope check | `gitnexus_detect_changes({scope: "staged"})` |
+| `rename` | Safe multi-file rename | `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` |
+| `cypher` | Custom graph queries | `gitnexus_cypher({query: "MATCH ..."})` |
+
+## Impact Risk Levels
+
+| Depth | Meaning | Action |
+|-------|---------|--------|
+| d=1 | WILL BREAK — direct callers/importers | MUST update these |
+| d=2 | LIKELY AFFECTED — indirect deps | Should test |
+| d=3 | MAY NEED TESTING — transitive | Test if critical path |
+
+## Resources
+
+| Resource | Use for |
+|----------|---------|
+| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
+| `gitnexus://repo/GitNexus/clusters` | All functional areas |
+| `gitnexus://repo/GitNexus/processes` | All execution flows |
+| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
+
+## Self-Check Before Finishing
+
+Before completing any code modification task, verify:
+1. `gitnexus_impact` was run for all modified symbols
+2. No HIGH/CRITICAL risk warnings were ignored
+3. `gitnexus_detect_changes()` confirms changes match expected scope
+4. All d=1 (WILL BREAK) dependents were updated
+
+## Keeping the Index Fresh
+
+After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
+
+```bash
+npx gitnexus analyze
+```
+
+If the index previously included embeddings, preserve them by adding `--embeddings`:
+
+```bash
+npx gitnexus analyze --embeddings
+```
+
+To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.embeddings` field shows the count (0 means no embeddings). **Running analyze without `--embeddings` will delete any previously generated embeddings.**
+
+> Claude Code users: A PostToolUse hook handles this automatically after `git commit` and `git merge`.
+
+## CLI
+
+| Task | Read this skill file |
+|------|---------------------|
+| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
+| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
+| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
+| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
+
+<!-- gitnexus:end -->

CONTRIBUTING.md

@@ -21,127 +21,30 @@ This project uses the [PolyForm Noncommercial License 1.0.0](https://polyformpro
 ## Branch and pull requests
 
 - Use short-lived branches off the default branch of the repo you are targeting.
-- **PR titles MUST follow the conventional-commit format** — `pr-labeler.yml` enforces this on every PR and auto-applies the matching label so release notes group the change correctly.
+- Prefer **conventional commits** (short prefix + description), for example:
+
+  ```text
+  feat: add graph export option
+  fix: correct MCP tool schema for query
+  test: cover cluster merge edge case
+  docs: clarify analyze flags
+  ```
+
+- **PR title:** `[area] Short description` (e.g. `[cli] Fix index refresh race`).
 - **PR description:** what changed, why, how to verify (commands), and any risk or rollback notes.
 
-### Pull request titles
-
-Format: `<type>[(scope)][!]: <subject>`
-
-Allowed types and the release-notes section each one lands in (defined in `.github/release.yml`):
-
-| Type | Label applied | Release-notes section |
-|------|---------------|-----------------------|
-| `feat` | `enhancement` | 🚀 Features |
-| `fix` | `bug` | 🐛 Bug Fixes |
-| `perf` | `performance` | 🏎️ Performance |
-| `refactor` | `refactor` | 🔄 Refactoring |
-| `test` | `test` | 🧪 Tests |
-| `ci` | `ci` | 👷 CI/CD |
-| `build` / `deps` | `dependencies` | 📦 Dependencies |
-| `docs` | `documentation` | (grouped under Other Changes unless a Docs section is added) |
-| `chore` / `revert` | `chore` | (excluded from release notes) |
-
-Append `!` to the type (e.g. `feat(api)!: drop /v1 endpoint`) or include `BREAKING CHANGE:` in the PR body to flag a breaking change — the labeler then adds the `breaking` label and the 💥 Breaking Changes section is rendered first.
-
-Examples:
-
-```text
-feat(web): add smart chat scroll
-fix(extractors): resolve silent contract mis-resolution
-perf: avoid O(n²) traversal in heritage walker
-chore(deps): bump vitest to 3.0.0
-ci: standardize workflow concurrency
-```
-
-Commits within a PR may use any style — only the **merged PR title** shows up in release notes, so that's the one the convention applies to.
-
 ## Before you open a PR
 
 - [ ] Tests pass for the packages you touched (`gitnexus` and/or `gitnexus-web`).
 - [ ] Typecheck passes: `npx tsc --noEmit` in `gitnexus/` and `npx tsc -b --noEmit` in `gitnexus-web/`.
 - [ ] No secrets, tokens, or machine-specific paths committed.
 - [ ] Documentation updated if behavior or public CLI/MCP contract changes.
-- [ ] Pre-commit hook runs clean (`.husky/pre-commit` — formatting via lint-staged + typecheck for staged packages; tests run in CI only).
+- [ ] Pre-commit hook runs clean (`.husky/pre-commit` — typecheck + unit tests for staged packages).
 
 ## Code review
 
 Maintainers may request changes for correctness, tests, performance, or consistency with existing patterns. Keeping diffs focused makes review faster.
 
-## GitHub Actions — Concurrency Convention
-
-Every workflow under `.github/workflows/` MUST declare a top-level `concurrency:` block using this convention:
-
-- **Group key** starts with `${{ github.workflow }}` so no two workflows can collide on the same group name. The discriminator that follows is chosen per event shape:
-  - Branch/tag scope: `${{ github.workflow }}-${{ github.ref }}`
-  - Per-PR scope (for `issue_comment`, `pull_request_review*`, `pull_request` meta events): `${{ github.workflow }}-${{ github.event.pull_request.number || github.event.issue.number }}`
-  - `workflow_run` scope (e.g. `ci-report.yml`): `${{ github.workflow }}-${{ github.event.workflow_run.pull_requests[0].number || format('{0}/{1}', github.event.workflow_run.head_repository.full_name, github.event.workflow_run.head_branch) }}` — the fork fallback must be stable across reruns (never `workflow_run.id`, which is per-run-unique and defeats serialization).
-  - Global single-slot (manual dispatch utilities): `${{ github.workflow }}`
-  - **Reusable workflows invoked via `workflow_call`:** do NOT use `${{ github.workflow }}` in the group key — in called-workflow context its evaluation is ambiguous and can resolve to the caller's name, which would deadlock against the caller's own group. Use a hardcoded literal prefix and a `github.event_name`-aware expression that falls through to `github.run_id` for reusable invocations (see `ci.yml` for the canonical form).
-  - **Merge queue (`merge_group`)**: when this event is added, use `${{ github.workflow }}-${{ github.event.merge_group.head_ref }}` with `cancel-in-progress: false` (every queue entry is a distinct ref; never cancel).
-- **`cancel-in-progress` policy:**
-
-  | Event | `cancel-in-progress` | Why |
-  |-------|----------------------|-----|
-  | `pull_request` CI run | `true` | New push supersedes old run |
-  | `push` to `main` | `false` | Every main commit gets validated |
-  | Tag push (`v*` publish) | `false` | Never cancel mid-publish |
-  | `push` to `main` for release-candidate | `false` | Never cancel mid-RC publish |
-  | `workflow_dispatch` (release/publish) | `false` | Manual runs are intentional |
-  | `workflow_run` (sticky-comment reports) | `false` | Serialize, don't race |
-  | Per-PR bot workflows (`@claude`, review) | `false` | Serialize comments per PR |
-  | PR-meta re-checks (pr-description-check) | `true` | Cheap, latest wins |
-  | Single-slot utilities (triage sweep) | `true` | Latest dispatch supersedes |
-
-- For workflows that serve multiple events at once (e.g. `ci.yml` handles `pull_request`, `push`, and `workflow_call`), make `cancel-in-progress` event-aware:
-
-  ```yaml
-  concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: ${{ github.event_name == 'pull_request' }}
-  ```
-
-- When adding a new workflow, copy the concurrency block from an existing workflow of the same event shape.
-
 ## AI-assisted contributions
 
 If you use coding agents, follow project context files (e.g. `AGENTS.md`, `CLAUDE.md`) and avoid drive-by refactors unrelated to the issue. Prefer incremental, test-backed changes.
-
-## Releases
-
-Two publish workflows ship `gitnexus` to npm:
-
-- **Stable** (`.github/workflows/publish.yml`) — triggered by pushing any `v*`
-  tag. Publishes to the `latest` dist-tag with a changelog-backed GitHub
-  release. Maintainers are expected to tag from `main` as a convention; the
-  workflow itself does not enforce branch reachability.
-- **Release Candidate** (`.github/workflows/release-candidate.yml`) — runs on
-  every push to `main` (typically a merged PR) plus manual dispatch. Docs-only
-  changes are skipped via `paths-ignore`. Publishes to the `rc` dist-tag with
-  version `X.Y.Z-rc.N` and a GitHub prerelease, where:
-  - `X.Y.Z` is selected automatically. On push (and on dispatch with
-    `bump: auto`, the default) the workflow **continues the active rc cycle**:
-    if the registry already has `X.Y.Z-rc.*` versions with `X.Y.Z` > current
-    `latest`, it reuses the highest such base; otherwise it patch-bumps
-    from `latest`. Dispatching with `bump: patch|minor|major` **resets**
-    the cycle from `latest`.
-  - `N` is auto-incremented against existing `X.Y.Z-rc.*` entries on the
-    registry. First rc for a given base is `rc.1`.
-
-  Idempotency: the workflow pushes an `rc/<HEAD_SHA>` marker tag and a
-  `v<RC>` release tag **atomically, before** calling `npm publish`. The guard
-  refuses to re-run once the marker exists, so a post-publish failure will
-  not mint a duplicate rc for the same commit. The `v<RC>` tag points at a
-  detached release commit whose `package.json` matches the npm tarball
-  exactly (traceable releases). Recovery after a partial failure:
-
-  ```bash
-  git push --delete origin rc/<HEAD_SHA> v<RC>
-  # then redispatch the workflow with force: true
-  ```
-
-The rc workflow never moves `latest`. To verify after a change, inspect dist-tags:
-
-```bash
-npm view gitnexus dist-tags
-```

Dockerfile.cli

@@ -1,57 +0,0 @@
-ARG BUILDPLATFORM
-ARG TARGETPLATFORM
-
-# ── Builder ────────────────────────────────────────────────────────────
-# Native modules (tree-sitter-*, onnxruntime-node, node-gyp builds for
-# tree-sitter-proto / tree-sitter-swift) require python3 + a C/C++ toolchain.
-FROM node:22-alpine AS builder
-
-WORKDIR /app
-
-# Toolchain for node-gyp / native builds.
-RUN apk add --no-cache python3 make g++ git
-
-# Build gitnexus-shared first — gitnexus depends on it as a workspace.
-COPY gitnexus-shared/package.json gitnexus-shared/package-lock.json ./gitnexus-shared/
-RUN npm ci --prefix gitnexus-shared
-COPY gitnexus-shared ./gitnexus-shared
-RUN npm run build --prefix gitnexus-shared
-
-# Copy the full gitnexus package before installing — `npm ci` triggers
-# `postinstall` (patches tree-sitter-swift, builds the vendored
-# tree-sitter-proto) and `prepare` (compiles TypeScript via scripts/build.js),
-# both of which need the source tree.
-COPY gitnexus ./gitnexus
-RUN npm ci --prefix gitnexus
-
-# Drop dev dependencies for a smaller runtime layer.
-RUN npm prune --omit=dev --prefix gitnexus
-
-# ── Runtime ────────────────────────────────────────────────────────────
-FROM node:22-alpine AS runtime
-
-# curl for the healthcheck; git so `gitnexus` can clone repos at runtime.
-RUN apk add --no-cache curl git
-
-WORKDIR /app
-
-# Pre-create the data directory and hand it to the unprivileged `node` user
-# so the bind-mounted volume is writable without root.
-RUN mkdir -p /data/gitnexus && chown -R node:node /data
-
-COPY --from=builder --chown=node:node /app/gitnexus/dist ./gitnexus/dist
-COPY --from=builder --chown=node:node /app/gitnexus/node_modules ./gitnexus/node_modules
-COPY --from=builder --chown=node:node /app/gitnexus/package.json ./gitnexus/package.json
-COPY --from=builder --chown=node:node /app/gitnexus/vendor ./gitnexus/vendor
-
-USER node
-
-# The web UI defaults to http://localhost:4747 — keep that contract.
-ENV GITNEXUS_HOME=/data/gitnexus \
-    NODE_ENV=production \
-    PORT=4747
-
-EXPOSE 4747
-
-# Bind to 0.0.0.0 so the server is reachable from the host's mapped port.
-CMD ["node", "gitnexus/dist/cli/index.js", "serve", "--host", "0.0.0.0", "--port", "4747"]

Dockerfile.web

@@ -1,35 +0,0 @@
-ARG BUILDPLATFORM
-ARG TARGETPLATFORM
-
-FROM --platform=$BUILDPLATFORM node:22-alpine AS builder
-
-WORKDIR /app
-
-COPY gitnexus-shared/package.json gitnexus-shared/package-lock.json ./gitnexus-shared/
-RUN npm ci --prefix gitnexus-shared
-
-COPY gitnexus-shared ./gitnexus-shared
-RUN npm run build --prefix gitnexus-shared
-
-COPY gitnexus-web/package.json gitnexus-web/package-lock.json ./gitnexus-web/
-RUN npm ci --prefix gitnexus-web
-
-COPY gitnexus-web ./gitnexus-web
-RUN npm run build --prefix gitnexus-web
-
-FROM node:22-alpine AS runtime
-
-RUN apk add --no-cache curl
-
-WORKDIR /app
-
-COPY --from=builder /app/gitnexus-web/dist ./dist
-COPY docker-server.mjs ./docker-server.mjs
-
-RUN chown -R node:node /app
-
-USER node
-
-EXPOSE 4173
-
-CMD ["node", "docker-server.mjs"]

GUARDRAILS.md

@@ -1,69 +1,72 @@
-# Guardrails — GitNexus
+# Guardrails — GitNexus (repo + agents)
 
-Rules for **human contributors** and **AI agents**. Complements `AGENTS.md` (workflows) and `CONTRIBUTING.md` (PR process).
+Rules for **human contributors** and **AI agents** working on this codebase or publishing artifacts. These complement `AGENTS.md` / `CLAUDE.md` (which focus on GitNexus-in-GitNexus workflows).
 
-## Scope (least privilege)
+## Scope (typical agent session)
 
-- **Read:** Source, tests, docs, public config as needed.
-- **Write:** Only files required for the fix or feature; no unrelated formatting or refactors.
-- **Execute:** Tests, typecheck, documented CLI commands. No destructive commands on user data without approval.
-- **Off-limits:** Other people's machines, production deployments you don't own, credentials you lack permission to use.
+When automating changes in this repository, treat scope as **least privilege**:
 
-Maintainer may widen scope per task.
+- **Read:** Source, tests, docs, public config as needed for the task.  
+- **Write:** Only files required for the requested fix or feature; avoid unrelated formatting or refactors.  
+- **Execute:** Tests, typecheck, and documented CLI commands; do not run destructive commands on user data outside the repo without explicit approval.  
+- **Off-limits:** Other people’s machines, production deployments you don’t own, and credentials you didn’t receive permission to use.
+
+Adjust explicitly if the maintainer defines a different scope for a task.
 
 ---
 
 ## Non-negotiables
 
-1. **Never commit secrets** — API keys, tokens, real `.env` values, private URLs, session cookies. Use `.env.example` with placeholders.
-2. **Never rename with find-and-replace** in GitNexus-indexed projects — use `rename` MCP tool with `dry_run: true` first, review `graph` vs `text_search` edits. No separate `gitnexus rename` CLI exists.
-3. **Run impact analysis before editing shared symbols** — `impact` (upstream) for functions/classes/methods others call. Do not ignore HIGH/CRITICAL without maintainer sign-off.
-4. **Run `detect_changes` before commit** — confirm diffs map to expected symbols/processes when the graph is available.
-5. **Preserve embeddings** — if `.gitnexus/meta.json` shows embeddings, use `npx gitnexus analyze --embeddings`; plain `analyze` drops them.
+1. **Never commit secrets** — API keys, tokens, `.env` with real values, private URLs, or session cookies. Use `.env.example` with placeholders only.  
+2. **Never rename symbols with blind find-and-replace** when working in a GitNexus-indexed project — use the **`rename` MCP tool** with **`dry_run: true` first**, then review `graph` vs `text_search` edits. (There is no separate `gitnexus rename` CLI; renaming goes through MCP or editor integration.)  
+3. **Run impact analysis before editing shared symbols** — use **`impact`** (upstream) for functions/classes/methods others call; do not ignore **HIGH** / **CRITICAL** risk without maintainer sign-off.  
+4. **Prefer `detect_changes` before commit** — confirm diffs map to expected symbols/processes when the graph is available.  
+5. **Preserve embeddings** — if `.gitnexus/meta.json` shows embeddings, run `npx gitnexus analyze --embeddings` when refreshing the index; plain `analyze` can drop them.
 
 ---
 
 ## Signs (recurring failure patterns)
 
-Format: **Trigger → Instruction → Reason**. Append new Signs when the same mistake repeats.
+Use this format: **Trigger → Instruction → Reason**.  
+Append new Signs here when the same mistake repeats (e.g. CI broken twice the same way).
 
-### Stale graph after edits
+### Sign: Stale graph after edits
 
-- **Trigger:** MCP warns index is behind `HEAD`, or search doesn't match latest commit.
-- **Do:** `npx gitnexus analyze` (plus `--embeddings` if used).
-- **Why:** Tools query LadybugDB from last analyze; git changes are invisible until re-indexed.
+- **Trigger:** MCP or resources warn the index is behind `HEAD`, or code search doesn’t match latest commit.  
+- **Instruction:** Run `npx gitnexus analyze` from the repo root (plus `--embeddings` if the project used them).  
+- **Reason:** Tools query LadybugDB built at last analyze; git changes are invisible until re-indexed.
 
-### Embeddings vanished after analyze
+### Sign: Embeddings vanished after analyze
 
-- **Trigger:** Semantic search quality drops; `stats.embeddings` in `meta.json` is 0 after refresh.
-- **Do:** `npx gitnexus analyze --embeddings`, confirm `meta.json` reflects stored embeddings.
-- **Why:** Embedding generation is opt-in; analyze without the flag does not preserve prior vectors.
+- **Trigger:** Semantic search quality drops; `stats.embeddings` in `.gitnexus/meta.json` is 0 after a refresh.  
+- **Instruction:** Re-run `npx gitnexus analyze --embeddings` and confirm `meta.json` reflects stored embeddings.  
+- **Reason:** Embedding generation is opt-in; analyze without the flag does not preserve prior vectors.
 
-### MCP lists no repos
+### Sign: MCP lists no repos
 
-- **Trigger:** MCP stderr says no indexed repos.
-- **Do:** `npx gitnexus analyze` in the target repo; verify `npx gitnexus list` shows it.
-- **Why:** MCP discovers repos via `~/.gitnexus/registry.json`, populated by analyze.
+- **Trigger:** MCP stderr says no indexed repos.  
+- **Instruction:** Run `npx gitnexus analyze` in the target repository; verify `npx gitnexus list` shows it.  
+- **Reason:** The MCP server discovers repos via `~/.gitnexus/registry.json`, populated by analyze.
 
-### Wrong repo in multi-repo setups
+### Sign: Wrong repo in multi-repo setups
 
-- **Trigger:** Query/impact results belong to another project.
-- **Do:** Call `list_repos`, then pass `repo` on subsequent tools.
-- **Why:** Default target is ambiguous when multiple repos are registered.
+- **Trigger:** Query/impact results clearly belong to another project.  
+- **Instruction:** Call `list_repos`, then pass **`repo`** on subsequent tools (or use per-workspace MCP config).  
+- **Reason:** Default target may be ambiguous when multiple repos are registered.
 
-### LadybugDB lock / "database busy"
+### Sign: LadybugDB lock / “database busy”
 
-- **Trigger:** Errors opening `.gitnexus/lbug` while MCP and analyze both run.
-- **Do:** Stop overlapping processes (one writer at a time). Retry analyze or restart MCP.
-- **Why:** Embedded DB expects single-process ownership.
+- **Trigger:** Errors opening `.gitnexus/lbug` while MCP and analyze both run.  
+- **Instruction:** Stop overlapping processes; one writer at a time. Retry analyze or restart MCP.  
+- **Reason:** Embedded DB expects single-process ownership of the store.
 
 ---
 
 ## Publishing & supply chain
 
-- **npm:** Do not publish from unreviewed automation. Bump version intentionally; tag releases to match `package.json`.
-- **Dependencies:** Minimal, auditable `package.json` changes; run tests and CI after lockfile updates.
-- **License:** PolyForm Noncommercial 1.0.0 — do not relicense without maintainer approval.
+- **npm:** Do not publish from unreviewed automation; follow maintainer release process. Bump version intentionally; tag releases to match `package.json`.  
+- **Dependencies:** Prefer minimal, auditable changes to `package.json`; run tests and CI after lockfile updates.  
+- **License:** This project ships under **PolyForm Noncommercial 1.0.0** — do not relicense or imply a different license in docs or metadata without maintainer approval.
 
 ---
 
@@ -71,15 +74,15 @@ Format: **Trigger → Instruction → Reason**. Append new Signs when the same m
 
 Stop and ask a **human maintainer** when:
 
-- Impact analysis shows HIGH/CRITICAL risk and the task still requires the change.
-- You need to alter CI, release, or security-sensitive config.
-- Requirements conflict (e.g. "speed up analyze" vs "must keep all embeddings on huge repo").
+- Impact analysis shows **HIGH** / **CRITICAL** risk and the task still requires the change.  
+- You need to alter **CI**, **release**, or **security-sensitive** config.  
+- Requirements conflict (e.g. “speed up analyze” vs “must keep all embeddings on huge repo”).  
 - You are unsure whether data loss is acceptable (`clean`, forced migrations, schema changes).
 
 ---
 
 ## Related docs
 
-- [ARCHITECTURE.md](ARCHITECTURE.md) — components and data flow
-- [RUNBOOK.md](RUNBOOK.md) — commands for recovery
-- [CONTRIBUTING.md](CONTRIBUTING.md) — PR and commit expectations
+- [ARCHITECTURE.md](ARCHITECTURE.md) — components and data flow.  
+- [RUNBOOK.md](RUNBOOK.md) — commands for recovery.  
+- [CONTRIBUTING.md](CONTRIBUTING.md) — PR and commit expectations.

MIGRATION.md

@@ -1,49 +1,5 @@
 # Migration Guide
 
-## `impact` tool may now return `{ status: 'ambiguous' }` (PR #888, issue #470)
-
-Before this change the `impact` MCP tool silently picked the first match
-when the `target` name hit multiple symbols (Class → Interface → Function
-→ Method → Constructor priority UNION). This often produced analysis for
-the wrong symbol with no signal back to the caller.
-
-After this change, when the resolver finds more than one viable match
-and the caller supplied none of `target_uid` / `file_path` / `kind`,
-`impact` returns a disambiguation response shaped like:
-
-```json
-{
-  "status": "ambiguous",
-  "message": "Found N symbols matching '<target>'. Use target_uid, file_path, or kind to disambiguate.",
-  "target": { "name": "<target>" },
-  "direction": "upstream",
-  "impactedCount": 0,
-  "risk": "UNKNOWN",
-  "candidates": [
-    { "uid": "...", "name": "...", "kind": "Function", "filePath": "...", "line": 42, "score": 0.76 }
-  ]
-}
-```
-
-### Do I need to migrate?
-
-**Probably not, but check for assumptions.** Callers that unconditionally
-read `result.byDepth` / `result.summary` / `result.affected_processes`
-without first checking `result.status` will now see `undefined` in the
-ambiguous case. The fix is to branch on `result.status === 'ambiguous'`
-first and follow up with `target_uid` (preferred) or `file_path` / `kind`.
-
-The `context` tool's ambiguous response is a strict superset of the
-existing shape — every candidate gains a `score` field, no existing field
-has changed. No migration required for `context` callers.
-
-### What happens on re-index?
-
-Nothing — this is an MCP-surface change only. The graph schema, indexer,
-and stored data are untouched.
-
----
-
 ## OVERRIDES → METHOD_OVERRIDES (PR #642)
 
 The `OVERRIDES` relationship type has been renamed to `METHOD_OVERRIDES` for

README.md

@@ -335,141 +335,6 @@ cd ../gitnexus-web && npm install
 npm run dev
 ```
 
-## Docker
-
-The official Docker setup ships **two signed images** orchestrated by `docker-compose.yaml`:
-
-| Image                                              | Purpose                                                                |
-| -------------------------------------------------- | ---------------------------------------------------------------------- |
-| `ghcr.io/abhigyanpatwari/gitnexus:latest`          | CLI / `gitnexus serve` backend (HTTP API on port `4747`, MCP, indexer) |
-| `ghcr.io/abhigyanpatwari/gitnexus-web:latest`      | Static web UI (port `4173`)                                            |
-
-> **Heads-up — image rename.** Earlier releases published the web UI under
-> `ghcr.io/abhigyanpatwari/gitnexus`. Starting with the introduction of the
-> bundled backend, that slug now hosts the CLI/server image and the UI moved
-> to `ghcr.io/abhigyanpatwari/gitnexus-web`. The previous tags remain
-> available for pulling, but new versions are only published under the new
-> slugs. Update your `docker run` / compose files accordingly (or just adopt
-> the bundled compose).
-
-### One-command setup
-
-```bash
-docker compose up -d
-```
-
-This starts the server on `http://localhost:4747` and the web UI on
-`http://localhost:4173`. The UI auto-detects the server because the browser
-runs on the host and reaches the container via the mapped port.
-
-A named volume (`gitnexus-data`) persists the global registry, indexes, and
-cloned repos at `/data/gitnexus` inside the server container. To make repos on
-your host machine indexable, set `WORKSPACE_DIR` before bringing the stack up:
-
-```bash
-WORKSPACE_DIR=$HOME/code docker compose up -d
-# Inside the server container the directory is mounted read-only at /workspace.
-docker compose exec gitnexus-server gitnexus index /workspace/my-repo
-```
-
-### Direct `docker run`
-
-```bash
-# Server
-docker run --rm -d \
-  --name gitnexus-server \
-  -p 4747:4747 \
-  -v gitnexus-data:/data/gitnexus \
-  ghcr.io/abhigyanpatwari/gitnexus:latest
-
-# Web UI
-docker run --rm -d \
-  --name gitnexus-web \
-  -p 4173:4173 \
-  ghcr.io/abhigyanpatwari/gitnexus-web:latest
-```
-
-Optional env file (override image tags, container names, ports, workspace dir):
-
-```bash
-cp .env.example .env
-docker compose --env-file .env up -d
-```
-
-### Versioning & supply-chain protection
-
-The Docker images are version-locked to the npm package:
-
-- Both images are **only published from `vX.Y.Z` git tags**, and the workflow
-  refuses to build unless the tag exactly matches `gitnexus/package.json`'s
-  version. So `ghcr.io/abhigyanpatwari/gitnexus:1.6.2` is byte-for-byte the
-  same release as `npm install gitnexus@1.6.2` — no drift, no floating
-  builds from `main`.
-- `:latest` is auto-promoted only from non-prerelease tags by the Docker
-  metadata action, so it always points at a real, npm-published version.
-
-Both images are signed with [Cosign keyless signing][cosign-keyless] using the
-workflow's GitHub OIDC identity, and shipped with build provenance and SBOM
-attestations. **This is your protection against supply-chain attacks**: even if
-an attacker republishes a same-named image elsewhere (or somehow pushes to a
-typo-squatted registry), they cannot forge a Cosign signature tied to
-`abhigyanpatwari/GitNexus`'s `docker.yml`. Always verify before pulling into
-sensitive environments:
-
-```bash
-cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
-  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
-  --certificate-oidc-issuer https://token.actions.githubusercontent.com
-```
-
-The regex pins the certificate identity to this repo's `docker.yml` workflow
-**run from a `v*` tag** — rejecting unsigned images, images signed by other
-workflows, and images signed from unprotected refs.
-
-You can also inspect the build provenance and SBOM:
-
-```bash
-cosign download attestation ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
-  --predicate-type https://slsa.dev/provenance/v1
-```
-
-#### Kubernetes: enforce signatures at admission
-
-For Kubernetes deployments, ship the bundled
-[`ClusterImagePolicy`](deploy/kubernetes/cluster-image-policy.yaml) so the
-[Sigstore policy-controller][policy-controller] rejects any GitNexus pod whose
-image is not signed by this repo's `docker.yml` running from a `vX.Y.Z` tag —
-the same identity the `cosign verify` snippet above pins.
-
-```bash
-# 1. Install the controller (one-time, cluster-wide)
-helm repo add sigstore https://sigstore.github.io/helm-charts && helm repo update
-helm install policy-controller -n cosign-system --create-namespace \
-  sigstore/policy-controller
-
-# 2. Opt your namespace in
-kubectl label namespace <your-ns> policy.sigstore.dev/include=true
-
-# 3. Apply the policy
-kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml
-```
-
-After this, attempting to deploy an unsigned image — or one signed by anything
-other than `abhigyanpatwari/GitNexus`'s `docker.yml` at a `v*` tag — fails the
-admission webhook before a pod is ever created. This turns the verifiable
-signature into an enforced policy, which is the supply-chain control most
-clusters actually need.
-
-[cosign-keyless]: https://docs.sigstore.dev/cosign/signing/overview/
-[policy-controller]: https://docs.sigstore.dev/policy-controller/overview/
-
-### Files
-
-- [Dockerfile.web](Dockerfile.web) — builds `gitnexus-shared` and `gitnexus-web`, then serves the production frontend.
-- [Dockerfile.cli](Dockerfile.cli) — builds the CLI/server (with its native deps) and runs `gitnexus serve --host 0.0.0.0`.
-- [docker-compose.yaml](docker-compose.yaml) — starts both signed images side by side.
-- [.env.example](.env.example) — overrides for image names, container names, ports, and the workspace mount.
-
 The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.
 
 **Local Backend Mode:** Run `gitnexus serve` and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.

TESTING.md

@@ -20,9 +20,9 @@ From repository root, unless noted:
 cd gitnexus
 npm install
 npm run build
-npm test                    # full suite: vitest run
-npm run test:unit           # unit only: vitest run test/unit
+npm test                    # unit: vitest run test/unit
 npm run test:integration    # integration suite
+npm run test:all
 npm run test:coverage
 npx tsc --noEmit            # typecheck (matches CI)
 ```
@@ -42,11 +42,8 @@ npm run test:e2e            # Playwright (requires gitnexus serve + npm run dev)
 
 A husky pre-commit hook (`.husky/pre-commit`) runs automatically on every `git commit`:
 
-1. **Formatting** — `lint-staged` runs prettier on staged files
-2. **`gitnexus-web/` files staged** → `tsc -b --noEmit`
-3. **`gitnexus/` files staged** → `tsc --noEmit`
-
-Tests do **not** run in the pre-commit hook — they run in CI (`ci-tests.yml`) only.
+- **`gitnexus-web/` files staged** → `tsc -b --noEmit` + `vitest run`
+- **`gitnexus/` files staged** → `tsc --noEmit` + `vitest run --project default`
 
 Skip with `git commit --no-verify` (use sparingly).
 
@@ -80,7 +77,7 @@ Re-run the full relevant suite when:
 
 GitHub Actions (`.github/workflows/ci.yml`) orchestrate:
 
-- **`ci-quality.yml`** — prettier format check, eslint lint, `tsc --noEmit` for `gitnexus/`, `tsc -b --noEmit` for `gitnexus-web/`
+- **`ci-quality.yml`** — `tsc --noEmit` for `gitnexus/` + `tsc -b --noEmit` for `gitnexus-web/`
 - **`ci-tests.yml`** — `vitest run` with coverage (ubuntu) + cross-platform (macOS, Windows)
 - **`ci-e2e.yml`** — Playwright E2E tests, gated on `gitnexus-web/**` changes
 

deploy/kubernetes/cluster-image-policy.yaml

@@ -1,64 +0,0 @@
-# Sigstore policy-controller ClusterImagePolicy for GitNexus container images.
-#
-# This enforces — at admission time — that every Pod pulling a
-# `ghcr.io/abhigyanpatwari/gitnexus` or `gitnexus-web` image is using a build
-# that was Cosign-keyless-signed by this repository's `docker.yml` workflow
-# running from a `vX.Y.Z` git tag. Unsigned images, images signed by other
-# workflows, and images signed from unprotected refs (e.g. `main`, PR branches)
-# are rejected.
-#
-# Prerequisites
-# -------------
-# 1. Install the Sigstore policy-controller in your cluster (Helm):
-#
-#      helm repo add sigstore https://sigstore.github.io/helm-charts
-#      helm repo update
-#      helm install policy-controller -n cosign-system --create-namespace \
-#        sigstore/policy-controller
-#
-# 2. Opt namespaces in to verification:
-#
-#      kubectl label namespace <your-ns> policy.sigstore.dev/include=true
-#
-# 3. Apply this policy:
-#
-#      kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml
-#
-# After this, `kubectl run --image=ghcr.io/abhigyanpatwari/gitnexus:<tag>` in
-# any opted-in namespace will only succeed if the image carries a valid
-# Sigstore signature with the pinned identity.
-#
-# References
-# - https://docs.sigstore.dev/policy-controller/overview/
-# - https://github.com/sigstore/policy-controller
-apiVersion: policy.sigstore.dev/v1beta1
-kind: ClusterImagePolicy
-metadata:
-  name: gitnexus-signed-images
-spec:
-  # Apply to both published GitNexus images on GHCR. Image references always
-  # carry a tag or digest at admission time, so these two globs cover every
-  # `gitnexus:<tag>`, `gitnexus@sha256:...`, `gitnexus-web:<tag>`, and
-  # `gitnexus-web@sha256:...` reference.
-  images:
-    - glob: 'ghcr.io/abhigyanpatwari/gitnexus*'
-  authorities:
-    - name: gitnexus-cosign-keyless
-      keyless:
-        # Public-good Sigstore Fulcio root.
-        url: https://fulcio.sigstore.dev
-        identities:
-          # Pin both the OIDC issuer (GitHub Actions) AND the exact workflow
-          # path running from a `vX.Y.Z` (or `vX.Y.Z-prerelease`) tag. Same
-          # regex the README's `cosign verify` example uses; it rejects:
-          #   * unsigned images
-          #   * signatures from any other repo / workflow
-          #   * signatures from non-tag refs (main, PRs, release branches)
-          #   * signatures from arbitrary non-semver tags
-          - issuer: https://token.actions.githubusercontent.com
-            subjectRegExp: ^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$
-      # Cross-check the signature against the public Rekor transparency log,
-      # so an attacker who briefly compromised Fulcio cannot retroactively
-      # mint a signature without leaving a public, append-only audit record.
-      ctlog:
-        url: https://rekor.sigstore.dev

docker-compose.yaml

@@ -1,45 +0,0 @@
-services:
-  gitnexus-server:
-    image: ${SERVER_IMAGE:-ghcr.io/abhigyanpatwari/gitnexus:latest}
-    container_name: ${SERVER_CONTAINER_NAME:-gitnexus-server}
-    # Map the server to the same host port the web UI expects by default
-    # (http://localhost:4747). The browser runs on the host, so the UI's
-    # built-in default works without any reconfiguration.
-    ports:
-      - '${SERVER_HOST_PORT:-4747}:4747'
-    volumes:
-      # Persist the global registry, indexes, and cloned repos across runs.
-      - gitnexus-data:/data/gitnexus
-      # Optional: mount a host workspace so `gitnexus index <path>` can see
-      # repos you already have on disk. The default points at an empty
-      # `./workspace/` sibling that compose will create on first start —
-      # it intentionally does NOT bind-mount the repo root, which would
-      # expose `.git`, `.env`, and CI secrets to the container.
-      # Override with `WORKSPACE_DIR=/abs/path/to/your/repos`.
-      - ${WORKSPACE_DIR:-./workspace}:/workspace:ro
-    restart: unless-stopped
-    healthcheck:
-      test: ['CMD', 'curl', '-fsS', 'http://localhost:4747/api/heartbeat']
-      interval: 30s
-      timeout: 5s
-      retries: 3
-      start_period: 15s
-
-  gitnexus-web:
-    image: ${WEB_IMAGE:-ghcr.io/abhigyanpatwari/gitnexus-web:latest}
-    container_name: ${WEB_CONTAINER_NAME:-gitnexus-web}
-    ports:
-      - '${WEB_HOST_PORT:-4173}:4173'
-    depends_on:
-      gitnexus-server:
-        condition: service_healthy
-    restart: unless-stopped
-    healthcheck:
-      test: ['CMD', 'curl', '-f', 'http://localhost:4173/']
-      interval: 30s
-      timeout: 5s
-      retries: 3
-      start_period: 10s
-
-volumes:
-  gitnexus-data:

docker-server.mjs

@@ -1,81 +0,0 @@
-import { createReadStream } from 'node:fs';
-import { stat } from 'node:fs/promises';
-import { createServer } from 'node:http';
-import { extname, join, normalize, sep } from 'node:path';
-
-const host = '0.0.0.0';
-const port = Number(process.env.PORT || '4173');
-const root = join(process.cwd(), 'dist');
-
-const contentTypes = {
-  '.css': 'text/css; charset=utf-8',
-  '.html': 'text/html; charset=utf-8',
-  '.js': 'text/javascript; charset=utf-8',
-  '.json': 'application/json; charset=utf-8',
-  '.map': 'application/json; charset=utf-8',
-  '.png': 'image/png',
-  '.svg': 'image/svg+xml',
-  '.txt': 'text/plain; charset=utf-8',
-  '.woff': 'font/woff',
-  '.woff2': 'font/woff2',
-};
-
-function resolvePath(urlPath) {
-  let decoded;
-  try {
-    decoded = decodeURIComponent(urlPath);
-  } catch {
-    return null;
-  }
-  if (decoded.includes('\0')) return null;
-  const cleanPath = normalize(decoded.replace(/^\/+/, ''));
-  const candidate = join(root, cleanPath);
-  if (candidate !== root && !candidate.startsWith(root + sep)) return null;
-  return candidate;
-}
-
-const server = createServer(async (req, res) => {
-  const requestPath = req.url?.split('?')[0] || '/';
-  let filePath = resolvePath(requestPath);
-
-  if (!filePath) {
-    res.writeHead(400);
-    res.end('Bad request');
-    return;
-  }
-
-  try {
-    const fileStat = await stat(filePath).catch(() => null);
-    if (fileStat?.isDirectory()) {
-      filePath = join(filePath, 'index.html');
-    } else if (!fileStat?.isFile()) {
-      filePath = join(root, 'index.html');
-    }
-
-    const finalStat = await stat(filePath).catch(() => null);
-    if (!finalStat?.isFile()) {
-      res.writeHead(404);
-      res.end('Not found');
-      return;
-    }
-
-    res.writeHead(200, {
-      'Cache-Control': filePath.includes('/assets/')
-        ? 'public, max-age=31536000, immutable'
-        : 'no-cache',
-      'Content-Type': contentTypes[extname(filePath)] || 'application/octet-stream',
-      'Cross-Origin-Opener-Policy': 'same-origin',
-      'Cross-Origin-Embedder-Policy': 'require-corp',
-    });
-    const stream = createReadStream(filePath);
-    stream.on('error', () => res.destroy());
-    stream.pipe(res);
-  } catch (error) {
-    res.writeHead(500);
-    res.end(error instanceof Error ? error.message : 'Internal server error');
-  }
-});
-
-server.listen(port, host, () => {
-  console.log(`gitnexus-web listening on http://${host}:${port}`);
-});

docker-server.test.mjs

@@ -1,107 +0,0 @@
-import { mkdir, mkdtemp, rm, unlink, writeFile } from 'node:fs/promises';
-import http, { createServer } from 'node:http';
-import { tmpdir } from 'node:os';
-import { dirname, join } from 'node:path';
-import { spawn } from 'node:child_process';
-import { fileURLToPath } from 'node:url';
-import { after, before, it } from 'node:test';
-import assert from 'node:assert/strict';
-
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const serverScript = join(__dirname, 'docker-server.mjs');
-
-function getFreePort() {
-  return new Promise((resolve) => {
-    const s = createServer();
-    s.listen(0, '127.0.0.1', () => {
-      const { port } = s.address();
-      s.close(() => resolve(port));
-    });
-  });
-}
-
-function rawGet(port, path) {
-  return new Promise((resolve, reject) => {
-    const req = http.request({ host: '127.0.0.1', port, path }, (res) => {
-      let body = '';
-      res.setEncoding('utf8');
-      res.on('data', (chunk) => {
-        body += chunk;
-      });
-      res.on('end', () => resolve({ status: res.statusCode, headers: res.headers, body }));
-    });
-    req.on('error', reject);
-    req.end();
-  });
-}
-
-async function waitForServer(port, retries = 30) {
-  for (let i = 0; i < retries; i++) {
-    try {
-      await rawGet(port, '/');
-      return;
-    } catch {
-      await new Promise((r) => setTimeout(r, 100));
-    }
-  }
-  throw new Error('Server did not start in time');
-}
-
-let tmpDir, serverPort, child;
-
-before(async () => {
-  tmpDir = await mkdtemp(join(tmpdir(), 'gitnexus-docker-test-'));
-  const distDir = join(tmpDir, 'dist');
-  const assetsDir = join(distDir, 'assets');
-  await mkdir(assetsDir, { recursive: true });
-  await writeFile(join(distDir, 'index.html'), '<html><body>spa</body></html>');
-  await writeFile(join(assetsDir, 'app.abc123.js'), 'console.log("app")');
-
-  serverPort = await getFreePort();
-  child = spawn(process.execPath, [serverScript], {
-    cwd: tmpDir,
-    env: { ...process.env, PORT: String(serverPort) },
-    stdio: 'pipe',
-  });
-  child.on('error', (err) => {
-    throw err;
-  });
-
-  await waitForServer(serverPort);
-});
-
-after(async () => {
-  child?.kill();
-  if (tmpDir) await rm(tmpDir, { recursive: true, force: true });
-});
-
-it('serves a valid asset with immutable cache header', async () => {
-  const res = await rawGet(serverPort, '/assets/app.abc123.js');
-  assert.equal(res.status, 200);
-  assert.match(res.headers['cache-control'], /immutable/);
-  assert.equal(res.headers['cross-origin-opener-policy'], 'same-origin');
-  assert.equal(res.headers['cross-origin-embedder-policy'], 'require-corp');
-});
-
-it('serves SPA fallback for unknown routes', async () => {
-  const res = await rawGet(serverPort, '/some/unknown/route');
-  assert.equal(res.status, 200);
-  assert.match(res.body, /spa/);
-  assert.match(res.headers['cache-control'], /no-cache/);
-});
-
-it('rejects path traversal with 400', async () => {
-  const res = await rawGet(serverPort, '/../../../etc/passwd');
-  assert.equal(res.status, 400);
-});
-
-it('rejects percent-encoded null bytes with 400', async () => {
-  const res = await rawGet(serverPort, '/foo%00bar');
-  assert.equal(res.status, 400);
-});
-
-it('returns 404 when dist/index.html is missing', async () => {
-  await unlink(join(tmpDir, 'dist', 'index.html'));
-  const res = await rawGet(serverPort, '/nonexistent-page');
-  assert.equal(res.status, 404);
-});

gitnexus-shared/src/graph/types.ts

@@ -131,20 +131,4 @@ export interface GraphRelationship {
   confidence: number;
   reason: string;
   step?: number;
-  /**
-   * Per-signal evidence trace for edges emitted by the scope-based
-   * resolution pipeline (RFC #909 Ring 2 PKG #925). Populated by
-   * `emit-references.ts` when draining `ReferenceIndex` into the graph
-   * so downstream query / audit tools can inspect *why* a given edge
-   * was emitted with its confidence value.
-   *
-   * Optional and additive — every existing edge emitter ignores this
-   * field, and every existing query continues to work whether or not
-   * an edge carries it.
-   */
-  evidence?: readonly {
-    readonly kind: string;
-    readonly weight: number;
-    readonly note?: string;
-  }[];
 }

gitnexus-shared/src/index.ts

@@ -23,128 +23,3 @@ export type { MroStrategy } from './mro-strategy.js';
 
 // Pipeline progress
 export type { PipelinePhase, PipelineProgress } from './pipeline.js';
-
-// ─── Scope-based resolution — RFC #909 (Ring 1 #910) ────────────────────────
-// Data model (RFC §2)
-export type { SymbolDefinition } from './scope-resolution/symbol-definition.js';
-export type {
-  ScopeId,
-  DefId,
-  ScopeKind,
-  Range,
-  Capture,
-  CaptureMatch,
-  BindingRef,
-  ImportEdge,
-  TypeRef,
-  Scope,
-  ResolutionEvidence,
-  Resolution,
-  Reference,
-  ReferenceIndex,
-  LookupParams,
-  RegistryContributor,
-  ParsedImport,
-  ParsedTypeBinding,
-  WorkspaceIndex,
-  Callsite,
-  ScopeLookup,
-} from './scope-resolution/types.js';
-
-// Evidence + tie-break constants (RFC Appendix A, Appendix B)
-export { EvidenceWeights, typeBindingWeightAtDepth } from './scope-resolution/evidence-weights.js';
-export { ORIGIN_PRIORITY } from './scope-resolution/origin-priority.js';
-export type { OriginForTieBreak } from './scope-resolution/origin-priority.js';
-
-// Language classification (RFC §6.1 Ring 3/4 governance)
-export {
-  LanguageClassifications,
-  isProductionLanguage,
-} from './scope-resolution/language-classification.js';
-export type { LanguageClassification } from './scope-resolution/language-classification.js';
-
-// Core indexes over per-file artifacts (RFC §3.1; Ring 2 SHARED #913)
-export { buildDefIndex } from './scope-resolution/def-index.js';
-export type { DefIndex } from './scope-resolution/def-index.js';
-export { buildModuleScopeIndex } from './scope-resolution/module-scope-index.js';
-export type { ModuleScopeIndex, ModuleScopeEntry } from './scope-resolution/module-scope-index.js';
-export { buildQualifiedNameIndex } from './scope-resolution/qualified-name-index.js';
-export type { QualifiedNameIndex } from './scope-resolution/qualified-name-index.js';
-
-// Strict type-reference resolver (RFC §4.6; Ring 2 SHARED #916)
-// `ScopeLookup` is defined in `./scope-resolution/types.js` and exported
-// from the type-export block above — not from this module.
-export { resolveTypeRef } from './scope-resolution/resolve-type-ref.js';
-export type { ResolveTypeRefContext } from './scope-resolution/resolve-type-ref.js';
-
-// ScopeExtractor output contracts (RFC §3.2 Phase 1; Ring 2 PKG #919)
-export type { ParsedFile } from './scope-resolution/parsed-file.js';
-export type { ReferenceSite, ReferenceKind, CallForm } from './scope-resolution/reference-site.js';
-
-// Method-dispatch materialized view over HeritageMap (RFC §3.1; Ring 2 SHARED #914)
-export { buildMethodDispatchIndex } from './scope-resolution/method-dispatch-index.js';
-export type {
-  MethodDispatchIndex,
-  MethodDispatchInput,
-} from './scope-resolution/method-dispatch-index.js';
-
-// SCC-aware cross-file finalize (RFC §3.2 Phase 2; Ring 2 SHARED #915)
-export { finalize } from './scope-resolution/finalize-algorithm.js';
-export type {
-  FinalizeInput,
-  FinalizeFile,
-  FinalizeHooks,
-  FinalizeOutput,
-  FinalizedScc,
-  FinalizeStats,
-} from './scope-resolution/finalize-algorithm.js';
-
-// Scope-aware registries + 7-step lookup (RFC §4; Ring 2 SHARED #917)
-export { buildClassRegistry } from './scope-resolution/registries/class-registry.js';
-export type { ClassRegistry } from './scope-resolution/registries/class-registry.js';
-export { buildMethodRegistry } from './scope-resolution/registries/method-registry.js';
-export type {
-  MethodRegistry,
-  MethodLookupOptions,
-} from './scope-resolution/registries/method-registry.js';
-export { buildFieldRegistry } from './scope-resolution/registries/field-registry.js';
-export type {
-  FieldRegistry,
-  FieldLookupOptions,
-} from './scope-resolution/registries/field-registry.js';
-export { lookupCore } from './scope-resolution/registries/lookup-core.js';
-export type { CoreLookupParams } from './scope-resolution/registries/lookup-core.js';
-export { lookupQualified } from './scope-resolution/registries/lookup-qualified.js';
-export type { LookupQualifiedParams } from './scope-resolution/registries/lookup-qualified.js';
-export { composeEvidence, confidenceFromEvidence } from './scope-resolution/registries/evidence.js';
-export type { RawSignals } from './scope-resolution/registries/evidence.js';
-export {
-  compareByConfidenceWithTiebreaks,
-  CONFIDENCE_EPSILON,
-} from './scope-resolution/registries/tie-breaks.js';
-export type { TieBreakKey } from './scope-resolution/registries/tie-breaks.js';
-export { CLASS_KINDS, METHOD_KINDS, FIELD_KINDS } from './scope-resolution/registries/context.js';
-export type {
-  RegistryContext,
-  RegistryProviders,
-  OwnerScopedContributor,
-  ArityVerdict,
-} from './scope-resolution/registries/context.js';
-
-// Scope tree spine + position lookup (RFC §2.2 + §3.1; Ring 2 SHARED #912)
-export { makeScopeId, clearScopeIdInternPool } from './scope-resolution/scope-id.js';
-export type { ScopeIdInput } from './scope-resolution/scope-id.js';
-export { buildScopeTree, ScopeTreeInvariantError } from './scope-resolution/scope-tree.js';
-export type { ScopeTree } from './scope-resolution/scope-tree.js';
-export { buildPositionIndex } from './scope-resolution/position-index.js';
-export type { PositionIndex } from './scope-resolution/position-index.js';
-
-// Shadow-mode diff + aggregation (RFC §6.3; Ring 2 SHARED #918)
-export { diffResolutions } from './scope-resolution/shadow/diff.js';
-export type {
-  ShadowAgreement,
-  ShadowCallsite,
-  ShadowDiff,
-} from './scope-resolution/shadow/diff.js';
-export { aggregateDiffs } from './scope-resolution/shadow/aggregate.js';
-export type { LanguageParityRow, ShadowParityReport } from './scope-resolution/shadow/aggregate.js';

gitnexus-shared/src/lbug/schema-constants.ts

@@ -30,7 +30,6 @@ export const NODE_TABLES = [
   'TypeAlias',
   'Const',
   'Static',
-  'Variable',
   'Property',
   'Record',
   'Delegate',

gitnexus-shared/src/mro-strategy.ts

@@ -1,46 +1,23 @@
 /**
- * MRO (Method Resolution Order) strategy — shared canonical definition.
+ * MRO (Method Resolution Order) strategy — shared between CLI and any
+ * future consumer that reasons about multiple-inheritance semantics.
  *
- * Lives in `gitnexus-shared` so `model/resolve.ts` and `mro-processor.ts` share
- * the type without importing the language registry (avoids circular coupling).
+ * Lives in `gitnexus-shared` so the low-level resolution module
+ * (`core/ingestion/model/resolve.ts`) does not need to import from
+ * `languages/` — keeping the `model/` layer free of language-registry
+ * coupling.
  *
- * `first-wins` (default, Java/C#/Kotlin/Go/Swift/Dart):
- *   BFS ancestor walk in declaration order; first match wins.
- *
- * `leftmost-base` (C++):
- *   BFS walk; HeritageMap preserves source insertion order, so BFS naturally
- *   picks the leftmost base in diamond inheritance.
- *
- * `c3` (Python):
- *   C3-linearization; falls back to BFS on cyclic/inconsistent hierarchy.
- *   See model/resolve.ts § c3Linearize.
- *
- * `implements-split` (Java/C#/Kotlin):
- *   Low-level lookup is BFS; graph-level mro-processor detects and warns on
- *   interface-default method ambiguity.
- *
- * `qualified-syntax` (Rust):
- *   No auto-resolution — `lookupMethodByOwnerWithMRO` returns undefined immediately.
- *   Rust requires explicit `<Type as Trait>::method` syntax.
- *
- * `ruby-mixin` (Ruby):
- *   Kind-aware walk that does NOT short-circuit on direct owner first (`prepend`
- *   must beat the class's own method). Walk order:
- *     1. Prepend providers (reverse declaration — last-prepended wins)
- *     2. Direct owner's own methods
- *     3. Include providers (reverse declaration)
- *     4. Transitive ancestors (BFS fallback)
- *   Singleton dispatch: caller passes `ancestryOverride` (extend providers only);
- *   becomes a simple left-to-right scan. Miss NEVER falls through to file-scoped
- *   lookup — null-routes or honors `fallback`.
- *
- * @see model/resolve.ts § lookupMethodByOwnerWithMRO
- * @see languages/ruby.ts § selectDispatch
+ * Strategy semantics:
+ * - `first-wins`:       BFS ancestor walk, first match wins (default).
+ * - `leftmost-base`:    BFS ancestor walk, leftmost base wins (C++).
+ * - `c3`:               C3-linearized ancestor order, first match wins (Python).
+ * - `implements-split`: BFS walk, first match wins (Java/C#/Kotlin) — full
+ *                       interface-default ambiguity is handled at graph level.
+ * - `qualified-syntax`: No auto-resolution (Rust — requires `<T as Trait>::m`).
  */
 export type MroStrategy =
   | 'first-wins'
   | 'c3'
   | 'leftmost-base'
   | 'implements-split'
-  | 'qualified-syntax'
-  | 'ruby-mixin';
+  | 'qualified-syntax';

gitnexus-shared/src/scope-resolution/def-index.ts

@@ -1,62 +0,0 @@
-/**
- * `DefIndex` — O(1) `DefId → SymbolDefinition` materialization.
- *
- * The global "what is this id?" lookup. Every per-kind registry (ClassRegistry,
- * MethodRegistry, FieldRegistry) returns `DefId[]` and resolves them back to
- * full `SymbolDefinition` records through this index — one central hash map,
- * one allocation per def.
- *
- * Part of RFC #909 Ring 2 SHARED — #913.
- *
- * Consumed by: #917 (`Registry.lookup` implementations), #915 (SCC finalize).
- */
-
-import type { SymbolDefinition } from './symbol-definition.js';
-import type { DefId } from './types.js';
-
-export interface DefIndex {
-  readonly byId: ReadonlyMap<DefId, SymbolDefinition>;
-  readonly size: number;
-  get(id: DefId): SymbolDefinition | undefined;
-  has(id: DefId): boolean;
-}
-
-/**
- * Build a `DefIndex` from a flat list of `SymbolDefinition` records.
- *
- * **Collision policy: first-write-wins.** `DefId` is meant to be unique
- * (`nodeId` is the stable graph identifier), so a collision indicates an
- * upstream bug — most likely the same symbol parsed twice or a duplicate
- * commit into the pipeline. Rather than silently overwriting with a later
- * definition that may be partial or wrong, the first record wins and
- * subsequent records for the same id are dropped. Pipeline bugs surface
- * later as `has(id) === true` but the def looking older than expected,
- * which is easier to debug than a silent overwrite.
- *
- * Pure function — safe to call repeatedly; no side effects.
- */
-export function buildDefIndex(defs: readonly SymbolDefinition[]): DefIndex {
-  const byId = new Map<DefId, SymbolDefinition>();
-  for (const def of defs) {
-    if (byId.has(def.nodeId)) continue; // first-write-wins
-    byId.set(def.nodeId, def);
-  }
-  return wrapIndex(byId);
-}
-
-// ─── Internal ───────────────────────────────────────────────────────────────
-
-function wrapIndex(byId: Map<DefId, SymbolDefinition>): DefIndex {
-  return {
-    byId,
-    get size() {
-      return byId.size;
-    },
-    get(id: DefId): SymbolDefinition | undefined {
-      return byId.get(id);
-    },
-    has(id: DefId): boolean {
-      return byId.has(id);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/evidence-weights.ts

@@ -1,90 +0,0 @@
-/**
- * `EvidenceWeights` — RFC Appendix A (authoritative values).
- *
- * Starting calibration for scope-based resolution. Shadow-first rollout
- * tunes these against legacy DAG parity. Every `ResolutionEvidence.weight`
- * value in the codebase MUST reference this map; inline magic numbers are a
- * lint violation. Extends issue #429 (centralize hardcoded confidence values).
- *
- * Evidence composes additively inside `composeEvidence`; the sum is capped
- * at 1.0 in `Resolution.confidence`.
- */
-
-/**
- * Authoritative weight map. Keys are a mix of `ResolutionEvidence.kind`
- * values and special modifiers (scope-chain depth, MRO depth decay,
- * unlinked-import multiplicative cap).
- */
-export const EvidenceWeights = {
-  // ─── Where-found signals (visibility) ─────────────────────────────────────
-  /** `BindingRef.origin === 'local'` */
-  local: 0.55,
-  /** `BindingRef.origin === 'import'` */
-  import: 0.45,
-  /** `BindingRef.origin === 'reexport'` */
-  reexport: 0.4,
-  /** `BindingRef.origin === 'namespace'` */
-  namespace: 0.4,
-  /** `BindingRef.origin === 'wildcard'` */
-  wildcard: 0.3,
-
-  // ─── Scope-chain deduction (per-hop) ──────────────────────────────────────
-  /** Deducted per parent-hop taken (depth-0 = 0, depth-1 = −0.02, …). */
-  scopeChainPerDepth: -0.02,
-
-  // ─── Receiver-type-binding signal (decays by MRO depth) ───────────────────
-  /**
-   * Weight applied when the receiver's type binding resolves to a class that
-   * declares the candidate as a method/field. Decays by MRO depth: direct
-   * class = index 0; 1 parent hop = index 1; etc. Falls back to the last
-   * value for depths beyond the table.
-   */
-  typeBindingByMroDepth: [0.5, 0.42, 0.36, 0.32, 0.3] as const,
-
-  // ─── Corroborating signals ────────────────────────────────────────────────
-  /** `def.ownerId === resolvedReceiver.def.id` (exact owner match). */
-  ownerMatch: 0.2,
-  /** Explanatory only — retained for debuggability. Never discriminates
-   *  because surviving candidates already passed `acceptedKinds`. */
-  kindMatch: 0.0,
-
-  // ─── Arity compatibility (from `provider.arityCompatibility`) ─────────────
-  /** `provider.arityCompatibility(...) === 'compatible'` */
-  arityMatchCompatible: 0.1,
-  /** `provider.arityCompatibility(...) === 'unknown'` */
-  arityMatchUnknown: 0.0,
-  /** `provider.arityCompatibility(...) === 'incompatible'` — penalizes;
-   *  candidates filtered only when a compatible candidate exists. */
-  arityMatchIncompatible: -0.15,
-
-  // ─── Global fallback (only when nothing lexically visible) ────────────────
-  /** Hit via `QualifiedNameIndex.byQualifiedName`. */
-  globalQualified: 0.35,
-  /** Fallback hit in a `byName` index (and nothing was lexically visible). */
-  globalName: 0.1,
-
-  // ─── Degraded signals ─────────────────────────────────────────────────────
-  /** Call/reference flowing through a `dynamic-unresolved` edge. */
-  dynamicImportUnresolved: 0.02,
-
-  // ─── Unresolved-import cap (multiplicative, applied per-signal) ───────────
-  /**
-   * Multiplicative cap on the edge-derived evidence signal
-   * (`import`/`wildcard`/`reexport`/`namespace`) when
-   * `ImportEdge.linkStatus === 'unresolved'`. Independent corroborating
-   * signals on the same candidate (`owner-match`, `arity-match`,
-   * `type-binding`) are NOT penalized.
-   */
-  unlinkedImportMultiplier: 0.5,
-} as const;
-
-/**
- * Look up the `type-binding` signal weight for a given MRO depth, falling
- * back to the last tabulated value for depths beyond the table.
- */
-export function typeBindingWeightAtDepth(mroDepth: number): number {
-  const table = EvidenceWeights.typeBindingByMroDepth;
-  if (mroDepth < 0) return table[0];
-  if (mroDepth >= table.length) return table[table.length - 1];
-  return table[mroDepth];
-}

gitnexus-shared/src/scope-resolution/finalize-algorithm.ts

@@ -1,663 +0,0 @@
-/**
- * `finalize` — cross-file finalize algorithm for the SemanticModel
- * (RFC §3.2 Phase 2; Ring 2 SHARED #915).
- *
- * Pure logic that takes per-file parse output (`ParsedImport[]` +
- * `SymbolDefinition[]`) and returns:
- *
- *   - Linked `ImportEdge[]` per module scope, with `targetModuleScope` and
- *     `targetDefId` filled where resolvable; edges that could not be
- *     resolved within the hard fixpoint cap are marked
- *     `linkStatus: 'unresolved'`.
- *   - Materialized `bindings` per module scope — local defs merged with
- *     imported / wildcard-expanded / re-exported names via the provider's
- *     `mergeBindings` precedence.
- *   - The SCC condensation of the import graph, exposed so disjoint SCCs
- *     can be processed in parallel by callers that want that.
- *
- * The algorithm is **SCC-aware**: it runs Tarjan SCC over the file-level
- * import graph, processes SCCs in reverse-topological order (leaves
- * first), and within each SCC runs a bounded fixpoint link pass capped at
- * `N = |edges in SCC|`. Cyclic imports finalize without hanging; malformed
- * inputs are bounded by the cap.
- *
- * **No language-specific logic.** Target resolution, wildcard expansion,
- * and binding precedence all go through caller-supplied hooks
- * (`resolveImportTarget`, `expandsWildcardTo`, `mergeBindings`) that
- * match the LanguageProvider surface from #911.
- *
- * **Dynamic imports rule.** `kind === 'dynamic-unresolved'` passes through
- * as an `ImportEdge { kind: 'dynamic-unresolved', targetFile: null }`
- * with no `BindingRef`. They are parse-time signals, not linkable targets.
- */
-
-import type { SymbolDefinition } from './symbol-definition.js';
-import type { BindingRef, ImportEdge, ParsedImport, ScopeId, WorkspaceIndex } from './types.js';
-
-// ─── Public contracts ───────────────────────────────────────────────────────
-
-/** Per-file input for the finalize pass. */
-export interface FinalizeFile {
-  readonly filePath: string;
-  /** The module scope id for this file; owns the finalized imports + bindings. */
-  readonly moduleScope: ScopeId;
-  readonly parsedImports: readonly ParsedImport[];
-  /**
-   * Defs exported from this file — the "what other files can import by name"
-   * surface. Typically those with `isExported: true` (the module's own
-   * declarations) plus, for multi-hop re-export chains, the re-exported
-   * names the parser chose to surface here.
-   *
-   * **Multi-hop re-export contract.** `finalize` resolves an edge
-   * `A → B (importedName: 'X')` by looking up `X` in `B.localDefs`. If B
-   * only has `export { X } from './C'` and the parser *does not* include
-   * `X` in `B.localDefs`, A's edge hits the fixpoint cap and is marked
-   * `linkStatus: 'unresolved'`. The fixpoint does NOT mutate `localDefs`
-   * across iterations — it is static input.
-   *
-   * Parsers that want multi-hop re-export chains to settle end-to-end must
-   * include re-exported names in the intermediate file's `localDefs` (with
-   * the original `DefId` of the source symbol). This keeps the algorithm
-   * O(1) per lookup and avoids graph-crawl during finalize.
-   */
-  readonly localDefs: readonly SymbolDefinition[];
-}
-
-/** Input to `finalize`. */
-export interface FinalizeInput {
-  readonly files: readonly FinalizeFile[];
-  /** Opaque workspace context forwarded to provider hooks. */
-  readonly workspaceIndex: WorkspaceIndex;
-}
-
-/**
- * Provider-supplied hooks. Mirror the optional LanguageProvider scope-
- * resolution hooks declared in #911; `finalize` calls them pure-ly and
- * expects pure answers.
- */
-export interface FinalizeHooks {
-  /**
-   * Resolve a raw import target to the concrete file path that owns it.
-   * Return `null` when no target file is resolvable (e.g., `np.foo` when
-   * `numpy` is external to the workspace).
-   */
-  resolveImportTarget(
-    targetRaw: string,
-    fromFile: string,
-    workspaceIndex: WorkspaceIndex,
-  ): string | null;
-
-  /**
-   * For a wildcard `import * from M`, return the names visible in the
-   * exporting module scope `M`. The finalize pass looks each name up in
-   * `M`'s local defs to produce a concrete `BindingRef`; names with no
-   * matching export are dropped.
-   */
-  expandsWildcardTo(targetModuleScope: ScopeId, workspaceIndex: WorkspaceIndex): readonly string[];
-
-  /**
-   * Merge `incoming` bindings into `existing` for a given name. Called
-   * once per name at each scope. Typical rules:
-   *   - Python: local > imported > wildcard (last-write-wins within tier).
-   *   - Rust: explicit `use` > glob; `pub use` overrides.
-   * Return value replaces the bucket entirely — no implicit append.
-   */
-  mergeBindings(
-    existing: readonly BindingRef[],
-    incoming: readonly BindingRef[],
-    scope: ScopeId,
-  ): readonly BindingRef[];
-}
-
-/** One SCC in the file-level import graph. */
-export interface FinalizedScc {
-  readonly files: readonly string[];
-  /** True iff this SCC has ≥ 2 files OR a single file that self-imports. */
-  readonly isCycle: boolean;
-}
-
-/**
- * Counters reported by `finalize`.
- *
- * **Counting granularity** — all edge counters are **per-`ParsedImport`**,
- * not per-materialized-`ImportEdge`. A single `wildcard` ParsedImport that
- * expands to N exports counts as one linked edge in these stats; the
- * materialized output (`FinalizeOutput.imports`) will have N edges for
- * that input. `dynamic-unresolved` ParsedImports count as linked (they
- * pass through with no `linkStatus`), so `linkedEdges` ≠ "has a
- * BindingRef" — use the `bindings` map for that.
- *
- * In other words: `totalEdges === input.parsedImports.length` summed
- * across files, and `linkedEdges + unresolvedEdges === totalEdges`.
- */
-export interface FinalizeStats {
-  readonly totalFiles: number;
-  /** Total `ParsedImport` records seen across all files. */
-  readonly totalEdges: number;
-  /**
-   * `ParsedImport`s whose finalized edge does NOT carry
-   * `linkStatus: 'unresolved'`. Includes `dynamic-unresolved` pass-throughs.
-   */
-  readonly linkedEdges: number;
-  /** `ParsedImport`s whose finalized edge carries `linkStatus: 'unresolved'`. */
-  readonly unresolvedEdges: number;
-  readonly sccCount: number;
-  readonly largestSccSize: number;
-}
-
-export interface FinalizeOutput {
-  /** Linked `ImportEdge[]` per module scope, in original input order. */
-  readonly imports: ReadonlyMap<ScopeId, readonly ImportEdge[]>;
-  /** Materialized bindings per module scope. */
-  readonly bindings: ReadonlyMap<ScopeId, ReadonlyMap<string, readonly BindingRef[]>>;
-  /** SCCs in reverse-topological order (leaves first). */
-  readonly sccs: readonly FinalizedScc[];
-  readonly stats: FinalizeStats;
-}
-
-// ─── Entry point ───────────────────────────────────────────────────────────
-
-export function finalize(input: FinalizeInput, hooks: FinalizeHooks): FinalizeOutput {
-  const byFilePath = new Map<string, FinalizeFile>();
-  for (const f of input.files) byFilePath.set(f.filePath, f);
-
-  // ── Phase 0: pre-resolve raw import targets (one syscall-equivalent per
-  // (file, parsedImport)). Edges with no resolvable target become
-  // `linkStatus: 'unresolved'` or, for dynamic-unresolved, pass through
-  // with `targetFile: null`.
-  const edgeIndex = new Map<string, ImportEdgeDraft[]>(); // filePath → drafts
-  let totalEdges = 0;
-
-  for (const file of input.files) {
-    const drafts: ImportEdgeDraft[] = [];
-    for (const parsed of file.parsedImports) {
-      const draft = makeEdgeDraft(parsed, file, hooks, input.workspaceIndex);
-      drafts.push(draft);
-      totalEdges++;
-    }
-    edgeIndex.set(file.filePath, drafts);
-  }
-
-  // ── Phase 1: build file-level import graph (only resolvable edges form
-  // graph edges; unresolvable ones are terminal and contribute no
-  // fixpoint obligation).
-  const graph = new Map<string, Set<string>>();
-  for (const file of input.files) {
-    graph.set(file.filePath, new Set());
-  }
-  for (const [fromFile, drafts] of edgeIndex) {
-    const edges = graph.get(fromFile)!;
-    for (const d of drafts) {
-      if (d.targetFile !== null && byFilePath.has(d.targetFile)) {
-        edges.add(d.targetFile);
-      }
-    }
-  }
-
-  // ── Phase 2: Tarjan SCC → reverse-topological list of SCCs.
-  const sccs = tarjanSccs(graph);
-
-  // ── Phase 3: process SCCs in reverse-topological order (leaves first).
-  // Within each SCC, run a bounded fixpoint that resolves intra-SCC edges.
-  // Edges leaving the SCC are already resolved (their target SCC is
-  // already finalized); edges inside the SCC may need multiple passes.
-  const linkedByScope = new Map<ScopeId, readonly ImportEdge[]>();
-  let linkedEdges = 0;
-
-  for (const scc of sccs) {
-    const sccFiles = new Set(scc.files);
-    const capacity = countEdgesWithin(edgeIndex, sccFiles);
-
-    // Run the fixpoint up to `capacity` iterations. Each iteration tries to
-    // resolve every still-unlinked edge in the SCC; stops early if a pass
-    // makes no progress.
-    let progressed = true;
-    let iterations = 0;
-    while (progressed && iterations < capacity) {
-      progressed = false;
-      iterations++;
-      for (const filePath of scc.files) {
-        const drafts = edgeIndex.get(filePath)!;
-        for (const draft of drafts) {
-          if (draft.finalized !== null) continue;
-          const finalized = tryFinalize(draft, byFilePath);
-          if (finalized !== null) {
-            draft.finalized = finalized;
-            progressed = true;
-          }
-        }
-      }
-    }
-
-    // Any drafts still not finalized within this SCC hit the cap → unresolved.
-    for (const filePath of scc.files) {
-      const drafts = edgeIndex.get(filePath)!;
-      for (const draft of drafts) {
-        if (draft.finalized !== null) continue;
-        draft.finalized = {
-          ...draft.base,
-          linkStatus: 'unresolved' as const,
-        };
-      }
-    }
-  }
-
-  // ── Phase 4: collect finalized `ImportEdge[]` per module scope, preserving
-  // input order within each file, and wildcard-expand where applicable.
-  for (const file of input.files) {
-    const drafts = edgeIndex.get(file.filePath)!;
-    const finalized: ImportEdge[] = [];
-    for (const d of drafts) {
-      const edge = d.finalized!;
-      if (d.source.kind === 'wildcard' && edge.linkStatus !== 'unresolved') {
-        // Produce one `wildcard-expanded` ImportEdge per exported name.
-        const expanded = expandWildcard(edge, byFilePath, hooks, input.workspaceIndex);
-        for (const e of expanded) finalized.push(e);
-      } else {
-        finalized.push(edge);
-      }
-      if (edge.linkStatus !== 'unresolved') linkedEdges++;
-    }
-    linkedByScope.set(file.moduleScope, Object.freeze(finalized));
-  }
-
-  // ── Phase 5: materialize module-scope bindings (local + imports + wildcards),
-  // delegating precedence to `provider.mergeBindings`.
-  const bindingsByScope = materializeBindings(input.files, linkedByScope, hooks);
-
-  // ── Stats.
-  const sccCount = sccs.length;
-  let largestSccSize = 0;
-  for (const scc of sccs) {
-    if (scc.files.length > largestSccSize) largestSccSize = scc.files.length;
-  }
-  const stats: FinalizeStats = {
-    totalFiles: input.files.length,
-    totalEdges,
-    linkedEdges,
-    unresolvedEdges: totalEdges - linkedEdges,
-    sccCount,
-    largestSccSize,
-  };
-
-  return Object.freeze({
-    imports: linkedByScope,
-    bindings: bindingsByScope,
-    sccs,
-    stats,
-  });
-}
-
-// ─── Internal: edge drafting (phase 0) ──────────────────────────────────────
-
-interface ImportEdgeDraft {
-  readonly source: ParsedImport;
-  readonly fromFile: string;
-  readonly fromScope: ScopeId;
-  readonly targetFile: string | null;
-  readonly base: ImportEdge;
-  finalized: ImportEdge | null;
-}
-
-function makeEdgeDraft(
-  parsed: ParsedImport,
-  file: FinalizeFile,
-  hooks: FinalizeHooks,
-  workspace: WorkspaceIndex,
-): ImportEdgeDraft {
-  // Dynamic-unresolved passes through — no `BindingRef`, no target file.
-  if (parsed.kind === 'dynamic-unresolved') {
-    const base: ImportEdge = {
-      localName: parsed.localName,
-      targetFile: null,
-      targetExportedName: '',
-      kind: 'dynamic-unresolved',
-    };
-    return {
-      source: parsed,
-      fromFile: file.filePath,
-      fromScope: file.moduleScope,
-      targetFile: null,
-      base,
-      finalized: base, // already fully finalized
-    };
-  }
-
-  const targetFile = hooks.resolveImportTarget(parsed.targetRaw ?? '', file.filePath, workspace);
-
-  // Edge is unresolvable at the file level — mark unresolved now.
-  if (targetFile === null) {
-    const edgeKind = parsed.kind === 'wildcard' ? 'wildcard-expanded' : parsed.kind;
-    const localName = parsed.kind === 'wildcard' ? '' : parsed.localName;
-    const targetExportedName = extractExportedName(parsed);
-    const base: ImportEdge = {
-      localName,
-      targetFile: null,
-      targetExportedName,
-      kind: edgeKind,
-      linkStatus: 'unresolved',
-    };
-    return {
-      source: parsed,
-      fromFile: file.filePath,
-      fromScope: file.moduleScope,
-      targetFile: null,
-      base,
-      finalized: base,
-    };
-  }
-
-  // Resolvable at the file level; intra-SCC fixpoint may still fail to fill
-  // in `targetDefId` (e.g., symbol not exported from target).
-  const edgeKind = parsed.kind === 'wildcard' ? 'wildcard-expanded' : parsed.kind;
-  const localName = parsed.kind === 'wildcard' ? '' : parsed.localName;
-  const targetExportedName = extractExportedName(parsed);
-  const base: ImportEdge = {
-    localName,
-    targetFile,
-    targetExportedName,
-    kind: edgeKind,
-  };
-  return {
-    source: parsed,
-    fromFile: file.filePath,
-    fromScope: file.moduleScope,
-    targetFile,
-    base,
-    finalized: null,
-  };
-}
-
-function extractExportedName(parsed: ParsedImport): string {
-  switch (parsed.kind) {
-    case 'named':
-    case 'alias':
-    case 'namespace':
-    case 'reexport':
-      return parsed.importedName;
-    case 'wildcard':
-    case 'dynamic-unresolved':
-      return '';
-  }
-}
-
-// ─── Internal: per-edge finalization (phase 3) ─────────────────────────────
-
-function tryFinalize(
-  draft: ImportEdgeDraft,
-  byFilePath: Map<string, FinalizeFile>,
-): ImportEdge | null {
-  const targetFile = draft.targetFile;
-  if (targetFile === null) return draft.base; // already terminal
-
-  const targetModule = byFilePath.get(targetFile);
-  if (targetModule === undefined) return draft.base; // external target — leave as-is
-
-  // Wildcards finalize at the file level; their per-name expansion happens
-  // in phase 4. At this stage we just record the target module scope.
-  if (draft.source.kind === 'wildcard') {
-    return {
-      ...draft.base,
-      targetModuleScope: targetModule.moduleScope,
-    };
-  }
-
-  // Namespace imports alias the target *module*; they don't name a
-  // specific export. Link the module scope unconditionally. If the target
-  // also exposes a def whose simple name matches `importedName` (some
-  // languages emit a synthetic module-def), pick it up as the `targetDefId`
-  // so consumers can reach the module as a symbol — but its absence is not
-  // a failure.
-  if (draft.source.kind === 'namespace') {
-    const moduleDef = findExportByName(targetModule.localDefs, extractExportedName(draft.source));
-    return {
-      ...draft.base,
-      targetModuleScope: targetModule.moduleScope,
-      ...(moduleDef !== undefined ? { targetDefId: moduleDef.nodeId } : {}),
-    };
-  }
-
-  // named / alias / reexport: look up the imported name in the target's
-  // local defs. Multi-hop re-export chains settle iteratively — each hop
-  // resolves once its prior hop is finalized.
-  const importedName = extractExportedName(draft.source);
-  const exported = findExportByName(targetModule.localDefs, importedName);
-
-  if (exported === undefined) {
-    // Target resolvable but the name isn't exported — keep trying in case a
-    // re-export inside the target's SCC surfaces it in a later iteration.
-    return null;
-  }
-
-  const transitiveVia = draft.source.kind === 'reexport' ? Object.freeze([targetFile]) : undefined;
-
-  return {
-    ...draft.base,
-    targetModuleScope: targetModule.moduleScope,
-    targetDefId: exported.nodeId,
-    ...(transitiveVia !== undefined ? { transitiveVia } : {}),
-  };
-}
-
-/**
- * The "simple" (unqualified) name of a def, for import-name matching.
- *
- * Canonical source: `def.qualifiedName` — the tail after the last `.` (or
- * the whole string if no dot). Defs without a qualifiedName can't be
- * resolved by name here and return `null`; callers treat that as "name
- * not exported" and either retry in a later fixpoint iteration or mark
- * the edge unresolved.
- */
-function deriveSimpleName(def: SymbolDefinition): string | null {
-  const q = def.qualifiedName;
-  if (q === undefined || q.length === 0) return null;
-  const dot = q.lastIndexOf('.');
-  return dot === -1 ? q : q.slice(dot + 1);
-}
-
-function findExportByName(
-  defs: readonly SymbolDefinition[],
-  name: string,
-): SymbolDefinition | undefined {
-  for (const d of defs) {
-    if (deriveSimpleName(d) === name) return d;
-  }
-  return undefined;
-}
-
-function countEdgesWithin(edgeIndex: Map<string, ImportEdgeDraft[]>, files: Set<string>): number {
-  let n = 0;
-  for (const filePath of files) {
-    const drafts = edgeIndex.get(filePath);
-    if (drafts === undefined) continue;
-    for (const d of drafts) {
-      if (d.targetFile !== null && files.has(d.targetFile)) n++;
-    }
-  }
-  // Guarantee at least one pass even for a trivial SCC (ensures deterministic
-  // fixpoint termination even when a single-file SCC has zero intra-SCC edges
-  // but still needs one settle pass).
-  return Math.max(n, 1);
-}
-
-// ─── Internal: wildcard expansion (phase 4) ────────────────────────────────
-
-function expandWildcard(
-  edge: ImportEdge,
-  byFilePath: Map<string, FinalizeFile>,
-  hooks: FinalizeHooks,
-  workspace: WorkspaceIndex,
-): readonly ImportEdge[] {
-  if (edge.targetModuleScope === undefined || edge.targetFile === null) {
-    return [edge]; // unresolvable wildcard survives as a single unlinked edge
-  }
-  const target = byFilePath.get(edge.targetFile);
-  if (target === undefined) return [edge];
-
-  const names = hooks.expandsWildcardTo(edge.targetModuleScope, workspace);
-  if (names.length === 0) return [];
-
-  const expanded: ImportEdge[] = [];
-  for (const name of names) {
-    const def = findExportByName(target.localDefs, name);
-    if (def === undefined) continue;
-    expanded.push({
-      localName: name,
-      targetFile: edge.targetFile,
-      targetExportedName: name,
-      kind: 'wildcard-expanded',
-      targetModuleScope: edge.targetModuleScope,
-      targetDefId: def.nodeId,
-    });
-  }
-  return expanded;
-}
-
-// ─── Internal: bindings materialization (phase 5) ───────────────────────────
-
-function materializeBindings(
-  files: readonly FinalizeFile[],
-  linkedByScope: ReadonlyMap<ScopeId, readonly ImportEdge[]>,
-  hooks: FinalizeHooks,
-): ReadonlyMap<ScopeId, ReadonlyMap<string, readonly BindingRef[]>> {
-  const out = new Map<ScopeId, ReadonlyMap<string, readonly BindingRef[]>>();
-
-  for (const file of files) {
-    const scopeBindings = new Map<string, readonly BindingRef[]>();
-
-    // Start with local defs as `origin: 'local'` bindings.
-    for (const def of file.localDefs) {
-      const name = deriveSimpleName(def);
-      if (name === null) continue;
-      const incoming: BindingRef[] = [{ def, origin: 'local' }];
-      const existing = scopeBindings.get(name) ?? [];
-      scopeBindings.set(name, hooks.mergeBindings(existing, incoming, file.moduleScope));
-    }
-
-    // Layer in finalized imports.
-    const imports = linkedByScope.get(file.moduleScope) ?? [];
-    for (const edge of imports) {
-      if (edge.targetDefId === undefined || edge.linkStatus === 'unresolved') continue;
-      // Every def the importing file needs to reach is in some other file's
-      // `localDefs`; walk all files to find it. In practice we could index
-      // this, but at finalize-time N(files) is small per workspace pass.
-      const def = findDefById(files, edge.targetDefId);
-      if (def === undefined) continue;
-
-      const origin: BindingRef['origin'] =
-        edge.kind === 'namespace'
-          ? 'namespace'
-          : edge.kind === 'wildcard-expanded'
-            ? 'wildcard'
-            : edge.kind === 'reexport'
-              ? 'reexport'
-              : 'import';
-      const fallback = deriveSimpleName(def);
-      const name = edge.localName.length > 0 ? edge.localName : fallback;
-      if (name === null) continue;
-      const incoming: BindingRef[] = [{ def, origin, via: edge }];
-      const existing = scopeBindings.get(name) ?? [];
-      scopeBindings.set(name, hooks.mergeBindings(existing, incoming, file.moduleScope));
-    }
-
-    // Freeze nested buckets for immutability.
-    const frozen = new Map<string, readonly BindingRef[]>();
-    for (const [name, refs] of scopeBindings) {
-      frozen.set(name, Object.freeze(refs.slice()));
-    }
-    out.set(file.moduleScope, frozen);
-  }
-
-  return out;
-}
-
-function findDefById(files: readonly FinalizeFile[], defId: string): SymbolDefinition | undefined {
-  for (const f of files) {
-    for (const d of f.localDefs) {
-      if (d.nodeId === defId) return d;
-    }
-  }
-  return undefined;
-}
-
-// ─── Internal: Tarjan SCC ──────────────────────────────────────────────────
-
-/**
- * Iterative Tarjan SCC. Returns SCCs in **reverse-topological** order
- * (leaves first — a property Tarjan gives for free, and the order
- * `finalize` wants so leaves are fully resolved before their dependents).
- */
-function tarjanSccs(graph: ReadonlyMap<string, ReadonlySet<string>>): FinalizedScc[] {
-  const index = new Map<string, number>();
-  const lowlink = new Map<string, number>();
-  const onStack = new Set<string>();
-  const stack: string[] = [];
-  const sccs: FinalizedScc[] = [];
-  let idx = 0;
-
-  // Iterative DFS to avoid stack overflow on deep import chains.
-  const allNodes = Array.from(graph.keys()).sort(); // deterministic order
-  const iterStack: Array<{ node: string; children: Iterator<string>; entered: boolean }> = [];
-
-  for (const root of allNodes) {
-    if (index.has(root)) continue;
-    iterStack.push({
-      node: root,
-      children: (graph.get(root) ?? new Set<string>()).values(),
-      entered: false,
-    });
-    while (iterStack.length > 0) {
-      const frame = iterStack[iterStack.length - 1]!;
-
-      if (!frame.entered) {
-        frame.entered = true;
-        index.set(frame.node, idx);
-        lowlink.set(frame.node, idx);
-        idx++;
-        stack.push(frame.node);
-        onStack.add(frame.node);
-      }
-
-      const nextChild = frame.children.next();
-      if (nextChild.done) {
-        // Post-visit: compute SCC membership if frame.node is a root.
-        if (lowlink.get(frame.node) === index.get(frame.node)) {
-          const scc: string[] = [];
-          let selfInCycle = false;
-          while (true) {
-            const w = stack.pop()!;
-            onStack.delete(w);
-            scc.push(w);
-            // A single-file self-loop counts as a cycle.
-            if (w === frame.node) {
-              selfInCycle = (graph.get(w) ?? new Set()).has(w);
-              break;
-            }
-          }
-          const isCycle = scc.length > 1 || selfInCycle;
-          sccs.push({ files: Object.freeze(scc), isCycle });
-        }
-        iterStack.pop();
-        // Propagate lowlink to parent.
-        if (iterStack.length > 0) {
-          const parent = iterStack[iterStack.length - 1]!;
-          lowlink.set(parent.node, Math.min(lowlink.get(parent.node)!, lowlink.get(frame.node)!));
-        }
-        continue;
-      }
-
-      const child = nextChild.value;
-      if (!index.has(child)) {
-        iterStack.push({
-          node: child,
-          children: (graph.get(child) ?? new Set<string>()).values(),
-          entered: false,
-        });
-      } else if (onStack.has(child)) {
-        lowlink.set(frame.node, Math.min(lowlink.get(frame.node)!, index.get(child)!));
-      }
-    }
-  }
-
-  return sccs;
-}

gitnexus-shared/src/scope-resolution/language-classification.ts

@@ -1,49 +0,0 @@
-/**
- * `LanguageClassification` — RFC §6.1 Ring 3 / Ring 4 governance.
- *
- * Classifies each `SupportedLanguages` member for the rollout. Ring 4 (DAG
- * retirement) is gated on *all production languages* being registry-primary
- * and stable for one release cycle; `experimental` and `quarantined`
- * languages do not block.
- *
- * Initial classification (locked in Ring 1 #910):
- *   - production: javascript, typescript, python, java, c, cpp, csharp, go,
- *                 ruby, rust, php, kotlin, swift, dart
- *   - experimental: vue (embedded-language / SFC complexity),
- *                   cobol (regex-provider path)
- *   - quarantined: (none)
- */
-
-import { SupportedLanguages } from '../languages.js';
-
-export type LanguageClassification = 'production' | 'experimental' | 'quarantined';
-
-/**
- * The canonical classification for each supported language. Governance
- * changes (promote `experimental` → `production`, quarantine a language, …)
- * update this map in a dedicated PR.
- */
-export const LanguageClassifications: Readonly<Record<SupportedLanguages, LanguageClassification>> =
-  {
-    [SupportedLanguages.JavaScript]: 'production',
-    [SupportedLanguages.TypeScript]: 'production',
-    [SupportedLanguages.Python]: 'production',
-    [SupportedLanguages.Java]: 'production',
-    [SupportedLanguages.C]: 'production',
-    [SupportedLanguages.CPlusPlus]: 'production',
-    [SupportedLanguages.CSharp]: 'production',
-    [SupportedLanguages.Go]: 'production',
-    [SupportedLanguages.Ruby]: 'production',
-    [SupportedLanguages.Rust]: 'production',
-    [SupportedLanguages.PHP]: 'production',
-    [SupportedLanguages.Kotlin]: 'production',
-    [SupportedLanguages.Swift]: 'production',
-    [SupportedLanguages.Dart]: 'production',
-    [SupportedLanguages.Vue]: 'experimental',
-    [SupportedLanguages.Cobol]: 'experimental',
-  };
-
-/** Convenience predicate: is this language gating Ring 4 retirement? */
-export function isProductionLanguage(lang: SupportedLanguages): boolean {
-  return LanguageClassifications[lang] === 'production';
-}

gitnexus-shared/src/scope-resolution/method-dispatch-index.ts

@@ -1,145 +0,0 @@
-/**
- * `MethodDispatchIndex` — materialized view of class hierarchies keyed by
- * `DefId` (RFC §3.1; Ring 2 SHARED #914).
- *
- * Two O(1)-access maps used by `Registry.lookupMethod` and interface-
- * dispatch callers:
- *
- *   - `mroByOwnerDefId`       : owner class → full MRO ancestor chain
- *                               (excludes the owner itself, in per-language
- *                               strategy order).
- *   - `implsByInterfaceDefId` : interface/trait → classes that implement it.
- *
- * **Not an MRO implementation.** The build function is a pure aggregator: it
- * asks the caller (via `computeMro` and `implementsOf` callbacks) for the
- * per-language answers and materializes the two-way index. MRO strategies
- * live where they already do today (`model/resolve.ts § c3Linearize`,
- * `languages/ruby.ts § selectDispatch`, etc.) — this index does not
- * reimplement them.
- *
- * Why callbacks and not a shared strategy registry: the five strategies
- * (Python C3, Ruby kind-aware, Java/Kotlin linear, Rust qualified-syntax,
- * COBOL none) already exist in the CLI package and depend on the CLI's
- * `HeritageMap` + `SemanticModel`. Pulling them into `gitnexus-shared` would
- * require migrating both — out of scope for #914. Callbacks let the shared
- * build stay pure while honoring existing strategies verbatim.
- *
- * Consumed by: #917 (`Registry.lookupMethod` MRO fast path, interface
- * dispatch resolver).
- */
-
-import type { DefId } from './types.js';
-
-// ─── Public contracts ───────────────────────────────────────────────────────
-
-export interface MethodDispatchIndex {
-  /**
-   * Full MRO ancestor chain per owner class (excludes the owner itself).
-   * Order reflects the per-language strategy used by `computeMro`.
-   */
-  readonly mroByOwnerDefId: ReadonlyMap<DefId, readonly DefId[]>;
-  /** Interfaces / traits → classes that implement them. */
-  readonly implsByInterfaceDefId: ReadonlyMap<DefId, readonly DefId[]>;
-
-  /** `mroByOwnerDefId.get`, with an empty frozen array on miss. */
-  mroFor(ownerDefId: DefId): readonly DefId[];
-  /** `implsByInterfaceDefId.get`, with an empty frozen array on miss. */
-  implementorsOf(interfaceDefId: DefId): readonly DefId[];
-}
-
-export interface MethodDispatchInput {
-  /**
-   * Owner defs to index (classes, structs, traits, interfaces — any kind
-   * that can appear on the owner side of a method-dispatch graph).
-   */
-  readonly owners: readonly DefId[];
-  /**
-   * Return the full MRO ancestor chain for `ownerDefId`, **excluding the
-   * owner itself**, in the order dictated by the owner's language-specific
-   * MRO strategy.
-   *
-   * Contract:
-   *   - Pure (no side effects).
-   *   - Deterministic per input.
-   *   - `undefined` not allowed — return `[]` when the owner has no parents.
-   */
-  readonly computeMro: (ownerDefId: DefId) => readonly DefId[];
-  /**
-   * Return the set of interface/trait defs that `ownerDefId` implements.
-   * Transitive inclusion (e.g., `implements` on a parent class) is the
-   * caller's choice — the build function simply inverts whatever is
-   * returned.
-   *
-   * Repeated IDs in the output are deduplicated automatically.
-   *
-   * **Call-count contract.** `implementsOf` is invoked **once per
-   * occurrence** of an owner in `input.owners`, not once per unique
-   * owner. Duplicate owners therefore re-invoke it; dedup happens at
-   * the bucket layer (after the callback returns). Callers with
-   * expensive `implementsOf` implementations should pass a deduplicated
-   * `owners` list. `computeMro`, by contrast, is memoized by the first-
-   * write-wins policy and fires at most once per unique owner.
-   */
-  readonly implementsOf: (ownerDefId: DefId) => readonly DefId[];
-}
-
-// ─── Builder ────────────────────────────────────────────────────────────────
-
-export function buildMethodDispatchIndex(input: MethodDispatchInput): MethodDispatchIndex {
-  const mroByOwnerDefId = new Map<DefId, readonly DefId[]>();
-  const implsBuilding = new Map<DefId, DefId[]>();
-  const implsSeen = new Map<DefId, Set<DefId>>();
-
-  for (const ownerId of input.owners) {
-    // First-write-wins on duplicate owner ids: a stable policy consistent
-    // with sibling indexes (#913 DefIndex / ModuleScopeIndex).
-    if (!mroByOwnerDefId.has(ownerId)) {
-      const chain = input.computeMro(ownerId);
-      mroByOwnerDefId.set(ownerId, Object.freeze(chain.slice()));
-    }
-
-    for (const ifaceId of input.implementsOf(ownerId)) {
-      let seen = implsSeen.get(ifaceId);
-      if (seen === undefined) {
-        seen = new Set<DefId>();
-        implsSeen.set(ifaceId, seen);
-      }
-      if (seen.has(ownerId)) continue;
-      seen.add(ownerId);
-
-      let bucket = implsBuilding.get(ifaceId);
-      if (bucket === undefined) {
-        bucket = [];
-        implsBuilding.set(ifaceId, bucket);
-      }
-      bucket.push(ownerId);
-    }
-  }
-
-  const implsByInterfaceDefId = new Map<DefId, readonly DefId[]>();
-  for (const [ifaceId, owners] of implsBuilding) {
-    implsByInterfaceDefId.set(ifaceId, Object.freeze(owners.slice()));
-  }
-
-  return wrapIndex(mroByOwnerDefId, implsByInterfaceDefId);
-}
-
-// ─── Internal ───────────────────────────────────────────────────────────────
-
-const EMPTY: readonly DefId[] = Object.freeze([]);
-
-function wrapIndex(
-  mroByOwnerDefId: Map<DefId, readonly DefId[]>,
-  implsByInterfaceDefId: Map<DefId, readonly DefId[]>,
-): MethodDispatchIndex {
-  return {
-    mroByOwnerDefId,
-    implsByInterfaceDefId,
-    mroFor(ownerDefId: DefId): readonly DefId[] {
-      return mroByOwnerDefId.get(ownerDefId) ?? EMPTY;
-    },
-    implementorsOf(interfaceDefId: DefId): readonly DefId[] {
-      return implsByInterfaceDefId.get(interfaceDefId) ?? EMPTY;
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/module-scope-index.ts

@@ -1,73 +0,0 @@
-/**
- * `ModuleScopeIndex` — O(1) `filePath → moduleScopeId` lookup.
- *
- * Every file parsed produces exactly one `Module` scope at its root. The
- * finalize algorithm needs to resolve `ImportEdge.targetFile` to a concrete
- * module scope id in constant time during the link pass; this index is that
- * mapping.
- *
- * Part of RFC #909 Ring 2 SHARED — #913.
- *
- * Consumed by: #915 (SCC finalize link pass), #923 (shadow harness when
- * resolving callsite file → enclosing module).
- */
-
-import type { ScopeId } from './types.js';
-
-export interface ModuleScopeIndex {
-  readonly byFilePath: ReadonlyMap<string, ScopeId>;
-  readonly size: number;
-  get(filePath: string): ScopeId | undefined;
-  has(filePath: string): boolean;
-}
-
-export interface ModuleScopeEntry {
-  readonly filePath: string;
-  readonly moduleScopeId: ScopeId;
-}
-
-/**
- * Build a `ModuleScopeIndex` from a flat list of `{ filePath, moduleScopeId }`
- * pairs.
- *
- * **Collision policy: first-write-wins.** A file should appear exactly once
- * in a single ingestion run; collisions indicate the same file was parsed
- * twice or a `filePath` normalization bug upstream. Dropping the later
- * entry preserves the first-stable id the rest of the pipeline may already
- * have registered against.
- *
- * **Caller contract: filePath keys must be pre-normalized.** This index
- * keys on the raw `filePath` string and does NOT canonicalize separators,
- * case, or trailing slashes. Callers upstream of this function must agree
- * on a canonical form (typically repo-root-relative, POSIX separators,
- * no trailing slash) before constructing entries — otherwise `C:\foo\bar.ts`,
- * `C:/foo/bar.ts`, and `foo/bar.ts` will all hash to distinct buckets and
- * `get()` will miss.
- *
- * Pure function — safe to call repeatedly; no side effects.
- */
-export function buildModuleScopeIndex(entries: readonly ModuleScopeEntry[]): ModuleScopeIndex {
-  const byFilePath = new Map<string, ScopeId>();
-  for (const { filePath, moduleScopeId } of entries) {
-    if (byFilePath.has(filePath)) continue; // first-write-wins
-    byFilePath.set(filePath, moduleScopeId);
-  }
-  return wrapIndex(byFilePath);
-}
-
-// ─── Internal ───────────────────────────────────────────────────────────────
-
-function wrapIndex(byFilePath: Map<string, ScopeId>): ModuleScopeIndex {
-  return {
-    byFilePath,
-    get size() {
-      return byFilePath.size;
-    },
-    get(filePath: string): ScopeId | undefined {
-      return byFilePath.get(filePath);
-    },
-    has(filePath: string): boolean {
-      return byFilePath.has(filePath);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/origin-priority.ts

@@ -1,30 +0,0 @@
-/**
- * `ORIGIN_PRIORITY` — RFC Appendix B (authoritative values).
- *
- * Tie-break ordering applied inside `Registry.lookup` Step 7 when
- * `|Δconfidence| < 0.001` between two `Resolution` candidates. Lower number
- * = stronger (wins the tie).
- *
- * Full tie-break order (§4.2 Step 7):
- *   confidence DESC → scope depth ASC → MRO depth ASC → ORIGIN_PRIORITY ASC
- *   → DefId.localeCompare
- */
-
-export type OriginForTieBreak =
-  | 'local'
-  | 'import'
-  | 'reexport'
-  | 'namespace'
-  | 'wildcard'
-  | 'global-qualified'
-  | 'global-name';
-
-export const ORIGIN_PRIORITY: Readonly<Record<OriginForTieBreak, number>> = {
-  local: 0,
-  import: 1,
-  reexport: 2,
-  namespace: 3,
-  wildcard: 4,
-  'global-qualified': 5,
-  'global-name': 6,
-};

gitnexus-shared/src/scope-resolution/parsed-file.ts

@@ -1,65 +0,0 @@
-/**
- * `ParsedFile` — the per-file artifact produced by `ScopeExtractor`
- * (RFC §3.2 Phase 1; Ring 2 PKG #919).
- *
- * The boundary between Phase 1 (extraction, per-file, parallelizable) and
- * Phase 2 (finalize, cross-file). One `ParsedFile` is emitted per source
- * file; the finalize orchestrator (#921) collects them into a workspace-
- * wide set and feeds them to the shared `finalize` algorithm (#915).
- *
- * ## Shape
- *
- *   - `scopes`           — every `Scope` created for this file, in tree-
- *                          topological order (module first, then children).
- *                          `Scope.bindings` carry **local-only** bindings at
- *                          this stage; finalize merges imports/wildcards on top.
- *   - `parsedImports`    — raw `ParsedImport[]` for this file; finalize
- *                          resolves each to a concrete `ImportEdge`.
- *   - `localDefs`        — defs structurally declared in this file. A
- *                          superset of every `Scope.ownedDefs` union.
- *                          Listed separately so `finalize` can dedup-index
- *                          without re-walking scopes.
- *   - `referenceSites`   — pre-resolution usage facts; populated by the
- *                          resolution phase into `ReferenceIndex`.
- *
- * ## What `ParsedFile` deliberately does NOT carry
- *
- *   - Linked `ImportEdge`s. Those are finalize output.
- *   - A `ScopeTree` instance. Callers build one from `scopes` (cheap —
- *     `buildScopeTree(parsedFile.scopes)`). Keeping the ParsedFile flat
- *     makes IPC serialization from worker threads straightforward.
- *   - Merged module-scope bindings. Finalize owns that materialization.
- *
- * ## Compatibility with `FinalizeFile`
- *
- * `FinalizeFile` (defined in `./finalize-algorithm.ts`) is a structural
- * subset of `ParsedFile` — `filePath`, `moduleScope`, `parsedImports`,
- * `localDefs`. A `ParsedFile` is trivially convertible to a `FinalizeFile`
- * by picking those four fields, so the finalize orchestrator threads
- * ParsedFile through to the shared algorithm without shape-shifting.
- */
-
-import type { Scope, ScopeId } from './types.js';
-import type { ParsedImport } from './types.js';
-import type { SymbolDefinition } from './symbol-definition.js';
-import type { ReferenceSite } from './reference-site.js';
-
-export interface ParsedFile {
-  readonly filePath: string;
-  /** `Scope.id` of the file's root `Module` scope. */
-  readonly moduleScope: ScopeId;
-  /**
-   * All scopes in this file, typically emitted in tree-topological order.
-   * Caller reconstructs a `ScopeTree` via `buildScopeTree(scopes)` when
-   * navigation or invariant re-validation is needed.
-   */
-  readonly scopes: readonly Scope[];
-  readonly parsedImports: readonly ParsedImport[];
-  /**
-   * All defs structurally declared in this file (classes, methods, fields,
-   * variables). Mirrors the union of `Scope.ownedDefs` across `scopes`,
-   * pre-flattened for O(N) consumption by finalize.
-   */
-  readonly localDefs: readonly SymbolDefinition[];
-  readonly referenceSites: readonly ReferenceSite[];
-}

gitnexus-shared/src/scope-resolution/position-index.ts

@@ -1,166 +0,0 @@
-/**
- * `PositionIndex` — O(log N_file) scope-at-position lookup
- * (RFC §3.1; Ring 2 SHARED #912).
- *
- * Per-file sorted array of `(range, scopeId)` entries, sorted by start
- * position ASC (`startLine`, then `startCol`). `atPosition(filePath, line,
- * col)` binary-searches for the last entry whose start ≤ (line, col), then
- * scans backward through the sorted prefix and returns the first entry
- * whose range contains the query position.
- *
- * **Why this works.** `ScopeTree`'s invariants (parent strictly contains
- * child; siblings don't overlap) guarantee that the scopes containing a
- * given point form an **ancestor chain**. When scanning backward through
- * entries sorted by start position ASC, the first scope we find that
- * contains the query is the innermost one — any deeper-starting scope
- * that also contained the query would appear *later* in the sorted array,
- * but we're only scanning entries with start ≤ query, so anything later
- * necessarily starts after the query and can't contain it.
- *
- * Expected complexity: `O(log N_file + D)` where `D` is the lexical depth
- * at the query position (typically ≤ 10). Worst-case degrades to `O(N_file)`
- * only under pathological inputs (many scopes starting at the same line).
- *
- * **Line/column conventions.** Matches `Range` in `types.ts`: lines are
- * 1-based, columns are 0-based. Ranges are **inclusive on both ends** —
- * a scope whose `endLine:endCol` equals the query position still contains
- * it. That matches how tree-sitter captures bodies (closing brace
- * included) and how closed PR #902's `enclosingFunctions` behaved.
- */
-
-import type { Range, Scope, ScopeId } from './types.js';
-
-export interface PositionIndex {
-  /** Total scope entries indexed across all files. */
-  readonly size: number;
-  /**
-   * Innermost scope containing `(line, col)` in `filePath`, or `undefined`
-   * when nothing contains it (position before file start, after file end,
-   * or filePath not indexed).
-   *
-   * **Touching-boundary semantics.** Ranges are inclusive on both ends.
-   * When two sibling scopes share a boundary point — e.g.
-   * `[5:0, 10:0]` and `[10:0, 15:0]`, which is legal under `ScopeTree`'s
-   * non-overlap invariant — a query at the shared point `(10, 0)` is
-   * contained by **both**. The innermost-wins tie-break rule applies as
-   * usual: since neither is nested inside the other, the one that
-   * **starts latest** wins, i.e. the **right** sibling. The mechanism
-   * is the backward scan through the start-position-sorted array (see
-   * `findLastStartLteIndex` below) — both siblings land before the
-   * upper-bound cursor, and the right sibling is scanned first. Queries at non-boundary positions between them naturally
-   * fall to the unique containing scope.
-   */
-  atPosition(filePath: string, line: number, col: number): ScopeId | undefined;
-}
-
-/**
- * Build a `PositionIndex` from a flat list of `Scope` records.
- *
- * Duplicate `id`s are tolerated and deduplicated — the caller's
- * `ScopeTree.buildScopeTree` is the authoritative validator of scope
- * identity, and the position index does not need to re-check that
- * invariant.
- */
-export function buildPositionIndex(scopes: readonly Scope[]): PositionIndex {
-  const entriesByFile = new Map<string, Entry[]>();
-  const seen = new Set<ScopeId>();
-
-  for (const scope of scopes) {
-    if (seen.has(scope.id)) continue;
-    seen.add(scope.id);
-
-    let bucket = entriesByFile.get(scope.filePath);
-    if (bucket === undefined) {
-      bucket = [];
-      entriesByFile.set(scope.filePath, bucket);
-    }
-    bucket.push({ id: scope.id, range: scope.range });
-  }
-
-  for (const bucket of entriesByFile.values()) {
-    bucket.sort(compareEntry);
-  }
-
-  return wrapIndex(entriesByFile, seen.size);
-}
-
-// ─── Internals ──────────────────────────────────────────────────────────────
-
-interface Entry {
-  readonly id: ScopeId;
-  readonly range: Range;
-}
-
-/**
- * Sort by start position ASC, breaking ties by end position DESC so that
- * larger (outer) scopes appear before their smaller (inner) co-starting
- * siblings in the array. Makes the backward-scan contract crisp: the
- * first containing hit from the end of the scanned prefix is the
- * innermost scope.
- */
-function compareEntry(a: Entry, b: Entry): number {
-  if (a.range.startLine !== b.range.startLine) return a.range.startLine - b.range.startLine;
-  if (a.range.startCol !== b.range.startCol) return a.range.startCol - b.range.startCol;
-  if (a.range.endLine !== b.range.endLine) return b.range.endLine - a.range.endLine;
-  return b.range.endCol - a.range.endCol;
-}
-
-/** Whether `(line, col)` is at or after `range`'s start. */
-function startIsAtOrBefore(range: Range, line: number, col: number): boolean {
-  if (range.startLine < line) return true;
-  if (range.startLine > line) return false;
-  return range.startCol <= col;
-}
-
-/** Whether `(line, col)` is at or before `range`'s end (inclusive). */
-function endIsAtOrAfter(range: Range, line: number, col: number): boolean {
-  if (range.endLine > line) return true;
-  if (range.endLine < line) return false;
-  return range.endCol >= col;
-}
-
-/**
- * Return the largest index `i` in `arr` where `arr[i].range` starts at or
- * before `(line, col)`. Returns `-1` if no entry starts ≤ the query.
- *
- * Classic "upper bound - 1" binary search: find the first entry that
- * starts *after* the query, then step back one.
- */
-function findLastStartLteIndex(arr: readonly Entry[], line: number, col: number): number {
-  let lo = 0;
-  let hi = arr.length;
-  while (lo < hi) {
-    const mid = (lo + hi) >>> 1;
-    if (startIsAtOrBefore(arr[mid]!.range, line, col)) {
-      lo = mid + 1;
-    } else {
-      hi = mid;
-    }
-  }
-  return lo - 1;
-}
-
-function wrapIndex(entriesByFile: Map<string, Entry[]>, size: number): PositionIndex {
-  return {
-    get size() {
-      return size;
-    },
-    atPosition(filePath: string, line: number, col: number): ScopeId | undefined {
-      const bucket = entriesByFile.get(filePath);
-      if (bucket === undefined || bucket.length === 0) return undefined;
-
-      const endIdx = findLastStartLteIndex(bucket, line, col);
-      if (endIdx < 0) return undefined;
-
-      // Scan backward; first containing hit is innermost (see file header).
-      for (let i = endIdx; i >= 0; i--) {
-        const entry = bucket[i]!;
-        if (endIsAtOrAfter(entry.range, line, col)) {
-          // `startIsAtOrBefore` is guaranteed true by the binary search.
-          return entry.id;
-        }
-      }
-      return undefined;
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/qualified-name-index.ts

@@ -1,92 +0,0 @@
-/**
- * `QualifiedNameIndex` — O(1) `qualifiedName → DefId[]` lookup across all kinds.
- *
- * Cross-kind fast path for qualified-name resolution
- * (`lookupQualified(qname, scope, params)` in RFC §4.5). Class, method,
- * field, and namespace defs all contribute to a single index here; consumers
- * filter the returned `DefId[]` by `p.acceptedKinds` at the call site.
- *
- * Returns `DefId[]` (not a single `DefId`) because multiple defs can legally
- * share a qualified name — partial classes in C#, method overloads, or
- * accidental cross-kind collisions. The lookup caller filters to the expected
- * kind(s) and ranks the survivors.
- *
- * Part of RFC #909 Ring 2 SHARED — #913.
- *
- * Consumed by: #917 (`Registry.lookup` qualified fast path, `resolveTypeRef`
- * dotted fallback via #916).
- */
-
-import type { SymbolDefinition } from './symbol-definition.js';
-import type { DefId } from './types.js';
-
-export interface QualifiedNameIndex {
-  readonly byQualifiedName: ReadonlyMap<string, readonly DefId[]>;
-  readonly size: number;
-  /** Returns all `DefId`s registered under this qualified name; empty frozen
-   *  array on miss so callers can iterate without null checks. */
-  get(qualifiedName: string): readonly DefId[];
-  has(qualifiedName: string): boolean;
-}
-
-/**
- * Build a `QualifiedNameIndex` from a flat list of `SymbolDefinition` records.
- *
- * Only defs with a non-empty `qualifiedName` contribute; defs without one are
- * silently skipped (not every kind carries a qualified name — anonymous or
- * top-level symbols, dynamic-unresolved imports, etc.).
- *
- * **Duplicate policy: appended in input order.** Each unique `(qname, DefId)`
- * pair contributes at most once — repeated entries for the same pair are
- * deduplicated. Distinct `DefId`s sharing a `qname` accumulate in insertion
- * order (stable output for deterministic lookup ranking at the call site).
- *
- * Pure function — safe to call repeatedly; no side effects.
- */
-export function buildQualifiedNameIndex(defs: readonly SymbolDefinition[]): QualifiedNameIndex {
-  const byQualifiedName = new Map<string, DefId[]>();
-  const seenPairs = new Set<string>();
-
-  for (const def of defs) {
-    const qname = def.qualifiedName;
-    if (qname === undefined || qname.length === 0) continue;
-
-    const pairKey = `${qname}\0${def.nodeId}`;
-    if (seenPairs.has(pairKey)) continue;
-    seenPairs.add(pairKey);
-
-    const bucket = byQualifiedName.get(qname);
-    if (bucket === undefined) {
-      byQualifiedName.set(qname, [def.nodeId]);
-    } else {
-      bucket.push(def.nodeId);
-    }
-  }
-
-  // Freeze bucket arrays so consumers can't mutate the index.
-  const frozen = new Map<string, readonly DefId[]>();
-  for (const [k, v] of byQualifiedName) {
-    frozen.set(k, Object.freeze(v.slice()));
-  }
-
-  return wrapIndex(frozen);
-}
-
-// ─── Internal ───────────────────────────────────────────────────────────────
-
-const EMPTY: readonly DefId[] = Object.freeze([]);
-
-function wrapIndex(byQualifiedName: Map<string, readonly DefId[]>): QualifiedNameIndex {
-  return {
-    byQualifiedName,
-    get size() {
-      return byQualifiedName.size;
-    },
-    get(qualifiedName: string): readonly DefId[] {
-      return byQualifiedName.get(qualifiedName) ?? EMPTY;
-    },
-    has(qualifiedName: string): boolean {
-      return byQualifiedName.has(qualifiedName);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/reference-site.ts

@@ -1,74 +0,0 @@
-/**
- * `ReferenceSite` — a pre-resolution usage fact collected by `ScopeExtractor`
- * (RFC §3.2 Phase 1; Ring 2 PKG #919).
- *
- * One record per `@reference.*` capture. The extractor records:
- *   - the name being referenced (method/field/class name),
- *   - the source range,
- *   - the innermost lexical scope containing the reference,
- *   - the reference kind (call, read, write, inherits, etc.),
- *   - optional call-form classification from `provider.classifyCallForm`,
- *   - optional explicit-receiver hint for dotted calls (`user.save()`),
- *   - optional arity for call sites.
- *
- * Reference sites are consumed by the resolution phase (RFC §3.2 Phase 4)
- * which routes each through `Registry.lookup` / `resolveTypeRef` and
- * emits the final `Reference` record into `ReferenceIndex`.
- *
- * **Pre-resolution only.** `ReferenceSite` intentionally carries no
- * `toDef`, `confidence`, or `evidence`. Those are populated by the
- * resolution step that reads this record and produces a `Reference`
- * (defined in `./types.ts`).
- */
-
-import type { Range, ScopeId } from './types.js';
-
-/**
- * What kind of usage this reference represents — the graph-edge kind
- * emitted after resolution (`CALLS`, `READS`, `WRITES`, etc.).
- *
- * Matches the `kind` field on `Reference` in `./types.ts` so the
- * resolution phase can pass it through without re-classification.
- */
-export type ReferenceKind =
-  | 'call'
-  | 'read'
-  | 'write'
-  | 'type-reference'
-  | 'inherits'
-  | 'import-use';
-
-/**
- * How a call site binds its target. Informs `Registry.lookup` Step 2
- * (type-binding path):
- *   - `'free'`   — bare call (no receiver); resolution via lexical chain.
- *   - `'member'` — dotted call (`x.foo()`); resolution via receiver type.
- *   - `'constructor'` — `new Foo()`; receiver is the class itself.
- *   - `'index'`  — index expression (`arr[0]`); rare as a dispatch site.
- *
- * Only meaningful for `kind === 'call'`; ignored for reads/writes.
- */
-export type CallForm = 'free' | 'member' | 'constructor' | 'index';
-
-export interface ReferenceSite {
-  /** The name being referenced (e.g., `'save'`, `'User'`, `'count'`). */
-  readonly name: string;
-  /** Source-text range of this reference. */
-  readonly atRange: Range;
-  /**
-   * Innermost lexical scope that contains `atRange`. Resolved by the
-   * extractor via position lookup and frozen here so the resolution
-   * phase doesn't re-compute it per call.
-   */
-  readonly inScope: ScopeId;
-  readonly kind: ReferenceKind;
-  /** Set when `kind === 'call'`. */
-  readonly callForm?: CallForm;
-  /**
-   * Explicit receiver for dotted calls (`user.save()` → `{ name: 'user' }`).
-   * Passed through to `Registry.lookup.explicitReceiver`.
-   */
-  readonly explicitReceiver?: { readonly name: string };
-  /** Argument count at the call site; used by `provider.arityCompatibility`. */
-  readonly arity?: number;
-}

gitnexus-shared/src/scope-resolution/registries/class-registry.ts

@@ -1,41 +0,0 @@
-/**
- * `ClassRegistry` — scope-aware lookup for class-like symbols
- * (RFC §4.4; Ring 2 SHARED #917).
- *
- * Thin wrapper over `lookupCore`, specialized for class kinds:
- *
- *   - `acceptedKinds` = Class / Interface / Enum / Struct / Union /
- *     Trait / TypeAlias / Typedef / Record / Delegate / Annotation /
- *     Template / Namespace.
- *   - `useReceiverTypeBinding` is **false** — classes are resolved by
- *     name through the lexical chain + global qualified fallback, not
- *     via a receiver type.
- *   - Arity filter is not applicable (classes are not called with
- *     argument counts at lookup time).
- */
-
-import type { Resolution, ScopeId } from '../types.js';
-import { lookupCore, type CoreLookupParams } from './lookup-core.js';
-import { CLASS_KINDS, type RegistryContext } from './context.js';
-
-export interface ClassRegistry {
-  /**
-   * Look up a class-like symbol by simple or dotted name anchored at
-   * `scope`. Returns a confidence-ranked `Resolution[]`; consume `[0]`
-   * for the best answer.
-   */
-  lookup(name: string, scope: ScopeId): readonly Resolution[];
-}
-
-export function buildClassRegistry(ctx: RegistryContext): ClassRegistry {
-  const params: CoreLookupParams = {
-    acceptedKinds: CLASS_KINDS,
-    useReceiverTypeBinding: false,
-    ownerScopedContributor: null,
-  };
-  return {
-    lookup(name: string, scope: ScopeId) {
-      return lookupCore(name, scope, params, ctx);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/registries/context.ts

@@ -1,110 +0,0 @@
-/**
- * `RegistryContext` — the injected state required by the scope-aware
- * registry lookups (RFC §4; Ring 2 SHARED #917).
- *
- * Bundles every Ring 2 index + every provider hook the 7-step algorithm
- * might consult. Threaded through `lookupCore` and the three public
- * registries unchanged; construction is the caller's responsibility
- * (typically once per workspace-indexing pass in Ring 2 PKG).
- *
- * The design intent is **pure-logic in `gitnexus-shared`, data + hooks
- * supplied by the caller**. Nothing here loads files, parses AST, or
- * reaches into the CLI package.
- */
-
-import type { NodeLabel } from '../../graph/types.js';
-import type { SymbolDefinition } from '../symbol-definition.js';
-import type { Callsite, DefId } from '../types.js';
-import type { DefIndex } from '../def-index.js';
-import type { QualifiedNameIndex } from '../qualified-name-index.js';
-import type { ModuleScopeIndex } from '../module-scope-index.js';
-import type { ScopeTree } from '../scope-tree.js';
-import type { MethodDispatchIndex } from '../method-dispatch-index.js';
-
-// ─── Provider hooks consumed by the registries ─────────────────────────────
-
-export interface RegistryProviders {
-  /**
-   * Language-specific arity compatibility between a callsite and a candidate
-   * `def`. Mirrors `LanguageProvider.arityCompatibility` from #911. Optional:
-   * when absent, every candidate receives `'unknown'` (neutral signal).
-   */
-  arityCompatibility?(callsite: Callsite, def: SymbolDefinition): ArityVerdict;
-}
-
-export type ArityVerdict = 'compatible' | 'unknown' | 'incompatible';
-
-// ─── Owner-scoped contributor (concrete shape for `RegistryContributor`) ────
-
-/**
- * Per-owner membership view plugged into `LookupParams.ownerScopedContributor`.
- *
- * When the caller knows a receiver is of type `Owner` (e.g., after
- * resolving an explicit receiver or via `self`), it can supply the
- * `Owner`'s own member bucket here. `lookupCore` treats hits from this
- * contributor as `origin: 'local'` inside the owner's body scope —
- * strongest-visibility evidence, unaffected by the scope-chain hop
- * deduction that punishes outer-scope hits.
- *
- * Ring 1's `RegistryContributor = unknown` opaque placeholder is narrowed
- * to this concrete shape here in Ring 2 SHARED (#917).
- */
-export interface OwnerScopedContributor {
-  /** The owner (class/struct/trait/interface) that bounds this view. */
-  readonly ownerDefId: DefId;
-  /**
-   * Methods / fields directly declared on the owner, keyed by simple name.
-   * Return empty array on miss; implementations should NOT walk the MRO —
-   * that's `MethodDispatchIndex`'s job, handled in the type-binding step.
-   */
-  byName(name: string): readonly SymbolDefinition[];
-}
-
-// ─── Top-level context threaded through every lookup ───────────────────────
-
-export interface RegistryContext {
-  readonly scopes: ScopeTree;
-  readonly defs: DefIndex;
-  readonly qualifiedNames: QualifiedNameIndex;
-  readonly moduleScopes: ModuleScopeIndex;
-  /**
-   * Method-dispatch index; required for method/field registries that
-   * honor `useReceiverTypeBinding`. Omit for class-only lookups.
-   */
-  readonly methodDispatch?: MethodDispatchIndex;
-  readonly providers: RegistryProviders;
-}
-
-// ─── Per-kind default `acceptedKinds` sets ─────────────────────────────────
-//
-// Exported so the three public registries stay declarative (each one just
-// points at the right constant + passes it to `lookupCore`).
-
-export const CLASS_KINDS: readonly NodeLabel[] = Object.freeze([
-  'Class',
-  'Interface',
-  'Enum',
-  'Struct',
-  'Union',
-  'Trait',
-  'TypeAlias',
-  'Typedef',
-  'Record',
-  'Delegate',
-  'Annotation',
-  'Template',
-  'Namespace',
-]);
-
-export const METHOD_KINDS: readonly NodeLabel[] = Object.freeze([
-  'Method',
-  'Function',
-  'Constructor',
-]);
-
-export const FIELD_KINDS: readonly NodeLabel[] = Object.freeze([
-  'Variable',
-  'Property',
-  'Const',
-  'Static',
-]);

gitnexus-shared/src/scope-resolution/registries/evidence.ts

@@ -1,196 +0,0 @@
-/**
- * `composeEvidence` — translate accumulated raw signals per candidate
- * into a `ResolutionEvidence[]` using the authoritative `EvidenceWeights`
- * map (RFC §4.3 + Appendix A; Ring 2 SHARED #917).
- *
- * Each `RawSignals` record describes what was observed about a candidate
- * during the 7-step walk: where it was found, at what depth, whether
- * anything corroborates it. This module turns those raw facts into the
- * typed evidence list attached to the outgoing `Resolution`.
- *
- * **Every weight comes from `EvidenceWeights`.** No inline magic numbers.
- * Extends issue #429 (centralize hardcoded confidence values).
- *
- * **Confidence compose rule.** Signals add; the sum is capped at 1.0 at
- * the call site (inside `lookupCore`). This module only emits the list;
- * it does NOT compute the capped sum so callers can inspect per-signal
- * contributions for debugging.
- */
-
-import type { BindingRef, ResolutionEvidence } from '../types.js';
-import { EvidenceWeights, typeBindingWeightAtDepth } from '../evidence-weights.js';
-
-/**
- * Raw signals observed for a single candidate during the 7-step walk.
- * Optional fields encode "this signal did not fire"; presence encodes
- * "emit an evidence record".
- */
-export interface RawSignals {
-  // ── Where-found ────────────────────────────────────────────────────────
-  /** Visibility origin of the binding that produced this candidate. */
-  readonly origin?: BindingRef['origin'] | 'global-qualified' | 'global-name';
-  /** Depth at which the binding was found (hops up from start scope). */
-  readonly scopeChainDepth?: number;
-  /** `ImportEdge` that brought the name in; present when origin is a non-local. */
-  readonly viaUnlinkedImport?: boolean;
-
-  // ── Type-binding path ──────────────────────────────────────────────────
-  /** Set when the candidate came via the receiver's type-binding MRO walk. */
-  readonly typeBindingMroDepth?: number;
-
-  // ── Corroborators ──────────────────────────────────────────────────────
-  /** `def.ownerId === resolvedReceiver.def.nodeId`. */
-  readonly ownerMatch?: boolean;
-  /** Always fires for candidates that pass `acceptedKinds`; weight 0. */
-  readonly kindMatch: true;
-
-  // ── Arity ──────────────────────────────────────────────────────────────
-  readonly arityVerdict?: 'compatible' | 'unknown' | 'incompatible';
-
-  // ── Dynamic-unresolved passthrough ─────────────────────────────────────
-  /** Candidate flows through a `kind: 'dynamic-unresolved'` ImportEdge. */
-  readonly dynamicUnresolved?: boolean;
-}
-
-/**
- * Compose the raw signals into a stable `ResolutionEvidence[]` list.
- *
- * Emission order mirrors the `EvidenceWeights` layout: where-found →
- * type-binding → corroborators → arity → degraded. Stable order makes
- * the per-signal contributions easy to reason about in tests and in the
- * shadow-mode parity dashboard.
- */
-export function composeEvidence(signals: RawSignals): readonly ResolutionEvidence[] {
-  const out: ResolutionEvidence[] = [];
-
-  // ── Where-found visibility ─────────────────────────────────────────────
-  if (signals.origin !== undefined) {
-    const baseWeight = getOriginWeight(signals.origin);
-    const capped = signals.viaUnlinkedImport
-      ? baseWeight * EvidenceWeights.unlinkedImportMultiplier
-      : baseWeight;
-    const evidenceKind = whereFoundEvidenceKind(signals.origin);
-    out.push({
-      kind: evidenceKind,
-      weight: capped,
-      ...(signals.viaUnlinkedImport
-        ? { note: `via unresolved import (${EvidenceWeights.unlinkedImportMultiplier}× cap)` }
-        : {}),
-    });
-  }
-
-  // ── Scope-chain depth deduction (per-hop, only meaningful for lexical
-  // hits where scopeChainDepth ≥ 1). Depth 0 = no deduction; depth N ≥ 1
-  // emits a single `scope-chain` evidence with the accumulated penalty.
-  if (signals.scopeChainDepth !== undefined && signals.scopeChainDepth > 0) {
-    out.push({
-      kind: 'scope-chain',
-      weight: EvidenceWeights.scopeChainPerDepth * signals.scopeChainDepth,
-      note: `depth=${signals.scopeChainDepth}`,
-    });
-  }
-
-  // ── Type-binding / MRO path ────────────────────────────────────────────
-  if (signals.typeBindingMroDepth !== undefined) {
-    out.push({
-      kind: 'type-binding',
-      weight: typeBindingWeightAtDepth(signals.typeBindingMroDepth),
-      note: `mroDepth=${signals.typeBindingMroDepth}`,
-    });
-  }
-
-  // ── Owner match (explanatory for debug) ────────────────────────────────
-  if (signals.ownerMatch === true) {
-    out.push({
-      kind: 'owner-match',
-      weight: EvidenceWeights.ownerMatch,
-    });
-  }
-
-  // ── Kind match (always present; weight 0; retained for debuggability) ──
-  out.push({
-    kind: 'kind-match',
-    weight: EvidenceWeights.kindMatch,
-  });
-
-  // ── Arity ──────────────────────────────────────────────────────────────
-  if (signals.arityVerdict !== undefined) {
-    const weight =
-      signals.arityVerdict === 'compatible'
-        ? EvidenceWeights.arityMatchCompatible
-        : signals.arityVerdict === 'incompatible'
-          ? EvidenceWeights.arityMatchIncompatible
-          : EvidenceWeights.arityMatchUnknown;
-    out.push({
-      kind: 'arity-match',
-      weight,
-      note: signals.arityVerdict,
-    });
-  }
-
-  // ── Dynamic-unresolved (degraded signal) ───────────────────────────────
-  if (signals.dynamicUnresolved === true) {
-    out.push({
-      kind: 'dynamic-import-unresolved',
-      weight: EvidenceWeights.dynamicImportUnresolved,
-    });
-  }
-
-  return out;
-}
-
-/**
- * Sum evidence weights and clamp to `[0, 1]`. Separate from `composeEvidence`
- * so tests and the parity dashboard can inspect the raw evidence list.
- */
-export function confidenceFromEvidence(evidence: readonly ResolutionEvidence[]): number {
-  let sum = 0;
-  for (const e of evidence) sum += e.weight;
-  if (sum < 0) return 0;
-  if (sum > 1) return 1;
-  return sum;
-}
-
-// ─── Internal ───────────────────────────────────────────────────────────────
-
-function getOriginWeight(origin: NonNullable<RawSignals['origin']>): number {
-  switch (origin) {
-    case 'local':
-      return EvidenceWeights.local;
-    case 'import':
-      return EvidenceWeights.import;
-    case 'reexport':
-      return EvidenceWeights.reexport;
-    case 'namespace':
-      return EvidenceWeights.namespace;
-    case 'wildcard':
-      return EvidenceWeights.wildcard;
-    case 'global-qualified':
-      return EvidenceWeights.globalQualified;
-    case 'global-name':
-      // Reserved for Ring 3 byName global index. `lookupCore` today only
-      // emits `'global-qualified'` (via `lookupQualified`, dotted-name
-      // fallback); no code path constructs `origin: 'global-name'` yet.
-      // Kept here so the Appendix A weight stays live and `composeEvidence`
-      // remains exhaustive over the origin union.
-      return EvidenceWeights.globalName;
-  }
-}
-
-function whereFoundEvidenceKind(
-  origin: NonNullable<RawSignals['origin']>,
-): ResolutionEvidence['kind'] {
-  switch (origin) {
-    case 'local':
-      return 'local';
-    case 'import':
-    case 'reexport':
-    case 'namespace':
-    case 'wildcard':
-      return 'import';
-    case 'global-qualified':
-      return 'global-qualified';
-    case 'global-name':
-      return 'global-name';
-  }
-}

gitnexus-shared/src/scope-resolution/registries/field-registry.ts

@@ -1,43 +0,0 @@
-/**
- * `FieldRegistry` — scope-aware lookup for field / property / variable
- * access (RFC §4.4; Ring 2 SHARED #917).
- *
- * Thin wrapper over `lookupCore`, specialized for data-member kinds:
- *
- *   - `acceptedKinds` = Variable / Property / Const / Static.
- *   - `useReceiverTypeBinding` is **true** — fields are resolved against
- *     the receiver type's MRO first, then via the lexical chain for
- *     free variables.
- *   - `callsite` is not meaningful for field access (no arity), but the
- *     `explicitReceiver` and `ownerScopedContributor` knobs are.
- */
-
-import type { Resolution, ScopeId } from '../types.js';
-import { lookupCore, type CoreLookupParams } from './lookup-core.js';
-import type { OwnerScopedContributor, RegistryContext } from './context.js';
-import { FIELD_KINDS } from './context.js';
-
-export interface FieldLookupOptions {
-  readonly explicitReceiver?: { readonly name: string };
-  readonly ownerScopedContributor?: OwnerScopedContributor;
-}
-
-export interface FieldRegistry {
-  lookup(name: string, scope: ScopeId, options?: FieldLookupOptions): readonly Resolution[];
-}
-
-export function buildFieldRegistry(ctx: RegistryContext): FieldRegistry {
-  return {
-    lookup(name: string, scope: ScopeId, options: FieldLookupOptions = {}) {
-      const params: CoreLookupParams = {
-        acceptedKinds: FIELD_KINDS,
-        useReceiverTypeBinding: true,
-        ownerScopedContributor: options.ownerScopedContributor ?? null,
-        ...(options.explicitReceiver !== undefined
-          ? { explicitReceiver: options.explicitReceiver }
-          : {}),
-      };
-      return lookupCore(name, scope, params, ctx);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/registries/lookup-core.ts

@@ -1,461 +0,0 @@
-/**
- * `lookupCore` — the shared 7-step canonical resolution algorithm
- * (RFC §4.2; Ring 2 SHARED #917).
- *
- * Pure function. Given a name, a starting scope, and per-kind parameters,
- * walks lexical scopes + optional type-binding MRO + optional owner
- * contributor + global qualified-name fallback, and returns a ranked
- * `Resolution[]` with per-candidate evidence.
- *
- * All three public registries (`ClassRegistry` / `MethodRegistry` /
- * `FieldRegistry`) dispatch into this function, differing only in the
- * parameters they pass. The CHOICE of which steps fire is expressed
- * through `LookupParams`, not through different algorithms per kind.
- *
- * ## Algorithm (RFC §4.2, verbatim names)
- *
- * **Step 1 — Lexical scope-chain walk.** From `startScope`, walk
- *   parent-ward. At each scope, consult `scope.bindings.get(name)`:
- *     - Filter candidates whose `def.type ∈ acceptedKinds`.
- *     - For each surviving candidate, record a raw signal with the
- *       binding's origin + the current scope-chain depth.
- *     - **Hard shadow.** If `bindings.get(name)` is non-empty (including
- *       non-kind-matching candidates), stop walking. The name is
- *       lexically bound here; outer scopes are not consulted.
- *
- * **Step 2 — Type-binding resolution.** When `useReceiverTypeBinding`
- *   is true, resolve the receiver's type at `startScope` (from
- *   `scope.typeBindings`), then walk the MRO via
- *   `MethodDispatchIndex.mroFor(ownerDefId)`. Membership per owner comes
- *   through `RegistryContext.methodDispatch` + owner lookups into
- *   `scope.ownedDefs`; each hit records a raw signal with the owner's
- *   MRO depth.
- *
- * **Step 3 — Owner-scoped contributor.** When
- *   `params.ownerScopedContributor` is present, merge its `byName(name)`
- *   hits with `origin: 'local'` (they are declared directly on the
- *   receiver). Distinct from Step 2 — Step 2 walks the MRO; Step 3 only
- *   looks at the directly-declared owner members.
- *
- * **Step 4 — Kind filter (emit `kind-match` evidence).** Already
- *   applied during Steps 1-3; this step just adds a `kind-match` signal
- *   at weight 0 to every candidate for debuggability (so the evidence
- *   array is self-describing).
- *
- * **Step 5 — Arity filter.** Call `providers.arityCompatibility(callsite,
- *   def)` per surviving candidate. Verdicts: `compatible` / `unknown` /
- *   `incompatible`. If at least one candidate is `compatible`, drop
- *   `incompatible` ones. Otherwise keep all (the penalty weight alone
- *   will rank them lower but they remain in the result).
- *
- * **Step 6 — Global fallback.** When Steps 1-3 produced **no**
- *   candidates and the name contains a `.`, consult the
- *   `QualifiedNameIndex` via `lookupQualified` — see §4.5. The `scope`
- *   argument is NOT passed here because global lookup is scope-agnostic.
- *
- * **Step 7 — Rank + tie-break.** Compose evidence, compute confidence
- *   (sum capped at 1.0), sort by the RFC Appendix B cascade.
- *
- * ## What this module does NOT do
- *
- *   - No AST reads (pure data in, pure data out).
- *   - No `gitnexus/` imports.
- *   - No language switches. Language-specific behavior flows exclusively
- *     through `providers.*` and the `params` object.
- *   - No caching. Callers that want memoization can wrap this function.
- */
-
-import type { NodeLabel } from '../../graph/types.js';
-import type { SymbolDefinition } from '../symbol-definition.js';
-import type {
-  BindingRef,
-  Callsite,
-  DefId,
-  LookupParams,
-  Resolution,
-  Scope,
-  ScopeId,
-} from '../types.js';
-import type { OriginForTieBreak } from '../origin-priority.js';
-import { composeEvidence, confidenceFromEvidence, type RawSignals } from './evidence.js';
-import { compareByConfidenceWithTiebreaks, type TieBreakKey } from './tie-breaks.js';
-import { lookupQualified } from './lookup-qualified.js';
-import type { ArityVerdict, OwnerScopedContributor, RegistryContext } from './context.js';
-
-// ─── Public entry point ─────────────────────────────────────────────────────
-
-/** Extended `LookupParams` narrowing `ownerScopedContributor` to the concrete shape. */
-export interface CoreLookupParams extends Omit<LookupParams, 'ownerScopedContributor'> {
-  readonly ownerScopedContributor: OwnerScopedContributor | null;
-  /** Call-site description forwarded to `arityCompatibility`. Optional — for non-call lookups. */
-  readonly callsite?: Callsite;
-}
-
-/**
- * Run the 7-step lookup. Returns a non-empty `Resolution[]` when any
- * candidate was found; an empty array otherwise. Callers consume `[0]`
- * for the best answer and optionally inspect the rest for alternates.
- */
-export function lookupCore(
-  name: string,
-  startScope: ScopeId,
-  params: CoreLookupParams,
-  ctx: RegistryContext,
-): readonly Resolution[] {
-  const acceptedKinds = new Set<NodeLabel>(params.acceptedKinds);
-  const perCandidate = new Map<DefId, CandidateState>();
-
-  // ── Step 1: lexical scope-chain walk ──────────────────────────────────
-  const lexicalShadowed = walkLexicalChain(name, startScope, acceptedKinds, ctx, perCandidate);
-
-  // ── Step 2: type-binding / MRO walk (methods/fields) ──────────────────
-  if (params.useReceiverTypeBinding && ctx.methodDispatch !== undefined) {
-    walkReceiverTypeBinding(name, startScope, acceptedKinds, params, ctx, perCandidate);
-  }
-
-  // ── Step 3: owner-scoped contributor ──────────────────────────────────
-  if (params.ownerScopedContributor !== null) {
-    seedFromOwnerScopedContributor(
-      name,
-      params.ownerScopedContributor,
-      acceptedKinds,
-      perCandidate,
-    );
-  }
-
-  // ── Step 4: kind-match evidence (emitted by composeEvidence directly) ──
-  // Handled inside `composeEvidence`.
-
-  // ── Step 5: arity filter ──────────────────────────────────────────────
-  if (params.callsite !== undefined) {
-    applyArityFilter(params.callsite, perCandidate, ctx);
-  }
-
-  // ── Step 6: global fallback (only when Steps 1-3 produced nothing) ──
-  if (perCandidate.size === 0 && !lexicalShadowed && name.includes('.')) {
-    const globals = lookupQualified(name, { acceptedKinds: params.acceptedKinds }, ctx);
-    if (globals.length > 0) return globals;
-  }
-
-  if (perCandidate.size === 0) return EMPTY;
-
-  // ── Step 7: compose evidence + rank ──────────────────────────────────
-  return rankCandidates(perCandidate);
-}
-
-// ─── Internal state ────────────────────────────────────────────────────────
-
-interface CandidateState {
-  readonly def: SymbolDefinition;
-  readonly signals: MutableRawSignals;
-  readonly tieBreakKey: MutableTieBreakKey;
-}
-
-interface MutableRawSignals {
-  origin?: BindingRef['origin'] | 'global-qualified' | 'global-name';
-  scopeChainDepth?: number;
-  viaUnlinkedImport?: boolean;
-  typeBindingMroDepth?: number;
-  ownerMatch?: boolean;
-  kindMatch: true;
-  arityVerdict?: ArityVerdict;
-  dynamicUnresolved?: boolean;
-}
-
-interface MutableTieBreakKey {
-  scopeDepth: number;
-  mroDepth: number;
-  origin: OriginForTieBreak;
-}
-
-function ensureCandidate(
-  perCandidate: Map<DefId, CandidateState>,
-  def: SymbolDefinition,
-): CandidateState {
-  const existing = perCandidate.get(def.nodeId);
-  if (existing !== undefined) return existing;
-  const fresh: CandidateState = {
-    def,
-    signals: { kindMatch: true },
-    tieBreakKey: { scopeDepth: 0, mroDepth: 0, origin: 'local' },
-  };
-  perCandidate.set(def.nodeId, fresh);
-  return fresh;
-}
-
-// ─── Step 1 implementation ─────────────────────────────────────────────────
-
-/**
- * Walk the lexical scope chain from `startScope` upward. Returns `true`
- * iff a scope with any `bindings.get(name)` entries was found — the
- * caller uses this to decide whether to run the global fallback.
- */
-function walkLexicalChain(
-  name: string,
-  startScope: ScopeId,
-  acceptedKinds: ReadonlySet<NodeLabel>,
-  ctx: RegistryContext,
-  perCandidate: Map<DefId, CandidateState>,
-): boolean {
-  let currentId: ScopeId | null = startScope;
-  let depth = 0;
-  const visited = new Set<ScopeId>();
-
-  while (currentId !== null) {
-    if (visited.has(currentId)) return false;
-    visited.add(currentId);
-
-    const scope: Scope | undefined = ctx.scopes.getScope(currentId);
-    if (scope === undefined) return false;
-
-    const bindings = scope.bindings.get(name);
-    if (bindings !== undefined && bindings.length > 0) {
-      for (const binding of bindings) {
-        if (!acceptedKinds.has(binding.def.type)) continue;
-        recordLexicalHit(perCandidate, binding, depth);
-      }
-      return true; // hard shadow regardless of kind-filter survivorship
-    }
-
-    currentId = scope.parent;
-    depth++;
-  }
-
-  return false;
-}
-
-function recordLexicalHit(
-  perCandidate: Map<DefId, CandidateState>,
-  binding: BindingRef,
-  scopeChainDepth: number,
-): void {
-  const state = ensureCandidate(perCandidate, binding.def);
-  state.signals.origin = binding.origin;
-  state.signals.scopeChainDepth = scopeChainDepth;
-  if (binding.via?.linkStatus === 'unresolved') {
-    state.signals.viaUnlinkedImport = true;
-  }
-  if (binding.via?.kind === 'dynamic-unresolved') {
-    state.signals.dynamicUnresolved = true;
-  }
-  state.tieBreakKey.scopeDepth = scopeChainDepth;
-  state.tieBreakKey.origin = binding.origin as OriginForTieBreak;
-}
-
-// ─── Step 2 implementation ─────────────────────────────────────────────────
-
-function walkReceiverTypeBinding(
-  name: string,
-  startScope: ScopeId,
-  acceptedKinds: ReadonlySet<NodeLabel>,
-  params: CoreLookupParams,
-  ctx: RegistryContext,
-  perCandidate: Map<DefId, CandidateState>,
-): void {
-  const ownerDefId = resolveReceiverOwner(startScope, params, ctx);
-  if (ownerDefId === undefined) return;
-
-  if (ctx.methodDispatch === undefined) return;
-
-  const ownerDef = ctx.defs.get(ownerDefId);
-  if (ownerDef === undefined) return;
-
-  // Walk the owner itself at depth 0, then its MRO chain.
-  const walk: DefId[] = [ownerDefId, ...ctx.methodDispatch.mroFor(ownerDefId)];
-
-  for (let mroDepth = 0; mroDepth < walk.length; mroDepth++) {
-    const currentOwnerId = walk[mroDepth]!;
-    const members = collectOwnedMembers(currentOwnerId, name, ctx);
-    for (const def of members) {
-      if (!acceptedKinds.has(def.type)) continue;
-      recordTypeBindingHit(perCandidate, def, mroDepth, ownerDefId);
-    }
-  }
-}
-
-function resolveReceiverOwner(
-  startScope: ScopeId,
-  params: CoreLookupParams,
-  ctx: RegistryContext,
-): DefId | undefined {
-  // Explicit receiver: consult the callsite scope's typeBindings for the
-  // named receiver; the attached TypeRef identifies the owner. Without a
-  // ready resolveTypeRef call (that module is separate), we do a direct
-  // lookup and trust the caller to have populated the binding.
-  if (params.explicitReceiver !== undefined) {
-    return lookupReceiverType(startScope, params.explicitReceiver.name, ctx);
-  }
-
-  // Implicit `self` / `this` — the scope's typeBindings should carry it.
-  for (const implicitName of IMPLICIT_RECEIVERS) {
-    const owner = lookupReceiverType(startScope, implicitName, ctx);
-    if (owner !== undefined) return owner;
-  }
-  return undefined;
-}
-
-const IMPLICIT_RECEIVERS: readonly string[] = Object.freeze(['self', 'this']);
-
-function lookupReceiverType(
-  startScope: ScopeId,
-  receiverName: string,
-  ctx: RegistryContext,
-): DefId | undefined {
-  let currentId: ScopeId | null = startScope;
-  const visited = new Set<ScopeId>();
-  while (currentId !== null) {
-    if (visited.has(currentId)) return undefined;
-    visited.add(currentId);
-
-    const scope = ctx.scopes.getScope(currentId);
-    if (scope === undefined) return undefined;
-
-    const typeRef = scope.typeBindings.get(receiverName);
-    if (typeRef !== undefined) {
-      // rawName must resolve to a def via qualifiedNames; if it doesn't, we
-      // can't claim the receiver type. No fallback — that's what
-      // `resolveTypeRef` would do, but we keep this path lean and let
-      // callers pre-resolve if they want the richer semantics.
-      const candidateIds = ctx.qualifiedNames.get(typeRef.rawName);
-      if (candidateIds.length === 1) return candidateIds[0];
-      // Ambiguous (≥ 2) or missing (0) — caller must pre-resolve via
-      // `resolveTypeRef` (#916) if they want the richer semantics. We
-      // intentionally do NOT re-implement a simple-name fallback here.
-      return undefined;
-    }
-    currentId = scope.parent;
-  }
-  return undefined;
-}
-
-function collectOwnedMembers(
-  ownerDefId: DefId,
-  memberName: string,
-  ctx: RegistryContext,
-): readonly SymbolDefinition[] {
-  // An owner's members are defs whose `ownerId === ownerDefId` and whose
-  // simple name matches `memberName`. We iterate `defs.byId` — O(D) per
-  // call today. A future by-owner index would make this O(K); tracked as
-  // a follow-up optimization before Ring 3 flips go production.
-  const out: SymbolDefinition[] = [];
-  for (const def of ctx.defs.byId.values()) {
-    if (def.ownerId !== ownerDefId) continue;
-    if (simpleNameOf(def) !== memberName) continue;
-    out.push(def);
-  }
-  return out;
-}
-
-function simpleNameOf(def: SymbolDefinition): string | undefined {
-  if (def.qualifiedName === undefined || def.qualifiedName.length === 0) return undefined;
-  const dot = def.qualifiedName.lastIndexOf('.');
-  return dot === -1 ? def.qualifiedName : def.qualifiedName.slice(dot + 1);
-}
-
-function recordTypeBindingHit(
-  perCandidate: Map<DefId, CandidateState>,
-  def: SymbolDefinition,
-  mroDepth: number,
-  receiverOwner: DefId,
-): void {
-  const state = ensureCandidate(perCandidate, def);
-  const existingMroDepth = state.signals.typeBindingMroDepth;
-  const firstHit = existingMroDepth === undefined;
-  // Only replace if this hit is shallower (smaller MRO depth). The local
-  // const lets TS narrow to `number` in the `else` branch so no `!`
-  // assertion is needed.
-  if (firstHit || mroDepth < existingMroDepth) {
-    state.signals.typeBindingMroDepth = mroDepth;
-    state.tieBreakKey.mroDepth = mroDepth;
-  }
-  if (def.ownerId === receiverOwner) {
-    state.signals.ownerMatch = true;
-  }
-  // Pure type-binding candidates (no lexical hit) would otherwise keep the
-  // `ensureCandidate` default `tieBreakKey.origin === 'local'`, making the
-  // Appendix B cascade lump them with local-origin candidates. Demote them
-  // to `'import'` — the strongest non-local origin — only when no earlier
-  // phase set an origin for this candidate. Lexical hits from Step 1 set
-  // `signals.origin` before Step 2 runs, so the guard skips them; Step 3
-  // (`seedFromOwnerScopedContributor`) runs AFTER Step 2 and unconditionally
-  // overrides `tieBreakKey.origin` back to `'local'` for direct-owner
-  // members, so any same-def overlap still ends up ranked correctly.
-  if (firstHit && state.signals.origin === undefined) {
-    state.tieBreakKey.origin = 'import';
-  }
-}
-
-// ─── Step 3 implementation ─────────────────────────────────────────────────
-
-function seedFromOwnerScopedContributor(
-  name: string,
-  contributor: OwnerScopedContributor,
-  acceptedKinds: ReadonlySet<NodeLabel>,
-  perCandidate: Map<DefId, CandidateState>,
-): void {
-  for (const def of contributor.byName(name)) {
-    if (!acceptedKinds.has(def.type)) continue;
-    const state = ensureCandidate(perCandidate, def);
-    // Treat the contributor's direct membership as `origin: 'local'` —
-    // strongest visibility, no scope-chain penalty.
-    state.signals.origin = 'local';
-    state.signals.scopeChainDepth = 0;
-    state.signals.ownerMatch = def.ownerId === contributor.ownerDefId;
-    state.tieBreakKey.origin = 'local';
-  }
-}
-
-// ─── Step 5 implementation ─────────────────────────────────────────────────
-
-function applyArityFilter(
-  callsite: Callsite,
-  perCandidate: Map<DefId, CandidateState>,
-  ctx: RegistryContext,
-): void {
-  const arityFn = ctx.providers.arityCompatibility;
-  if (arityFn === undefined) {
-    // No provider → record 'unknown' for every candidate; keeps signal
-    // shape uniform for composeEvidence.
-    for (const state of perCandidate.values()) {
-      state.signals.arityVerdict = 'unknown';
-    }
-    return;
-  }
-
-  let anyCompatible = false;
-  for (const state of perCandidate.values()) {
-    const verdict = arityFn(callsite, state.def);
-    state.signals.arityVerdict = verdict;
-    if (verdict === 'compatible') anyCompatible = true;
-  }
-
-  if (!anyCompatible) return;
-
-  // Filter: when at least one compatible candidate exists, drop incompatibles.
-  for (const [defId, state] of perCandidate) {
-    if (state.signals.arityVerdict === 'incompatible') {
-      perCandidate.delete(defId);
-    }
-  }
-}
-
-// ─── Step 7 implementation ─────────────────────────────────────────────────
-
-function rankCandidates(perCandidate: Map<DefId, CandidateState>): readonly Resolution[] {
-  const resolutions: Resolution[] = [];
-  const tieKeys = new Map<string, TieBreakKey>();
-
-  for (const state of perCandidate.values()) {
-    const evidence = composeEvidence(state.signals as RawSignals);
-    const confidence = confidenceFromEvidence(evidence);
-    resolutions.push({ def: state.def, confidence, evidence });
-    tieKeys.set(state.def.nodeId, { ...state.tieBreakKey });
-  }
-
-  resolutions.sort((a, b) => compareByConfidenceWithTiebreaks(a, b, tieKeys));
-  return Object.freeze(resolutions);
-}
-
-// ─── Constants ──────────────────────────────────────────────────────────────
-
-const EMPTY: readonly Resolution[] = Object.freeze([]);

gitnexus-shared/src/scope-resolution/registries/lookup-qualified.ts

@@ -1,71 +0,0 @@
-/**
- * `lookupQualified` — qualified-name fast path (RFC §4.5; Ring 2 SHARED #917).
- *
- * Consults `QualifiedNameIndex` directly, filters by `acceptedKinds`, and
- * returns `Resolution[]` with `origin: 'global-qualified'` evidence. Used by:
- *
- *   - `resolveTypeRef` dotted fallback (#916)
- *   - `Registry.lookup` Step 6 when no lexical candidate survived
- *   - Explicit dotted identifiers in Cypher / MCP tools where the caller
- *     knows the target's canonical qualified name
- *
- * **Strict + deterministic.** No receiver-type resolution, no scope walk.
- * Every surviving candidate gets the same base confidence (from
- * `EvidenceWeights.globalQualified`), then the tie-break cascade
- * disambiguates.
- */
-
-import type { NodeLabel } from '../../graph/types.js';
-import type { Resolution } from '../types.js';
-import { composeEvidence, confidenceFromEvidence } from './evidence.js';
-import { compareByConfidenceWithTiebreaks, type TieBreakKey } from './tie-breaks.js';
-import type { RegistryContext } from './context.js';
-
-export interface LookupQualifiedParams {
-  readonly acceptedKinds: readonly NodeLabel[];
-}
-
-/**
- * Look up a canonical qualified name (e.g., `app.models.User`) across all
- * defs, filtered by `acceptedKinds`. Returns an empty array when the name
- * is not indexed or no candidate matches the kind filter.
- *
- * Callers consume `[0]` for the strict single-return answer; the remainder
- * carries alternate candidates (partial classes, overloads, accidental
- * cross-kind hits) ordered by the tie-break cascade.
- */
-export function lookupQualified(
-  qualifiedName: string,
-  params: LookupQualifiedParams,
-  ctx: RegistryContext,
-): readonly Resolution[] {
-  const defIds = ctx.qualifiedNames.get(qualifiedName);
-  if (defIds.length === 0) return EMPTY;
-
-  const acceptedKinds = new Set<NodeLabel>(params.acceptedKinds);
-
-  const resolutions: Resolution[] = [];
-  const tieKeys = new Map<string, TieBreakKey>();
-
-  for (const defId of defIds) {
-    const def = ctx.defs.get(defId);
-    if (def === undefined) continue;
-    if (!acceptedKinds.has(def.type)) continue;
-
-    const evidence = composeEvidence({ origin: 'global-qualified', kindMatch: true });
-    const confidence = confidenceFromEvidence(evidence);
-    resolutions.push({ def, confidence, evidence });
-    tieKeys.set(def.nodeId, {
-      scopeDepth: 0,
-      mroDepth: 0,
-      origin: 'global-qualified',
-    });
-  }
-
-  if (resolutions.length === 0) return EMPTY;
-
-  resolutions.sort((a, b) => compareByConfidenceWithTiebreaks(a, b, tieKeys));
-  return Object.freeze(resolutions);
-}
-
-const EMPTY: readonly Resolution[] = Object.freeze([]);

gitnexus-shared/src/scope-resolution/registries/method-registry.ts

@@ -1,54 +0,0 @@
-/**
- * `MethodRegistry` — scope-aware lookup for method / function / constructor
- * dispatch (RFC §4.4; Ring 2 SHARED #917).
- *
- * Thin wrapper over `lookupCore`, specialized for callable kinds:
- *
- *   - `acceptedKinds` = Method / Function / Constructor.
- *   - `useReceiverTypeBinding` is **true** — the type-binding + MRO walk
- *     (Step 2) is the primary evidence path for receiver-dispatched calls.
- *   - `callsite.arity` flows through to `provider.arityCompatibility`
- *     when provided. When the provider is absent, arity evidence is
- *     `unknown` (neutral signal).
- */
-
-import type { Callsite, Resolution, ScopeId } from '../types.js';
-import { lookupCore, type CoreLookupParams } from './lookup-core.js';
-import type { OwnerScopedContributor, RegistryContext } from './context.js';
-import { METHOD_KINDS } from './context.js';
-
-/**
- * Extra per-call parameters that vary across call sites but NOT across
- * registries. Kept as a separate shape so `MethodRegistry.lookup` stays
- * concise while still exposing the explicit-receiver + owner-contributor +
- * arity knobs the RFC algorithm needs.
- */
-export interface MethodLookupOptions {
-  /** Call-site arity for `provider.arityCompatibility`. */
-  readonly callsite?: Callsite;
-  /** Explicit receiver (e.g., `user` in `user.save()`). See §4.1. */
-  readonly explicitReceiver?: { readonly name: string };
-  /** Optional per-owner contributor (Step 3). */
-  readonly ownerScopedContributor?: OwnerScopedContributor;
-}
-
-export interface MethodRegistry {
-  lookup(name: string, scope: ScopeId, options?: MethodLookupOptions): readonly Resolution[];
-}
-
-export function buildMethodRegistry(ctx: RegistryContext): MethodRegistry {
-  return {
-    lookup(name: string, scope: ScopeId, options: MethodLookupOptions = {}) {
-      const params: CoreLookupParams = {
-        acceptedKinds: METHOD_KINDS,
-        useReceiverTypeBinding: true,
-        ownerScopedContributor: options.ownerScopedContributor ?? null,
-        ...(options.callsite !== undefined ? { callsite: options.callsite } : {}),
-        ...(options.explicitReceiver !== undefined
-          ? { explicitReceiver: options.explicitReceiver }
-          : {}),
-      };
-      return lookupCore(name, scope, params, ctx);
-    },
-  };
-}

gitnexus-shared/src/scope-resolution/registries/tie-breaks.ts

@@ -1,76 +0,0 @@
-/**
- * `compareByConfidenceWithTiebreaks` — the RFC §4.2 Step 7 total order
- * over `Resolution` candidates (Ring 2 SHARED #917).
- *
- * Primary key is confidence (DESC). Remaining ties within `CONFIDENCE_EPSILON`
- * fall through a deterministic cascade so the same inputs always produce
- * the same winner, independent of insertion order.
- *
- * Tie-break cascade (per RFC Appendix B):
- *
- *   1. confidence DESC                       (primary)
- *   2. scope depth ASC                       (nearer lexical scope wins)
- *   3. MRO depth ASC                         (nearer class in hierarchy wins)
- *   4. `ORIGIN_PRIORITY` ASC                 (local > import > … > global-name)
- *   5. DefId.localeCompare                   (final deterministic tiebreaker)
- *
- * The per-candidate inputs needed beyond `Resolution.confidence` —
- * `scopeDepth`, `mroDepth`, `origin` — are supplied via a sidecar
- * `TieBreakKey` so the comparator stays pure and `Resolution` itself
- * doesn't need to carry book-keeping fields.
- */
-
-import { ORIGIN_PRIORITY, type OriginForTieBreak } from '../origin-priority.js';
-import type { Resolution } from '../types.js';
-
-export const CONFIDENCE_EPSILON = 0.001;
-
-/** Side-information per candidate used for secondary tie-breaks. */
-export interface TieBreakKey {
-  readonly scopeDepth: number;
-  readonly mroDepth: number;
-  readonly origin: OriginForTieBreak;
-}
-
-/**
- * Pure comparator suitable for `Array.prototype.sort`. Return value follows
- * the JavaScript convention: negative → `a` wins, positive → `b` wins.
- *
- * **Important:** `keys` is keyed by `Resolution.def.nodeId`, not by array
- * index — stable across reorderings. Missing keys fall back to neutral
- * values (`scopeDepth: 0`, `mroDepth: 0`, `origin: 'local'`), which means
- * the tie-break degrades gracefully to defId-lexicographic ordering when
- * side-info is unavailable. That keeps the total order deterministic
- * even on malformed inputs.
- */
-export function compareByConfidenceWithTiebreaks(
-  a: Resolution,
-  b: Resolution,
-  keys: ReadonlyMap<string, TieBreakKey>,
-): number {
-  // Primary: confidence DESC, treating values within epsilon as equal.
-  const delta = b.confidence - a.confidence;
-  if (Math.abs(delta) >= CONFIDENCE_EPSILON) return delta < 0 ? -1 : 1;
-
-  const ka = keys.get(a.def.nodeId) ?? DEFAULT_KEY;
-  const kb = keys.get(b.def.nodeId) ?? DEFAULT_KEY;
-
-  // Secondary: scope depth ASC.
-  if (ka.scopeDepth !== kb.scopeDepth) return ka.scopeDepth - kb.scopeDepth;
-
-  // Tertiary: MRO depth ASC.
-  if (ka.mroDepth !== kb.mroDepth) return ka.mroDepth - kb.mroDepth;
-
-  // Quaternary: ORIGIN_PRIORITY ASC.
-  const po = ORIGIN_PRIORITY[ka.origin] - ORIGIN_PRIORITY[kb.origin];
-  if (po !== 0) return po;
-
-  // Final: DefId lexicographic, locale-aware for deterministic cross-platform output.
-  return a.def.nodeId.localeCompare(b.def.nodeId);
-}
-
-const DEFAULT_KEY: TieBreakKey = Object.freeze({
-  scopeDepth: 0,
-  mroDepth: 0,
-  origin: 'local',
-});

gitnexus-shared/src/scope-resolution/resolve-type-ref.ts

@@ -1,148 +0,0 @@
-/**
- * `resolveTypeRef` — strict single-return resolver for `TypeRef`s
- * (RFC §4.6; Ring 2 SHARED #916).
- *
- * Narrower contract than `Registry.lookup`: no name-only global fallback, no
- * confidence ranking, no arity check. Used by `Registry.lookup` Step 2 (type-
- * binding propagation) and by any caller that wants the single best type-
- * target for an annotation without paying for the full evidence pipeline.
- *
- * **Algorithm (strict).** Walk the scope chain from `ref.declaredAtScope`:
- *
- *   1. At each scope, inspect `bindings.get(ref.rawName)`:
- *      - If one of the bindings is a **type-kind** def with a **strict origin**
- *        (`'local' | 'import' | 'namespace' | 'reexport'`), return it.
- *      - If any binding for this name exists at this scope but none qualifies
- *        (e.g., a local variable named `User` shadows an outer import of class
- *        `User`), return `null`. The nearer binding shadows; we do NOT fall
- *        through to the global qualified-name index.
- *      - Otherwise continue to the parent scope.
- *   2. If the raw name is a dotted path (e.g., `'models.User'`) and the scope
- *      walk produced no match, consult `QualifiedNameIndex.byQualifiedName`.
- *      Only accept **exactly one** type-kind hit — anything ambiguous returns
- *      `null` rather than a guess.
- *   3. Return `null`.
- *
- * **What `'strict' origins' means.** `'wildcard'` is intentionally excluded.
- * A wildcard-expanded name (`from x import *`) is too loose to use as an
- * anchor for type resolution — it gives no signal about whether the name was
- * actually imported. `Registry.lookup` may accept wildcard bindings at its
- * own discretion (with lower evidence weight); `resolveTypeRef` does not.
- *
- * **What 'type-kind' means.** The subset of `NodeLabel` that a type annotation
- * may legitimately reference: class-like, interface-like, enum-like, and
- * alias-like kinds. See `TYPE_KINDS` below.
- *
- * Pure function — safe to call repeatedly; no side effects.
- */
-
-import type { NodeLabel } from '../graph/types.js';
-import type { SymbolDefinition } from './symbol-definition.js';
-import type { BindingRef, ScopeId, ScopeLookup, TypeRef } from './types.js';
-import type { DefIndex } from './def-index.js';
-import type { QualifiedNameIndex } from './qualified-name-index.js';
-
-// ─── Public contracts ───────────────────────────────────────────────────────
-
-/**
- * All inputs `resolveTypeRef` needs from the semantic model. Bundled into a
- * context object so the call site stays short and the interface is stable as
- * additional indexes get threaded through in later rings.
- */
-export interface ResolveTypeRefContext {
-  readonly scopes: ScopeLookup;
-  readonly defIndex: DefIndex;
-  readonly qualifiedNameIndex: QualifiedNameIndex;
-}
-
-// ─── Strict policy constants ────────────────────────────────────────────────
-
-/** `'wildcard'` is deliberately absent. See file header. */
-const STRICT_ORIGINS: ReadonlySet<BindingRef['origin']> = new Set<BindingRef['origin']>([
-  'local',
-  'import',
-  'namespace',
-  'reexport',
-]);
-
-/**
- * `NodeLabel` values that may appear on the RHS of a type annotation.
- *
- * Includes the usual class-like and interface-like kinds plus the alias-like
- * ones (`TypeAlias`, `Typedef`). `Namespace` is excluded — it is a scope
- * container, not a value type. `Function` / `Method` / `Variable` are
- * excluded by design: a `rawName` bound to them at a strict origin is a
- * *shadowing* binding, which the algorithm short-circuits to `null`.
- *
- * `'Type'` (the generic `NodeLabel` value) is also excluded — verified
- * against `gitnexus/src/core/ingestion/` at the time of writing, no
- * production extractor emits `type: 'Type'` for annotation-relevant
- * symbols. Should a future extractor start emitting it, add `'Type'`
- * here and add a test asserting the new path.
- */
-const TYPE_KINDS: ReadonlySet<NodeLabel> = new Set<NodeLabel>([
-  'Class',
-  'Interface',
-  'Enum',
-  'Struct',
-  'Union',
-  'Trait',
-  'TypeAlias',
-  'Typedef',
-  'Record',
-  'Delegate',
-  'Annotation',
-  'Template',
-]);
-
-// ─── Main entry point ──────────────────────────────────────────────────────
-
-export function resolveTypeRef(ref: TypeRef, ctx: ResolveTypeRefContext): SymbolDefinition | null {
-  // Phase 1: scope-chain walk anchored at the declaration site.
-  let currentId: ScopeId | null = ref.declaredAtScope;
-  const visited = new Set<ScopeId>();
-
-  while (currentId !== null) {
-    // Cycle guard — a well-formed scope tree never loops, but a bug in the
-    // construction path should fail fast here rather than hanging.
-    if (visited.has(currentId)) return null;
-    visited.add(currentId);
-
-    const scope = ctx.scopes.getScope(currentId);
-    if (scope === undefined) return null; // broken chain = unresolvable
-
-    const bindings = scope.bindings.get(ref.rawName);
-    if (bindings !== undefined && bindings.length > 0) {
-      // At least one binding exists at this scope → it is the shadowing site.
-      // Either one of them qualifies, or the name is shadowed by a non-type.
-      for (const binding of bindings) {
-        if (!STRICT_ORIGINS.has(binding.origin)) continue;
-        if (TYPE_KINDS.has(binding.def.type)) {
-          return binding.def;
-        }
-      }
-      // Shadowed by a non-type / non-strict-origin binding. Fail fast — no
-      // global fallback, no walk to the parent.
-      return null;
-    }
-
-    currentId = scope.parent;
-  }
-
-  // Phase 2: dotted fallback via `QualifiedNameIndex`. Only accept a unique
-  // type-kind hit; anything ambiguous returns null (strict: no guesses).
-  if (ref.rawName.includes('.')) {
-    const candidates = ctx.qualifiedNameIndex.get(ref.rawName);
-    let onlyTypeDef: SymbolDefinition | null = null;
-    for (const defId of candidates) {
-      const def = ctx.defIndex.get(defId);
-      if (def === undefined) continue;
-      if (!TYPE_KINDS.has(def.type)) continue;
-      if (onlyTypeDef !== null) return null; // ambiguous
-      onlyTypeDef = def;
-    }
-    if (onlyTypeDef !== null) return onlyTypeDef;
-  }
-
-  return null;
-}

gitnexus-shared/src/scope-resolution/scope-id.ts

@@ -1,57 +0,0 @@
-/**
- * `ScopeId` canonical constructor + string intern pool
- * (RFC §2.2; Ring 2 SHARED #912).
- *
- * `ScopeId` is a deterministic string derived from the scope's file path,
- * byte range, and kind:
- *
- *   scope:{filePath}#{startLine}:{startCol}-{endLine}:{endCol}:{kind}
- *
- * Two scopes produced by reparsing the same file at the same positions are
- * `===`-equal as strings. Beyond the canonical shape, `makeScopeId` also
- * **interns** the string through a process-local pool, so repeated calls
- * with structurally identical inputs return the same string reference —
- * making `Map<ScopeId, ...>` lookups and cache keys identity-fast.
- *
- * The intern pool is unbounded. The number of distinct `ScopeId`s across a
- * single indexing run is O(total scopes in workspace), which is bounded by
- * source-text size and already in memory; interning adds no asymptotic
- * pressure. `clearScopeIdInternPool` is exported for test isolation.
- */
-
-import type { Range } from './types.js';
-import type { ScopeId, ScopeKind } from './types.js';
-
-/** Inputs required to construct a canonical `ScopeId`. */
-export interface ScopeIdInput {
-  readonly filePath: string;
-  readonly range: Range;
-  readonly kind: ScopeKind;
-}
-
-/**
- * Build a canonical `ScopeId` from its structural parts and intern it.
- *
- * Pure + referentially transparent: given the same input shape, always
- * returns the same string reference for the lifetime of the pool.
- */
-export function makeScopeId(input: ScopeIdInput): ScopeId {
-  const raw = `scope:${input.filePath}#${input.range.startLine}:${input.range.startCol}-${input.range.endLine}:${input.range.endCol}:${input.kind}`;
-  const existing = INTERN_POOL.get(raw);
-  if (existing !== undefined) return existing;
-  INTERN_POOL.set(raw, raw);
-  return raw;
-}
-
-/**
- * Drop the intern pool. Intended for test setup/teardown — production code
- * should not need this, since the pool's memory usage is bounded by the
- * number of live scopes and cleaning it mid-run would break identity
- * equality for existing scope ids.
- */
-export function clearScopeIdInternPool(): void {
-  INTERN_POOL.clear();
-}
-
-/** Internal: shared intern pool (process-local). */
-const INTERN_POOL = new Map<string, string>();

gitnexus-shared/src/scope-resolution/scope-tree.ts

@@ -1,254 +0,0 @@
-/**
- * `ScopeTree` — the lexical-scope spine of the `SemanticModel`
- * (RFC §2.2 + §3.1; Ring 2 SHARED #912).
- *
- * Generalizes the `enclosingFunctions` pattern from closed PR #902 to
- * arbitrary `ScopeKind`s. Owns the (parent ↔ children) relationship
- * derived from each `Scope.parent` pointer, and validates the structural
- * invariants a well-formed scope tree must satisfy.
- *
- * Invariants enforced at build time (throw on violation):
- *
- *   - Every non-`Module` scope has a non-null parent.
- *   - Every parent pointer references a scope that was also supplied to
- *     `buildScopeTree`.
- *   - Parent range **strictly contains** child range.
- *   - Sibling ranges under the same parent do not overlap.
- *   - Parent and child live in the same `filePath`. (Cross-file parent
- *     pointers would be a category error — a `File` scope is not the
- *     parent of another file's scopes; imports do that job.)
- *
- * Satisfies the `ScopeLookup` contract (defined in `./types.js`), so
- * `resolveTypeRef` (#916) and the scope-aware registries (#917) can take a
- * `ScopeTree` directly without adapters.
- *
- * Immutable surface: `byId` is a `ReadonlyMap`; children arrays are
- * `Object.freeze`d; miss lookups return a shared frozen empty array.
- */
-
-import type { Scope, ScopeId, ScopeLookup, Range } from './types.js';
-
-// ─── Public contract ────────────────────────────────────────────────────────
-
-export interface ScopeTree extends ScopeLookup {
-  readonly size: number;
-  readonly byId: ReadonlyMap<ScopeId, Scope>;
-
-  getScope(id: ScopeId): Scope | undefined;
-  getParent(id: ScopeId): Scope | undefined;
-  /** Child `ScopeId`s of `id`, in input order. Frozen empty array on miss. */
-  getChildren(id: ScopeId): readonly ScopeId[];
-  /**
-   * Ancestor chain from the immediate parent up to (and including) the
-   * root module scope. Excludes the starting scope itself. Frozen empty
-   * array on miss / for a root scope.
-   */
-  getAncestors(id: ScopeId): readonly ScopeId[];
-  has(id: ScopeId): boolean;
-}
-
-// ─── Build errors ───────────────────────────────────────────────────────────
-
-/**
- * Thrown by `buildScopeTree` when the input violates a structural
- * invariant. Carries the offending ids + the invariant name so failed
- * extraction pipelines can report actionable diagnostics.
- */
-export class ScopeTreeInvariantError extends Error {
-  constructor(
-    readonly invariant:
-      | 'non-module-requires-parent'
-      | 'parent-not-found'
-      | 'parent-must-contain-child'
-      | 'sibling-ranges-overlap'
-      | 'parent-must-share-filepath'
-      | 'duplicate-scope-id',
-    message: string,
-  ) {
-    super(message);
-    this.name = 'ScopeTreeInvariantError';
-  }
-}
-
-// ─── Builder ───────────────────────────────────────────────────────────────
-
-/**
- * Build an immutable `ScopeTree` from a flat list of `Scope` records.
- *
- * Throws `ScopeTreeInvariantError` on the first invariant violation; a
- * malformed tree is a bug in the extraction pipeline, not a data case for
- * consumers to handle, so fail-fast is the correct posture.
- */
-export function buildScopeTree(scopes: readonly Scope[]): ScopeTree {
-  const byId = new Map<ScopeId, Scope>();
-  const childrenById = new Map<ScopeId, ScopeId[]>();
-
-  // ── Pass 1: collect by id + duplicate check ───────────────────────────
-  for (const scope of scopes) {
-    if (byId.has(scope.id)) {
-      throw new ScopeTreeInvariantError(
-        'duplicate-scope-id',
-        `Two scopes share id '${scope.id}'. Scope ids must be unique per tree.`,
-      );
-    }
-    byId.set(scope.id, scope);
-  }
-
-  // ── Pass 2: validate parent pointers + build children buckets ─────────
-  for (const scope of scopes) {
-    if (scope.parent === null) {
-      if (scope.kind !== 'Module') {
-        throw new ScopeTreeInvariantError(
-          'non-module-requires-parent',
-          `Scope '${scope.id}' has kind '${scope.kind}' but no parent. Only 'Module' scopes may be root-level.`,
-        );
-      }
-      continue;
-    }
-
-    const parent = byId.get(scope.parent);
-    if (parent === undefined) {
-      throw new ScopeTreeInvariantError(
-        'parent-not-found',
-        `Scope '${scope.id}' references parent '${scope.parent}' which is not part of this tree.`,
-      );
-    }
-    if (parent.filePath !== scope.filePath) {
-      throw new ScopeTreeInvariantError(
-        'parent-must-share-filepath',
-        `Scope '${scope.id}' (${scope.filePath}) has parent '${parent.id}' in a different file (${parent.filePath}). Parent/child scopes must share filePath.`,
-      );
-    }
-    if (!rangeStrictlyContains(parent.range, scope.range)) {
-      throw new ScopeTreeInvariantError(
-        'parent-must-contain-child',
-        `Parent scope '${parent.id}' at ${formatRange(parent.range)} does not strictly contain child '${scope.id}' at ${formatRange(scope.range)}.`,
-      );
-    }
-
-    let bucket = childrenById.get(parent.id);
-    if (bucket === undefined) {
-      bucket = [];
-      childrenById.set(parent.id, bucket);
-    }
-    bucket.push(scope.id);
-  }
-
-  // ── Pass 3: sibling-overlap check ─────────────────────────────────────
-  for (const [parentId, childIds] of childrenById) {
-    if (childIds.length < 2) continue;
-    // Sort siblings by (startLine, startCol) for an O(n log n) pairwise
-    // scan instead of O(n²) all-pairs.
-    const children = childIds.map((id) => byId.get(id)!).slice();
-    children.sort((a, b) => comparePosition(a.range, b.range));
-    for (let i = 1; i < children.length; i++) {
-      const prev = children[i - 1]!;
-      const curr = children[i]!;
-      if (rangesOverlap(prev.range, curr.range)) {
-        throw new ScopeTreeInvariantError(
-          'sibling-ranges-overlap',
-          `Sibling scopes under parent '${parentId}' overlap: '${prev.id}' ${formatRange(prev.range)} and '${curr.id}' ${formatRange(curr.range)}.`,
-        );
-      }
-    }
-  }
-
-  // Freeze children arrays so the surface is truly read-only.
-  const frozenChildren = new Map<ScopeId, readonly ScopeId[]>();
-  for (const [parentId, childIds] of childrenById) {
-    frozenChildren.set(parentId, Object.freeze(childIds.slice()));
-  }
-
-  return freezeTree(byId, frozenChildren);
-}
-
-// ─── Internals ──────────────────────────────────────────────────────────────
-
-const EMPTY_CHILDREN: readonly ScopeId[] = Object.freeze([]);
-
-function freezeTree(
-  byId: Map<ScopeId, Scope>,
-  childrenById: Map<ScopeId, readonly ScopeId[]>,
-): ScopeTree {
-  return {
-    byId,
-    get size() {
-      return byId.size;
-    },
-    getScope(id: ScopeId): Scope | undefined {
-      return byId.get(id);
-    },
-    getParent(id: ScopeId): Scope | undefined {
-      const scope = byId.get(id);
-      if (scope === undefined || scope.parent === null) return undefined;
-      return byId.get(scope.parent);
-    },
-    getChildren(id: ScopeId): readonly ScopeId[] {
-      return childrenById.get(id) ?? EMPTY_CHILDREN;
-    },
-    getAncestors(id: ScopeId): readonly ScopeId[] {
-      const start = byId.get(id);
-      if (start === undefined || start.parent === null) return EMPTY_CHILDREN;
-      const out: ScopeId[] = [];
-      const visited = new Set<ScopeId>([id]);
-      let cursor: ScopeId | null = start.parent;
-      while (cursor !== null && !visited.has(cursor)) {
-        visited.add(cursor);
-        out.push(cursor);
-        const next = byId.get(cursor);
-        cursor = next === undefined ? null : next.parent;
-      }
-      return Object.freeze(out);
-    },
-    has(id: ScopeId): boolean {
-      return byId.has(id);
-    },
-  };
-}
-
-/**
- * `outer` strictly contains `inner` when `outer`'s start is at or before
- * `inner`'s start, `outer`'s end is at or after `inner`'s end, and they are
- * not the exact same range. Equal ranges are rejected — a child cannot
- * occupy the exact same span as its parent.
- */
-function rangeStrictlyContains(outer: Range, inner: Range): boolean {
-  if (
-    outer.startLine === inner.startLine &&
-    outer.startCol === inner.startCol &&
-    outer.endLine === inner.endLine &&
-    outer.endCol === inner.endCol
-  ) {
-    return false;
-  }
-  const outerStartsAtOrBefore =
-    outer.startLine < inner.startLine ||
-    (outer.startLine === inner.startLine && outer.startCol <= inner.startCol);
-  const outerEndsAtOrAfter =
-    outer.endLine > inner.endLine ||
-    (outer.endLine === inner.endLine && outer.endCol >= inner.endCol);
-  return outerStartsAtOrBefore && outerEndsAtOrAfter;
-}
-
-/**
- * Two ranges overlap when neither finishes before the other begins. Ranges
- * that merely touch at a single boundary point (`a.end === b.start`) do
- * NOT overlap — this matches tree-sitter's half-open-like range semantics
- * and the typical "sibling blocks meet but don't overlap" pattern.
- */
-function rangesOverlap(a: Range, b: Range): boolean {
-  const aEndsBeforeB =
-    a.endLine < b.startLine || (a.endLine === b.startLine && a.endCol <= b.startCol);
-  const bEndsBeforeA =
-    b.endLine < a.startLine || (b.endLine === a.startLine && b.endCol <= a.startCol);
-  return !(aEndsBeforeB || bEndsBeforeA);
-}
-
-function comparePosition(a: Range, b: Range): number {
-  if (a.startLine !== b.startLine) return a.startLine - b.startLine;
-  return a.startCol - b.startCol;
-}
-
-function formatRange(r: Range): string {
-  return `${r.startLine}:${r.startCol}-${r.endLine}:${r.endCol}`;
-}

gitnexus-shared/src/scope-resolution/shadow/aggregate.ts

@@ -1,188 +0,0 @@
-/**
- * Shadow-mode aggregation — per-language parity %, per-evidence-kind
- * breakdown of divergences. Consumed by the parity dashboard (RING2-PKG-5).
- *
- * Pure functions; no I/O. The harness persists per-run JSON; the dashboard
- * reads `.gitnexus/shadow-parity/latest.json` and renders.
- *
- * Related types — `ShadowAgreement`, `ShadowCallsite`, `ShadowDiff` — are
- * defined alongside `diffResolutions` in `./diff.ts` and re-exported
- * through the top-level `gitnexus-shared` barrel. Consumers import all
- * three from `gitnexus-shared`, not from this module.
- *
- * Part of RFC #909 Ring 2 SHARED — #918.
- */
-
-import type { SupportedLanguages } from '../../languages.js';
-import type { ResolutionEvidence } from '../types.js';
-import type { ShadowAgreement, ShadowDiff } from './diff.js';
-
-// ─── Aggregated report shape ────────────────────────────────────────────────
-
-export interface LanguageParityRow {
-  readonly language: SupportedLanguages;
-  readonly totalCalls: number;
-  readonly bothAgree: number;
-  readonly onlyLegacy: number;
-  readonly onlyNew: number;
-  readonly bothDisagree: number;
-  readonly bothEmpty: number;
-  /**
-   * Fraction in [0, 1]. Numerator = `bothAgree`; denominator = "calls where
-   * at least one side resolved" = `totalCalls - bothEmpty`.
-   *
-   * When the denominator is 0 (all calls for this language were
-   * `both-empty`), returns 0. Callers rendering the dashboard should treat
-   * a 0 parity alongside `totalCalls === bothEmpty` as "no signal" rather
-   * than "total disagreement".
-   */
-  readonly parity: number;
-  /**
-   * Divergence signals broken down by `ResolutionEvidence.kind`. Sourced
-   * from `ShadowDiff.evidenceDelta` on non-agreeing rows only — `both-agree`
-   * and `both-empty` do not contribute.
-   */
-  readonly evidenceBreakdown: ReadonlyMap<ResolutionEvidence['kind'], number>;
-}
-
-export interface ShadowParityReport {
-  readonly generatedAt: string; // ISO 8601
-  readonly perLanguage: readonly LanguageParityRow[];
-  readonly overall: Omit<LanguageParityRow, 'language' | 'evidenceBreakdown'>;
-}
-
-// ─── Public API ─────────────────────────────────────────────────────────────
-
-/**
- * Aggregate a stream of `ShadowDiff` records into a `ShadowParityReport`,
- * bucketed by language. Pure function.
- *
- * - `perLanguage` rows are sorted alphabetically by `SupportedLanguages`
- *   value for stable JSON output (the dashboard reads
- *   `.gitnexus/shadow-parity/latest.json` and diffing snapshots is useful).
- * - `overall` is the column-wise sum across languages.
- * - `generatedAt` is injected via the `now` parameter so tests stay
- *   deterministic; production callers let it default to `new Date()`.
- */
-export function aggregateDiffs(
-  diffs: readonly { readonly language: SupportedLanguages; readonly diff: ShadowDiff }[],
-  now: Date = new Date(),
-): ShadowParityReport {
-  const perLanguageMap = new Map<SupportedLanguages, MutableCounts>();
-
-  for (const { language, diff } of diffs) {
-    let counts = perLanguageMap.get(language);
-    if (!counts) {
-      counts = makeEmptyCounts();
-      perLanguageMap.set(language, counts);
-    }
-    tallyDiff(counts, diff);
-  }
-
-  const perLanguage: LanguageParityRow[] = Array.from(perLanguageMap.entries())
-    .map(([language, counts]) => buildRow(language, counts))
-    .sort((a, b) => a.language.localeCompare(b.language));
-
-  const overall = buildOverallRow(perLanguage);
-
-  return {
-    generatedAt: now.toISOString(),
-    perLanguage,
-    overall,
-  };
-}
-
-// ─── Internal helpers ───────────────────────────────────────────────────────
-
-interface MutableCounts {
-  totalCalls: number;
-  bothAgree: number;
-  onlyLegacy: number;
-  onlyNew: number;
-  bothDisagree: number;
-  bothEmpty: number;
-  evidenceBreakdown: Map<ResolutionEvidence['kind'], number>;
-}
-
-function makeEmptyCounts(): MutableCounts {
-  return {
-    totalCalls: 0,
-    bothAgree: 0,
-    onlyLegacy: 0,
-    onlyNew: 0,
-    bothDisagree: 0,
-    bothEmpty: 0,
-    evidenceBreakdown: new Map(),
-  };
-}
-
-function tallyDiff(counts: MutableCounts, diff: ShadowDiff): void {
-  counts.totalCalls += 1;
-  incrementAgreement(counts, diff.agreement);
-  if (diff.agreement === 'both-agree' || diff.agreement === 'both-empty') return;
-  for (const ev of diff.evidenceDelta) {
-    counts.evidenceBreakdown.set(ev.kind, (counts.evidenceBreakdown.get(ev.kind) ?? 0) + 1);
-  }
-}
-
-function incrementAgreement(counts: MutableCounts, agreement: ShadowAgreement): void {
-  switch (agreement) {
-    case 'both-agree':
-      counts.bothAgree += 1;
-      return;
-    case 'only-legacy':
-      counts.onlyLegacy += 1;
-      return;
-    case 'only-new':
-      counts.onlyNew += 1;
-      return;
-    case 'both-disagree':
-      counts.bothDisagree += 1;
-      return;
-    case 'both-empty':
-      counts.bothEmpty += 1;
-      return;
-  }
-}
-
-function buildRow(language: SupportedLanguages, counts: MutableCounts): LanguageParityRow {
-  const resolved = counts.totalCalls - counts.bothEmpty;
-  const parity = resolved > 0 ? counts.bothAgree / resolved : 0;
-  return {
-    language,
-    totalCalls: counts.totalCalls,
-    bothAgree: counts.bothAgree,
-    onlyLegacy: counts.onlyLegacy,
-    onlyNew: counts.onlyNew,
-    bothDisagree: counts.bothDisagree,
-    bothEmpty: counts.bothEmpty,
-    parity,
-    // Freeze via `new Map` on a sorted-kind copy so downstream consumers
-    // can't mutate the aggregator's internal state.
-    evidenceBreakdown: new Map(
-      Array.from(counts.evidenceBreakdown.entries()).sort(([a], [b]) => a.localeCompare(b)),
-    ),
-  };
-}
-
-function buildOverallRow(
-  perLanguage: readonly LanguageParityRow[],
-): Omit<LanguageParityRow, 'language' | 'evidenceBreakdown'> {
-  let totalCalls = 0;
-  let bothAgree = 0;
-  let onlyLegacy = 0;
-  let onlyNew = 0;
-  let bothDisagree = 0;
-  let bothEmpty = 0;
-  for (const row of perLanguage) {
-    totalCalls += row.totalCalls;
-    bothAgree += row.bothAgree;
-    onlyLegacy += row.onlyLegacy;
-    onlyNew += row.onlyNew;
-    bothDisagree += row.bothDisagree;
-    bothEmpty += row.bothEmpty;
-  }
-  const resolved = totalCalls - bothEmpty;
-  const parity = resolved > 0 ? bothAgree / resolved : 0;
-  return { totalCalls, bothAgree, onlyLegacy, onlyNew, bothDisagree, bothEmpty, parity };
-}

gitnexus-shared/src/scope-resolution/shadow/diff.ts

@@ -1,126 +0,0 @@
-/**
- * Shadow-mode diff logic — RFC §6.3.
- *
- * Pure comparison logic for shadow mode. Takes two `Resolution[]` (legacy
- * DAG result + new scope-based registry result) and produces a structured
- * diff record for the parity dashboard.
- *
- * Consumed by the Ring 2 PKG shadow harness (#923), which dual-runs each
- * call through legacy + new paths, diffs results, and persists per-run JSON
- * for the parity dashboard.
- *
- * Part of RFC #909 Ring 2 SHARED — #918.
- */
-
-import type { Resolution, ResolutionEvidence } from '../types.js';
-
-// ─── Diff record shape ──────────────────────────────────────────────────────
-
-export type ShadowAgreement =
-  | 'both-agree' // top match identical (same DefId)
-  | 'only-legacy' // legacy resolved; new did not
-  | 'only-new' // new resolved; legacy did not
-  | 'both-disagree' // both resolved, but to different targets
-  | 'both-empty'; // both returned empty
-
-export interface ShadowDiff {
-  readonly callsite: ShadowCallsite;
-  readonly legacy: Resolution | null;
-  readonly newResult: Resolution | null;
-  readonly agreement: ShadowAgreement;
-  /**
-   * Symmetric difference of the two top resolutions' `evidence` arrays,
-   * keyed on `ResolutionEvidence.kind`.
-   *
-   * - For `'both-agree'` and `'both-empty'` agreements, always empty.
-   * - For `'both-disagree'`, contains evidence kinds present on exactly one
-   *   side (not in both).
-   * - For `'only-legacy'`, contains all of legacy's top evidence.
-   * - For `'only-new'`, contains all of new's top evidence.
-   */
-  readonly evidenceDelta: readonly ResolutionEvidence[];
-}
-
-export interface ShadowCallsite {
-  readonly filePath: string;
-  readonly line: number;
-  readonly col: number;
-  readonly calledName: string;
-}
-
-// ─── Public API ─────────────────────────────────────────────────────────────
-
-/**
- * Compare two `Resolution[]` arrays (top matches at `[0]`) and produce a
- * `ShadowDiff`. Pure function.
- *
- * Agreement rules:
- * - both arrays empty → `'both-empty'`, `evidenceDelta: []`
- * - legacy empty, new non-empty → `'only-new'`, `evidenceDelta` = new's top evidence
- * - legacy non-empty, new empty → `'only-legacy'`, `evidenceDelta` = legacy's top evidence
- * - both non-empty, same top `def.nodeId` → `'both-agree'`, `evidenceDelta: []`
- * - both non-empty, different top `def.nodeId` → `'both-disagree'`,
- *   `evidenceDelta` = symmetric difference by `ResolutionEvidence.kind`
- *   (first occurrence of a kind-only-on-legacy then kind-only-on-new; order
- *   preserved from input arrays)
- *
- * Evidence-delta rationale: callers aggregating divergences want to know
- * which signal kinds explain a disagreement. Keying on `kind` (not full
- * equality over `weight`/`note`) avoids spurious deltas when the same
- * signal fires with slightly different calibration weights on each side.
- */
-export function diffResolutions(
-  callsite: ShadowCallsite,
-  legacy: readonly Resolution[],
-  newResult: readonly Resolution[],
-): ShadowDiff {
-  const legacyTop: Resolution | null = legacy.length > 0 ? legacy[0] : null;
-  const newTop: Resolution | null = newResult.length > 0 ? newResult[0] : null;
-
-  const agreement: ShadowAgreement = (() => {
-    if (legacyTop === null && newTop === null) return 'both-empty';
-    if (legacyTop === null) return 'only-new';
-    if (newTop === null) return 'only-legacy';
-    return legacyTop.def.nodeId === newTop.def.nodeId ? 'both-agree' : 'both-disagree';
-  })();
-
-  const evidenceDelta = computeEvidenceDelta(legacyTop, newTop, agreement);
-
-  return {
-    callsite,
-    legacy: legacyTop,
-    newResult: newTop,
-    agreement,
-    evidenceDelta,
-  };
-}
-
-// ─── Internal helpers ───────────────────────────────────────────────────────
-
-/**
- * Symmetric difference of two evidence arrays, keyed on
- * `ResolutionEvidence.kind`. Preserves input order: legacy-only signals
- * first (in legacy's original order), then new-only signals (in new's order).
- *
- * For `'both-agree'` / `'both-empty'` the delta is empty by contract. For
- * `'only-legacy'` / `'only-new'` one side's evidence is the delta (nothing to
- * subtract against).
- */
-function computeEvidenceDelta(
-  legacy: Resolution | null,
-  newResult: Resolution | null,
-  agreement: ShadowAgreement,
-): readonly ResolutionEvidence[] {
-  if (agreement === 'both-agree' || agreement === 'both-empty') return [];
-  if (agreement === 'only-legacy') return legacy!.evidence;
-  if (agreement === 'only-new') return newResult!.evidence;
-
-  // both-disagree: symmetric difference keyed on `kind`
-  const legacyKinds = new Set(legacy!.evidence.map((e) => e.kind));
-  const newKinds = new Set(newResult!.evidence.map((e) => e.kind));
-
-  const onlyInLegacy = legacy!.evidence.filter((e) => !newKinds.has(e.kind));
-  const onlyInNew = newResult!.evidence.filter((e) => !legacyKinds.has(e.kind));
-
-  return [...onlyInLegacy, ...onlyInNew];
-}

gitnexus-shared/src/scope-resolution/symbol-definition.ts

@@ -1,35 +0,0 @@
-/**
- * `SymbolDefinition` — the canonical shape of an indexed symbol record.
- *
- * Historically defined in `gitnexus/src/core/ingestion/model/symbol-table.ts`;
- * moved into `gitnexus-shared` as part of RFC #909 Ring 1 (#910) so the
- * scope-resolution types that reference it can live in the shared package
- * alongside their consumers (`gitnexus/` and `gitnexus-web/`).
- *
- * Shape is unchanged from the prior local definition.
- */
-
-import type { NodeLabel } from '../graph/types.js';
-
-export interface SymbolDefinition {
-  nodeId: string;
-  filePath: string;
-  type: NodeLabel;
-  /** Canonical dot-separated qualified type name for class-like symbols
-   *  (e.g. `App.Models.User`). Falls back to the simple symbol name when no
-   *  package/namespace/module scope exists or no explicit qualified metadata is provided. */
-  qualifiedName?: string;
-  parameterCount?: number;
-  /** Number of required (non-optional, non-default) parameters.
-   *  Enables range-based arity filtering: argCount >= requiredParameterCount && argCount <= parameterCount. */
-  requiredParameterCount?: number;
-  /** Per-parameter type names for overload disambiguation (e.g. ['int', 'String']).
-   *  Populated when parameter types are resolvable from AST (any typed language). */
-  parameterTypes?: string[];
-  /** Raw return type text extracted from AST (e.g. 'User', 'Promise<User>') */
-  returnType?: string;
-  /** Declared type for non-callable symbols — fields/properties (e.g. 'Address', 'List<User>') */
-  declaredType?: string;
-  /** Links Method/Constructor/Property to owning Class/Struct/Trait nodeId */
-  ownerId?: string;
-}

gitnexus-shared/src/scope-resolution/types.ts

@@ -1,432 +0,0 @@
-/**
- * Scope-resolution type definitions — RFC §2 data model (authoritative source).
- *
- * See: https://www.notion.so/346dc50b6ed281cfaacbe480bf231d50
- *
- * Anti-drift rule: every type, interface, and enum defined here is the single
- * source of truth. Later code that references these names must import them
- * from `gitnexus-shared`; it must not re-define them locally.
- *
- * Lifecycle contract (RFC §2.8): scopes are **constructed during extraction,
- * linked during finalize, immutable after finalize**. All fields are
- * `readonly` at the type level; `Object.freeze` is applied at runtime in dev
- * builds. `ReferenceIndex` is the sole structure populated after freeze — by
- * resolution, before emission.
- */
-
-import type { NodeLabel } from '../graph/types.js';
-import type { SymbolDefinition } from './symbol-definition.js';
-
-// ─── §2.1 Type aliases ──────────────────────────────────────────────────────
-
-/** Stable per-(file, range, kind) scope identifier; interned for identity-fast equality. */
-export type ScopeId = string;
-
-/** Stable symbol-definition identifier (graph nodeId). */
-export type DefId = string;
-
-/** Kinds of lexical scope a `Scope` node can represent. */
-export type ScopeKind =
-  | 'Module' // file root
-  | 'Namespace' // C++ namespace, C# namespace, Kotlin package-object, Rust mod
-  | 'Class' // class/struct/trait/interface body
-  | 'Function' // function/method/closure/lambda body
-  | 'Block' // { ... }, if-body, for-body, with-body, match arms
-  | 'Expression'; // comprehensions, for-init, pattern bindings, lambda param lists
-
-// ─── Range + Capture (parser-agnostic) ──────────────────────────────────────
-
-/** Source-text range. 1-based `startLine`/`endLine`; 0-based `startCol`/`endCol`. */
-export interface Range {
-  readonly startLine: number;
-  readonly startCol: number;
-  readonly endLine: number;
-  readonly endCol: number;
-}
-
-/**
- * Tagged capture emitted by a LanguageProvider's `emitScopeCaptures` hook.
- *
- * Parser-agnostic: tree-sitter queries and COBOL's regex tagger both produce
- * `Capture[]`. The central `ScopeExtractor` consumes captures without
- * knowing which parser produced them.
- */
-export interface Capture {
-  /** Capture name, including leading `@` (e.g., `'@scope.module'`, `'@declaration.class'`). */
-  readonly name: string;
-  readonly range: Range;
-  /** The captured source text. */
-  readonly text: string;
-}
-
-/**
- * A grouping of `Capture`s that came from a single query match (e.g., one
- * `@import.statement` match carries `@import.source`, `@import.name`,
- * `@import.alias?` as child captures). Keyed by capture name for O(1)
- * child access.
- */
-export type CaptureMatch = Readonly<Record<string, Capture>>;
-
-// ─── Hook input/output types (RFC §5.2) ─────────────────────────────────────
-
-/**
- * Provider-interpreted raw import, consumed by finalize (Phase 2) to produce
- * linked `ImportEdge[]`. The provider's `interpretImport` hook turns a
- * `CaptureMatch` for an `@import.statement` into one of these; the central
- * finalize algorithm resolves `targetRaw` to a concrete file via
- * `resolveImportTarget` and materializes the final `ImportEdge`.
- *
- * Discriminated union — each variant carries only the fields that make sense
- * for its kind. Invalid shapes (e.g., a `namespace` import with an alias-like
- * `importedName` mismatch) are compile errors, not latent bugs. `'wildcard-
- * expanded'` is deliberately NOT a variant: that kind is finalize output only,
- * produced when `expandsWildcardTo` materializes a wildcard against target
- * exports — a provider must never emit it at parse time.
- */
-export type ParsedImport =
-  /**
-   * Per-name import without rename.
-   *
-   * Examples:
-   *   - Python `from foo import X`   → `{ kind: 'named', localName: 'X', importedName: 'X', targetRaw: 'foo' }`
-   *   - TS `import { X } from './foo'` → `{ kind: 'named', localName: 'X', importedName: 'X', targetRaw: './foo' }`
-   *   - Java `import foo.bar.X`       → `{ kind: 'named', localName: 'X', importedName: 'X', targetRaw: 'foo.bar' }`
-   */
-  | {
-      readonly kind: 'named';
-      readonly localName: string;
-      readonly importedName: string;
-      readonly targetRaw: string;
-    }
-  /**
-   * Per-name import with rename.
-   *
-   * Examples:
-   *   - Python `from foo import X as Y`   → `{ kind: 'alias', localName: 'Y', importedName: 'X', alias: 'Y', targetRaw: 'foo' }`
-   *   - TS `import { X as Y } from './foo'` → `{ kind: 'alias', localName: 'Y', importedName: 'X', alias: 'Y', targetRaw: './foo' }`
-   */
-  | {
-      readonly kind: 'alias';
-      readonly localName: string;
-      readonly importedName: string;
-      readonly alias: string;
-      readonly targetRaw: string;
-    }
-  /**
-   * Qualified module handle, with or without rename. `importedName` is the
-   * module being aliased; `localName` is the scope-visible handle (often the
-   * same unless renamed).
-   *
-   * Examples:
-   *   - Python `import numpy`            → `{ kind: 'namespace', localName: 'numpy', importedName: 'numpy', targetRaw: 'numpy' }`
-   *   - Python `import numpy as np`      → `{ kind: 'namespace', localName: 'np',    importedName: 'numpy', targetRaw: 'numpy' }`
-   *   - TS `import * as np from 'numpy'` → `{ kind: 'namespace', localName: 'np',    importedName: 'numpy', targetRaw: 'numpy' }`
-   *   - Go `import foo "pkg/bar"`        → `{ kind: 'namespace', localName: 'foo',   importedName: 'bar',   targetRaw: 'pkg/bar' }`
-   */
-  | {
-      readonly kind: 'namespace';
-      /** Scope-visible handle (e.g. `np` in `import numpy as np`; `numpy` when unaliased). */
-      readonly localName: string;
-      /** Module being aliased (e.g. `numpy` in `import numpy as np`). */
-      readonly importedName: string;
-      readonly targetRaw: string;
-    }
-  /**
-   * Syntactically-detectable parse-time re-export. Finalize may still produce
-   * `ImportEdge { kind: 'reexport', transitiveVia }` when flattening chains;
-   * this variant preserves the *parse-time* signal so finalize doesn't have
-   * to re-derive it from scratch.
-   *
-   * Examples:
-   *   - TS `export { X } from './y'`       → `{ kind: 'reexport', localName: 'X', importedName: 'X', targetRaw: './y' }`
-   *   - TS `export { X as Y } from './y'`  → `{ kind: 'reexport', localName: 'Y', importedName: 'X', alias: 'Y', targetRaw: './y' }`
-   *   - Rust `pub use foo::bar`            → `{ kind: 'reexport', localName: 'bar', importedName: 'bar', targetRaw: 'foo' }`
-   */
-  | {
-      readonly kind: 'reexport';
-      /** Name as re-exported in the current module. */
-      readonly localName: string;
-      /** Name in the source module. */
-      readonly importedName: string;
-      readonly targetRaw: string;
-      /** Set when the re-export renames the symbol (e.g. `export { X as Y } from './y'`). */
-      readonly alias?: string;
-    }
-  /**
-   * Wildcard import — brings every exported name from the target module into
-   * the importing scope. The finalize algorithm expands this into one
-   * `BindingRef` per exported name via the provider's `expandsWildcardTo`
-   * hook, producing the finalize-only `ImportEdge` kind `'wildcard-expanded'`.
-   *
-   * Examples:
-   *   - Python `from foo import *`   → `{ kind: 'wildcard', targetRaw: 'foo' }`
-   *   - JS `export * from './foo'`   → `{ kind: 'wildcard', targetRaw: './foo' }`
-   *   - Rust `pub use foo::*`         → `{ kind: 'wildcard', targetRaw: 'foo' }`
-   */
-  | {
-      readonly kind: 'wildcard';
-      readonly targetRaw: string;
-    }
-  /**
-   * Runtime-computed target — the import path is not a static literal at
-   * parse time. Providers SHOULD emit the unresolvable expression's source
-   * text as `targetRaw` to aid diagnostics; `null` only when no string form
-   * exists.
-   *
-   * Examples:
-   *   - JS `await import(expr)`                          → `{ kind: 'dynamic-unresolved', localName: '', targetRaw: 'expr' }`
-   *   - Python `importlib.import_module(f'pkg.{name}')`  → `{ kind: 'dynamic-unresolved', localName: '', targetRaw: "f'pkg.{name}'" }`
-   */
-  | {
-      readonly kind: 'dynamic-unresolved';
-      readonly localName: string;
-      /** Source text of the unresolved expression when available; `null` otherwise. */
-      readonly targetRaw: string | null;
-    };
-
-/**
- * Provider-interpreted type binding. The provider's `interpretTypeBinding`
- * hook turns a `CaptureMatch` (e.g., `@type-binding.parameter`) into one of
- * these; the central extractor attaches the resulting `TypeRef` to the
- * appropriate scope's `typeBindings` map.
- */
-export interface ParsedTypeBinding {
-  /** The name being bound (parameter name, `self`, assignment LHS, …). */
-  readonly boundName: string;
-  /** The raw type name as written in source (`'User'`, `'models.User'`, …). */
-  readonly rawTypeName: string;
-  readonly source: TypeRef['source'];
-}
-
-/**
- * Cross-file workspace index consumed by finalize-phase hooks
- * (`resolveImportTarget`, `expandsWildcardTo`). Opaque placeholder in Ring 1;
- * concretely typed in Ring 2 SHARED (#915).
- */
-export type WorkspaceIndex = unknown;
-
-// `ScopeTree` is exported from `./scope-tree.js` as of Ring 2 SHARED (#912).
-// The former opaque placeholder lived here during Ring 1; removed now that
-// the concrete type exists. Consumers import from `gitnexus-shared` directly.
-
-/**
- * Minimal scope-lookup contract: map a `ScopeId` back to its `Scope` record.
- *
- * Lives in the data-model layer so both `ScopeTree` (§3.1) and
- * `resolveTypeRef` / `Registry.lookup` (§4) can depend on it without
- * inverting each other. `ScopeTree` is the canonical implementation;
- * tests and future alternative containers may supply their own.
- */
-export interface ScopeLookup {
-  getScope(id: ScopeId): Scope | undefined;
-}
-
-/** Call-site description passed to `arityCompatibility`. */
-export interface Callsite {
-  /** Number of arguments at the call site. */
-  readonly arity: number;
-}
-
-// ─── §2.4 ImportEdge ────────────────────────────────────────────────────────
-
-/**
- * A cross-file import edge attached to a module/namespace scope.
- *
- * Raw (unlinked) edges are emitted during parse (Phase 1); `targetModuleScope`
- * and `targetDefId` are filled in during finalize (Phase 2) via SCC-aware
- * bounded-fixpoint linking (RFC §3.2).
- */
-export interface ImportEdge {
-  /** How this scope sees the imported name (after alias). */
-  readonly localName: string;
-  /** Exporting file; `null` only when `kind === 'dynamic-unresolved'`. */
-  readonly targetFile: string | null;
-  /** The name under which the target exports this symbol. */
-  readonly targetExportedName: string;
-  /** Pre-resolved at finalize: the module scope of the exporting file. */
-  readonly targetModuleScope?: ScopeId;
-  /** Pre-resolved at finalize: the exported symbol's `DefId`. */
-  readonly targetDefId?: DefId;
-  readonly kind:
-    | 'named'
-    | 'alias'
-    | 'namespace'
-    | 'wildcard-expanded'
-    | 'reexport'
-    | 'dynamic-unresolved';
-  /** Re-export chain, for provenance (e.g., `['./y']` when re-exported via `./y`). */
-  readonly transitiveVia?: readonly string[];
-  /** Set to `'unresolved'` when the SCC fixpoint could not link this edge. */
-  readonly linkStatus?: 'unresolved';
-}
-
-// ─── §2.3 BindingRef ────────────────────────────────────────────────────────
-
-/**
- * A name binding visible at a scope, with provenance.
- *
- * Provenance stays at the visibility layer — a name being visible because it
- * is local vs imported vs wildcard-expanded vs re-exported is a property of
- * the binding itself. This keeps evidence emission and `import-use` reference
- * stamping first-class instead of reconstructing provenance from a side table.
- */
-export interface BindingRef {
-  readonly def: SymbolDefinition;
-  readonly origin: 'local' | 'import' | 'namespace' | 'wildcard' | 'reexport';
-  /** Non-null for non-local origins; carries the `ImportEdge` that brought the name into this scope. */
-  readonly via?: ImportEdge;
-}
-
-// ─── §2.5 TypeRef ───────────────────────────────────────────────────────────
-
-/**
- * A reference to a named type, anchored at its declaration site.
- *
- * Design choice: raw name + declaration-site scope, resolved at lookup time.
- * Pre-resolution would invert the extraction/resolution wall. Deferred thunks
- * add no capability. Structured type systems are months of work per language.
- * This shape keeps V1 tractable while preserving correctness for aliases,
- * re-exports, and nested modules. Generics deferred to V2 via `typeArgs`.
- */
-export interface TypeRef {
-  /** The name as written in source (e.g., `'User'`, `'models.User'`, `'List'`). */
-  readonly rawName: string;
-  /** Anchor for resolving `rawName` — the scope where the annotation/inference was written. */
-  readonly declaredAtScope: ScopeId;
-  readonly source:
-    | 'annotation'
-    | 'parameter-annotation'
-    | 'return-annotation'
-    | 'self'
-    | 'assignment-inferred'
-    | 'constructor-inferred'
-    | 'receiver-propagated';
-  /** Reserved for V2+: generic type arguments (`List<User>` → `[TypeRef('User')]`). V1 ignores. */
-  readonly typeArgs?: readonly TypeRef[];
-}
-
-// ─── §2.2 Scope ─────────────────────────────────────────────────────────────
-
-/**
- * The canonical lexical-scope node. Forms the spine of the SemanticModel.
- *
- * ScopeId shape (RFC §2.2): `scope:{filePath}#{startLine}:{startCol}-{endLine}:{endCol}:{kind}`
- * — deterministic, stable across reparses of the same source, interned.
- */
-export interface Scope {
-  readonly id: ScopeId;
-  readonly parent: ScopeId | null;
-  readonly kind: ScopeKind;
-  readonly range: Range;
-  readonly filePath: string;
-
-  /** Names visible from this scope. Provenance preserved via `BindingRef.origin`. */
-  readonly bindings: ReadonlyMap<string, readonly BindingRef[]>;
-
-  /** Defs structurally owned by this scope (e.g., methods owned by a class body scope). */
-  readonly ownedDefs: readonly SymbolDefinition[];
-
-  /** Import edges attached to this scope. Mostly module/namespace scopes, but some
-   *  languages allow local imports (Python `def f(): from x import Y`, Rust
-   *  fn-local `use`, TS dynamic `import()`). */
-  readonly imports: readonly ImportEdge[];
-
-  /** Local type facts visible from this scope (parameter annotations, `self` binding, etc.). */
-  readonly typeBindings: ReadonlyMap<string, TypeRef>;
-}
-
-// ─── §2.6 Resolution + ResolutionEvidence ───────────────────────────────────
-
-/**
- * One piece of evidence for a `Resolution`. Multiple signals corroborate a
- * single match; their weights compose additively to produce `confidence`.
- *
- * Weights come from `EvidenceWeights` (see `./evidence-weights.ts`).
- */
-export interface ResolutionEvidence {
-  readonly kind:
-    | 'local'
-    | 'scope-chain'
-    | 'import'
-    | 'type-binding'
-    | 'owner-match'
-    | 'kind-match'
-    | 'arity-match'
-    | 'global-name'
-    | 'global-qualified'
-    | 'dynamic-import-unresolved';
-  /** Signal weight, sourced from `EvidenceWeights`. Additive; sum capped at 1.0. */
-  readonly weight: number;
-  /** Optional debug annotation (e.g., `'matched via self: User'`). */
-  readonly note?: string;
-}
-
-/**
- * A ranked resolution candidate returned by `ClassRegistry.lookup` /
- * `MethodRegistry.lookup` / `FieldRegistry.lookup`. Evidence composes
- * additively; callers read `[0]` for the one-shot answer or inspect the
- * evidence trace for debugging.
- */
-export interface Resolution {
-  readonly def: SymbolDefinition;
-  /** Σ of `evidence[].weight`, capped at 1.0. */
-  readonly confidence: number;
-  readonly evidence: readonly ResolutionEvidence[];
-  /** Optional debug trace: scopes walked to reach `def`. */
-  readonly path?: readonly ScopeId[];
-}
-
-// ─── §2.7 Reference + ReferenceIndex ────────────────────────────────────────
-
-/**
- * A post-resolution usage fact: some code at `atRange` inside `fromScope`
- * references `toDef` with the given confidence/evidence. Materialized by the
- * resolution phase; emitted as graph edges (`CALLS`/`READS`/`WRITES`/etc.)
- * during the emit phase.
- */
-export interface Reference {
-  /** Innermost lexical scope containing `atRange`. */
-  readonly fromScope: ScopeId;
-  readonly toDef: DefId;
-  /** Location of the reference in source. */
-  readonly atRange: Range;
-  readonly kind: 'call' | 'read' | 'write' | 'type-reference' | 'inherits' | 'import-use';
-  readonly confidence: number;
-  readonly evidence: readonly ResolutionEvidence[];
-}
-
-/**
- * Two-way index over `Reference` records, populated during the resolution
- * phase. Scopes stay immutable after finalize; references accumulate here.
- */
-export interface ReferenceIndex {
-  readonly bySourceScope: ReadonlyMap<ScopeId, readonly Reference[]>;
-  readonly byTargetDef: ReadonlyMap<DefId, readonly Reference[]>;
-}
-
-// ─── §4.1 LookupParams ──────────────────────────────────────────────────────
-
-/**
- * Opaque placeholder for the per-kind registry passed as the owner-scoped
- * contributor. Typed concretely in Ring 2 SHARED (#917); kept as `unknown`
- * here so Ring 1 can ship without pulling in the registry implementation.
- */
-export type RegistryContributor = unknown;
-
-/**
- * Parameters accepted by `Registry.lookup`. Three registries (Class/Method/
- * Field) run the same 7-step algorithm with different parameter tuples; see
- * RFC §4.4 for per-registry specializations.
- */
-export interface LookupParams {
-  readonly acceptedKinds: readonly NodeLabel[];
-  /** Class lookups: false. Method/Field lookups: true. */
-  readonly useReceiverTypeBinding: boolean;
-  readonly ownerScopedContributor: RegistryContributor | null;
-  /** Optional arity hint fed to `provider.arityCompatibility`. */
-  readonly arityHint?: number;
-  /** Explicit receiver name (e.g., `'user'` in `user.save()`). When present,
-   *  the receiver's type binding at the callsite scope is used; otherwise
-   *  the enclosing method's implicit `self`/`this` is consulted. See §4.1. */
-  readonly explicitReceiver?: { readonly name: string };
-}

gitnexus-web/e2e/multi-repo-scoping.spec.ts

@@ -61,22 +61,13 @@ test.beforeAll(async () => {
   }
 });
 
-// Auto-connect downloads the full graph from the backend; under parallel
-// workers in CI the same backend serves multiple downloads concurrently, so
-// reaching the "Ready" state can take noticeably longer than a single-worker
-// run. Match the 45s budget used by waitForGraphLoaded() in
-// server-connect.spec.ts which has been stable on the same backend.
-const READY_TIMEOUT_MS = 45_000;
-
 test.describe('Multi-Repo Scoping', () => {
   test('auto-connect via ?server= sets ?project= in URL', async ({ page }) => {
     // Navigate with ?server= param (the bookmarkable shortcut)
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
 
     // Wait for graph to load
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // URL should now contain ?project= with the repo name
     const url = new URL(page.url());
@@ -86,14 +77,8 @@ test.describe('Multi-Repo Scoping', () => {
   });
 
   test('?server= is preserved in URL for F5 recovery', async ({ page }) => {
-    // Two sequential auto-connects (initial + reload), each up to READY_TIMEOUT_MS,
-    // can exceed the default 60s test timeout under parallel workers.
-    test.slow();
-
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // URL should still have ?server=
     const url = new URL(page.url());
@@ -101,16 +86,12 @@ test.describe('Multi-Repo Scoping', () => {
 
     // F5 should reconnect (not show onboarding)
     await page.reload();
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
   });
 
   test('node count in status bar matches backend data', async ({ page }) => {
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // Fetch expected node count from backend
     const res = await fetch(`${BACKEND_URL}/api/repo?repo=${encodeURIComponent(firstRepoName)}`);

gitnexus-web/e2e/onboarding.spec.ts

@@ -26,10 +26,7 @@ async function enterExploringView(page: import('@playwright/test').Page) {
     // Landing screen may not appear (e.g. ?server auto-connect)
   }
 
-  // Match the 45s budget used by waitForGraphLoaded() in
-  // server-connect.spec.ts; under parallel CI workers, downloading the full
-  // graph can occasionally exceed 30s.
-  await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 45_000 });
+  await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 }
 
 // ── Flow 1: Onboarding (no server running) ─────────────────────────────────
@@ -247,10 +244,6 @@ test.describe('Flow 3: Analyze form', () => {
 test.describe('Flow 4: Repo dropdown in exploring view', () => {
   const SKIP_MSG = 'Requires running gitnexus server with indexed repos';
 
-  // enterExploringView() can take up to ~45s under parallel CI workers; combined
-  // with the dropdown interactions this can exceed the default 60s test budget.
-  test.slow();
-
   test.beforeAll(async () => {
     if (process.env.E2E) return;
     try {

gitnexus-web/e2e/repo-switching.spec.ts

@@ -84,20 +84,11 @@ test.describe('Hold-queue timeout error', () => {
 
 // ── 2. ?project= URL persistence ─────────────────────────────────────────────
 
-// Auto-connect downloads the full graph from the backend; under parallel
-// workers in CI the same backend serves multiple downloads concurrently, so
-// reaching the "Ready" state can take noticeably longer than a single-worker
-// run. Match the 45s budget used by waitForGraphLoaded() in
-// server-connect.spec.ts which has been stable on the same backend.
-const READY_TIMEOUT_MS = 45_000;
-
 test.describe('?project= URL persistence', () => {
   test('?project= is set in URL after connecting via ?server=', async ({ page }) => {
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
 
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     const url = new URL(page.url());
     const project = url.searchParams.get('project');
@@ -107,20 +98,12 @@ test.describe('?project= URL persistence', () => {
   });
 
   test('?project= is still present after F5 reload', async ({ page }) => {
-    // Two sequential auto-connects (initial + reload), each up to READY_TIMEOUT_MS,
-    // can exceed the default 60s test timeout under parallel workers.
-    test.slow();
-
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // After connect, URL has ?server=&project= — F5 re-uses both params
     await page.reload();
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     const url = new URL(page.url());
     expect(url.searchParams.get('project')).toBeTruthy();
@@ -139,9 +122,7 @@ test.describe('?project= auto-connect', () => {
       `/?server=${encodeURIComponent(BACKEND_URL)}&project=${encodeURIComponent(firstRepoName)}`,
     );
 
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // ?project= in URL should match what we passed in
     const url = new URL(page.url());
@@ -174,9 +155,7 @@ test.describe('Windows path normalization', () => {
 
     await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
 
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({
-      timeout: READY_TIMEOUT_MS,
-    });
+    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
 
     // URL ?project= must be the short basename, NOT the full Windows path
     const url = new URL(page.url());

gitnexus-web/package-lock.json

@@ -29,7 +29,7 @@
         "langchain": "^1.2.10",
         "lru-cache": "^11.2.4",
         "lucide-react": "^0.562.0",
-        "mermaid": "^11.14.0",
+        "mermaid": "^11.12.2",
         "mnemonist": "^0.39.0",
         "pandemonium": "^2.4.0",
         "react": "^18.3.1",
@@ -39,7 +39,7 @@
         "react-zoom-pan-pinch": "^3.7.0",
         "remark-gfm": "^4.0.1",
         "sigma": "^3.0.2",
-        "tailwindcss": "^4.2.2",
+        "tailwindcss": "^4.1.18",
         "uuid": "^13.0.0",
         "zod": "^3.25.76"
       },
@@ -57,12 +57,12 @@
         "@vercel/node": "^5.5.16",
         "@vitejs/plugin-react": "^5.1.0",
         "@vitest/coverage-v8": "^3.2.4",
-        "jsdom": "^29.0.2",
+        "jsdom": "^29.0.0",
         "tree-sitter-wasms": "^0.1.13",
         "typescript": "^5.4.5",
         "vite": "^5.2.0",
         "vitest": "^3.2.4",
-        "wait-on": "^9.0.5"
+        "wait-on": "^8.0.5"
       },
       "engines": {
         "node": ">=20.0.0"
@@ -129,49 +129,39 @@
       }
     },
     "node_modules/@asamuzakjp/css-color": {
-      "version": "5.1.11",
-      "resolved": "https://registry.npmjs.org/@asamuzakjp/css-color/-/css-color-5.1.11.tgz",
-      "integrity": "sha512-KVw6qIiCTUQhByfTd78h2yD1/00waTmm9uy/R7Ck/ctUyAPj+AEDLkQIdJW0T8+qGgj3j5bpNKK7Q3G+LedJWg==",
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/css-color/-/css-color-5.0.1.tgz",
+      "integrity": "sha512-2SZFvqMyvboVV1d15lMf7XiI3m7SDqXUuKaTymJYLN6dSGadqp+fVojqJlVoMlbZnlTmu3S0TLwLTJpvBMO1Aw==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@asamuzakjp/generational-cache": "^1.0.1",
-        "@csstools/css-calc": "^3.2.0",
-        "@csstools/css-color-parser": "^4.1.0",
+        "@csstools/css-calc": "^3.1.1",
+        "@csstools/css-color-parser": "^4.0.2",
         "@csstools/css-parser-algorithms": "^4.0.0",
-        "@csstools/css-tokenizer": "^4.0.0"
+        "@csstools/css-tokenizer": "^4.0.0",
+        "lru-cache": "^11.2.6"
       },
       "engines": {
         "node": "^20.19.0 || ^22.12.0 || >=24.0.0"
       }
     },
     "node_modules/@asamuzakjp/dom-selector": {
-      "version": "7.0.10",
-      "resolved": "https://registry.npmjs.org/@asamuzakjp/dom-selector/-/dom-selector-7.0.10.tgz",
-      "integrity": "sha512-KyOb19eytNSELkmdqzZZUXWCU25byIlOld5qVFg0RYdS0T3tt7jeDByxk9hIAC73frclD8GKrHttr0SUjKCCdQ==",
+      "version": "7.0.3",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/dom-selector/-/dom-selector-7.0.3.tgz",
+      "integrity": "sha512-Q6mU0Z6bfj6YvnX2k9n0JxiIwrCFN59x/nWmYQnAqP000ruX/yV+5bp/GRcF5T8ncvfwJQ7fgfP74DlpKExILA==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@asamuzakjp/generational-cache": "^1.0.1",
         "@asamuzakjp/nwsapi": "^2.3.9",
         "bidi-js": "^1.0.3",
         "css-tree": "^3.2.1",
-        "is-potential-custom-element-name": "^1.0.1"
+        "is-potential-custom-element-name": "^1.0.1",
+        "lru-cache": "^11.2.7"
       },
       "engines": {
         "node": "^20.19.0 || ^22.12.0 || >=24.0.0"
       }
     },
-    "node_modules/@asamuzakjp/generational-cache": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/@asamuzakjp/generational-cache/-/generational-cache-1.0.1.tgz",
-      "integrity": "sha512-wajfB8KqzMCN2KGNFdLkReeHncd0AslUSrvHVvvYWuU8ghncRJoA50kT3zP9MVL0+9g4/67H+cdvBskj9THPzg==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": "^20.19.0 || ^22.12.0 || >=24.0.0"
-      }
-    },
     "node_modules/@asamuzakjp/nwsapi": {
       "version": "2.3.9",
       "resolved": "https://registry.npmjs.org/@asamuzakjp/nwsapi/-/nwsapi-2.3.9.tgz",
@@ -543,40 +533,54 @@
       "license": "MIT"
     },
     "node_modules/@chevrotain/cst-dts-gen": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/cst-dts-gen/-/cst-dts-gen-12.0.0.tgz",
-      "integrity": "sha512-fSL4KXjTl7cDgf0B5Rip9Q05BOrYvkJV/RrBTE/bKDN096E4hN/ySpcBK5B24T76dlQ2i32Zc3PAE27jFnFrKg==",
+      "version": "11.0.3",
+      "resolved": "https://registry.npmjs.org/@chevrotain/cst-dts-gen/-/cst-dts-gen-11.0.3.tgz",
+      "integrity": "sha512-BvIKpRLeS/8UbfxXxgC33xOumsacaeCKAjAeLyOn7Pcp95HiRbrpl14S+9vaZLolnbssPIUuiUd8IvgkRyt6NQ==",
       "license": "Apache-2.0",
       "dependencies": {
-        "@chevrotain/gast": "12.0.0",
-        "@chevrotain/types": "12.0.0"
+        "@chevrotain/gast": "11.0.3",
+        "@chevrotain/types": "11.0.3",
+        "lodash-es": "4.17.21"
       }
     },
+    "node_modules/@chevrotain/cst-dts-gen/node_modules/lodash-es": {
+      "version": "4.17.21",
+      "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.17.21.tgz",
+      "integrity": "sha512-mKnC+QJ9pWVzv+C4/U3rRsHapFfHvQFoFB92e52xeyGMcX6/OlIl78je1u8vePzYZSkkogMPJ2yjxxsb89cxyw==",
+      "license": "MIT"
+    },
     "node_modules/@chevrotain/gast": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/gast/-/gast-12.0.0.tgz",
-      "integrity": "sha512-1ne/m3XsIT8aEdrvT33so0GUC+wkctpUPK6zU9IlOyJLUbR0rg4G7ZiApiJbggpgPir9ERy3FRjT6T7lpgetnQ==",
+      "version": "11.0.3",
+      "resolved": "https://registry.npmjs.org/@chevrotain/gast/-/gast-11.0.3.tgz",
+      "integrity": "sha512-+qNfcoNk70PyS/uxmj3li5NiECO+2YKZZQMbmjTqRI3Qchu8Hig/Q9vgkHpI3alNjr7M+a2St5pw5w5F6NL5/Q==",
       "license": "Apache-2.0",
       "dependencies": {
-        "@chevrotain/types": "12.0.0"
+        "@chevrotain/types": "11.0.3",
+        "lodash-es": "4.17.21"
       }
     },
+    "node_modules/@chevrotain/gast/node_modules/lodash-es": {
+      "version": "4.17.21",
+      "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.17.21.tgz",
+      "integrity": "sha512-mKnC+QJ9pWVzv+C4/U3rRsHapFfHvQFoFB92e52xeyGMcX6/OlIl78je1u8vePzYZSkkogMPJ2yjxxsb89cxyw==",
+      "license": "MIT"
+    },
     "node_modules/@chevrotain/regexp-to-ast": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/regexp-to-ast/-/regexp-to-ast-12.0.0.tgz",
-      "integrity": "sha512-p+EW9MaJwgaHguhoqwOtx/FwuGr+DnNn857sXWOi/mClXIkPGl3rn7hGNWvo31HA3vyeQxjqe+H36yZJwYU8cA==",
+      "version": "11.0.3",
+      "resolved": "https://registry.npmjs.org/@chevrotain/regexp-to-ast/-/regexp-to-ast-11.0.3.tgz",
+      "integrity": "sha512-1fMHaBZxLFvWI067AVbGJav1eRY7N8DDvYCTwGBiE/ytKBgP8azTdgyrKyWZ9Mfh09eHWb5PgTSO8wi7U824RA==",
       "license": "Apache-2.0"
     },
     "node_modules/@chevrotain/types": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/types/-/types-12.0.0.tgz",
-      "integrity": "sha512-S+04vjFQKeuYw0/eW3U52LkAHQsB1ASxsPGsLPUyQgrZ2iNNibQrsidruDzjEX2JYfespXMG0eZmXlhA6z7nWA==",
+      "version": "11.0.3",
+      "resolved": "https://registry.npmjs.org/@chevrotain/types/-/types-11.0.3.tgz",
+      "integrity": "sha512-gsiM3G8b58kZC2HaWR50gu6Y1440cHiJ+i3JUvcp/35JchYejb2+5MVeJK0iKThYpAa/P2PYFV4hoi44HD+aHQ==",
       "license": "Apache-2.0"
     },
     "node_modules/@chevrotain/utils": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/utils/-/utils-12.0.0.tgz",
-      "integrity": "sha512-lB59uJoaGIfOOL9knQqQRfhl9g7x8/wqFkp13zTdkRu1huG9kg6IJs1O8hqj9rs6h7orGxHJUKb+mX3rPbWGhA==",
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+      "resolved": "https://registry.npmjs.org/dagre-d3-es/-/dagre-d3-es-7.0.13.tgz",
+      "integrity": "sha512-efEhnxpSuwpYOKRm/L5KbqoZmNNukHa/Flty4Wp62JRvgH2ojwVgPgdYyr4twpieZnyRDdIH7PY2mopX26+j2Q==",
       "license": "MIT",
       "dependencies": {
         "d3": "^7.9.0",
@@ -5827,9 +6064,9 @@
       }
     },
     "node_modules/joi": {
-      "version": "18.1.2",
-      "resolved": "https://registry.npmjs.org/joi/-/joi-18.1.2.tgz",
-      "integrity": "sha512-rF5MAmps5esSlhCA+N1b6IYHDw9j/btzGaqfgie522jS02Ju/HXBxamlXVlKEHAxoMKQL77HWI8jlqWsFuekZA==",
+      "version": "18.0.2",
+      "resolved": "https://registry.npmjs.org/joi/-/joi-18.0.2.tgz",
+      "integrity": "sha512-RuCOQMIt78LWnktPoeBL0GErkNaJPTBGcYuyaBvUOQSpcpcLfWrHPPihYdOGbV5pam9VTWbeoF7TsGiHugcjGA==",
       "dev": true,
       "license": "BSD-3-Clause",
       "dependencies": {
@@ -5839,7 +6076,7 @@
         "@hapi/pinpoint": "^2.0.1",
         "@hapi/tlds": "^1.1.1",
         "@hapi/topo": "^6.0.2",
-        "@standard-schema/spec": "^1.1.0"
+        "@standard-schema/spec": "^1.0.0"
       },
       "engines": {
         "node": ">= 20"
@@ -5861,14 +6098,14 @@
       "license": "MIT"
     },
     "node_modules/jsdom": {
-      "version": "29.0.2",
-      "resolved": "https://registry.npmjs.org/jsdom/-/jsdom-29.0.2.tgz",
-      "integrity": "sha512-9VnGEBosc/ZpwyOsJBCQ/3I5p7Q5ngOY14a9bf5btenAORmZfDse1ZEheMiWcJ3h81+Fv7HmJFdS0szo/waF2w==",
+      "version": "29.0.0",
+      "resolved": "https://registry.npmjs.org/jsdom/-/jsdom-29.0.0.tgz",
+      "integrity": "sha512-9FshNB6OepopZ08unmmGpsF7/qCjxGPbo3NbgfJAnPeHXnsODE9WWffXZtRFRFe0ntzaAOcSKNJFz8wiyvF1jQ==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@asamuzakjp/css-color": "^5.1.5",
-        "@asamuzakjp/dom-selector": "^7.0.6",
+        "@asamuzakjp/css-color": "^5.0.1",
+        "@asamuzakjp/dom-selector": "^7.0.2",
         "@bramus/specificity": "^2.4.2",
         "@csstools/css-syntax-patches-for-csstree": "^1.1.1",
         "@exodus/bytes": "^1.15.0",
@@ -5882,7 +6119,7 @@
         "saxes": "^6.0.0",
         "symbol-tree": "^3.2.4",
         "tough-cookie": "^6.0.1",
-        "undici": "^7.24.5",
+        "undici": "^7.24.3",
         "w3c-xmlserializer": "^5.0.0",
         "webidl-conversions": "^8.0.1",
         "whatwg-mimetype": "^5.0.0",
@@ -5915,9 +6152,9 @@
       }
     },
     "node_modules/jsdom/node_modules/undici": {
-      "version": "7.25.0",
-      "resolved": "https://registry.npmjs.org/undici/-/undici-7.25.0.tgz",
-      "integrity": "sha512-xXnp4kTyor2Zq+J1FfPI6Eq3ew5h6Vl0F/8d9XU5zZQf1tX9s2Su1/3PiMmUANFULpmksxkClamIZcaUqryHsQ==",
+      "version": "7.24.3",
+      "resolved": "https://registry.npmjs.org/undici/-/undici-7.24.3.tgz",
+      "integrity": "sha512-eJdUmK/Wrx2d+mnWWmwwLRyA7OQCkLap60sk3dOK4ViZR7DKwwptwuIvFBg2HaiP9ESaEdhtpSymQPvytpmkCA==",
       "dev": true,
       "license": "MIT",
       "engines": {
@@ -6058,21 +6295,19 @@
       }
     },
     "node_modules/langium": {
-      "version": "4.2.2",
-      "resolved": "https://registry.npmjs.org/langium/-/langium-4.2.2.tgz",
-      "integrity": "sha512-JUshTRAfHI4/MF9dH2WupvjSXyn8JBuUEWazB8ZVJUtXutT0doDlAv1XKbZ1Pb5sMexa8FF4CFBc0iiul7gbUQ==",
+      "version": "3.3.1",
+      "resolved": "https://registry.npmjs.org/langium/-/langium-3.3.1.tgz",
+      "integrity": "sha512-QJv/h939gDpvT+9SiLVlY7tZC3xB2qK57v0J04Sh9wpMb6MP1q8gB21L3WIo8T5P1MSMg3Ep14L7KkDCFG3y4w==",
       "license": "MIT",
       "dependencies": {
-        "@chevrotain/regexp-to-ast": "~12.0.0",
-        "chevrotain": "~12.0.0",
-        "chevrotain-allstar": "~0.4.1",
+        "chevrotain": "~11.0.3",
+        "chevrotain-allstar": "~0.3.0",
         "vscode-languageserver": "~9.0.1",
         "vscode-languageserver-textdocument": "~1.0.11",
-        "vscode-uri": "~3.1.0"
+        "vscode-uri": "~3.0.8"
       },
       "engines": {
-        "node": ">=20.10.0",
-        "npm": ">=10.2.3"
+        "node": ">=16.0.0"
       }
     },
     "node_modules/langsmith": {
@@ -6378,16 +6613,16 @@
       }
     },
     "node_modules/lodash": {
-      "version": "4.18.1",
-      "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.18.1.tgz",
-      "integrity": "sha512-dMInicTPVE8d1e5otfwmmjlxkZoUpiVLwyeTdUsi/Caj/gfzzblBcCE5sRHV/AsjuCmxWrte2TNGSYuCeCq+0Q==",
+      "version": "4.17.23",
+      "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.23.tgz",
+      "integrity": "sha512-LgVTMpQtIopCi79SJeDiP0TfWi5CNEc/L/aRdTh3yIvmZXTnheWpKjSZhnvMl8iXbC1tFg9gdHHDMLoV7CnG+w==",
       "dev": true,
       "license": "MIT"
     },
     "node_modules/lodash-es": {
-      "version": "4.18.1",
-      "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.18.1.tgz",
-      "integrity": "sha512-J8xewKD/Gk22OZbhpOVSwcs60zhd95ESDwezOFuA3/099925PdHJ7OFHNTGtajL3AlZkykD32HykiMo+BIBI8A==",
+      "version": "4.17.22",
+      "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.17.22.tgz",
+      "integrity": "sha512-XEawp1t0gxSi9x01glktRZ5HDy0HXqrM0x5pXQM98EaI0NxO6jVM7omDOxsuEo5UIASAnm2bRp1Jt/e0a2XU8Q==",
       "license": "MIT"
     },
     "node_modules/longest-streak": {
@@ -6837,28 +7072,27 @@
       }
     },
     "node_modules/mermaid": {
-      "version": "11.14.0",
-      "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-11.14.0.tgz",
-      "integrity": "sha512-GSGloRsBs+JINmmhl0JDwjpuezCsHB4WGI4NASHxL3fHo3o/BRXTxhDLKnln8/Q0lRFRyDdEjmk1/d5Sn1Xz8g==",
+      "version": "11.12.2",
+      "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-11.12.2.tgz",
+      "integrity": "sha512-n34QPDPEKmaeCG4WDMGy0OT6PSyxKCfy2pJgShP+Qow2KLrvWjclwbc3yXfSIf4BanqWEhQEpngWwNp/XhZt6w==",
       "license": "MIT",
       "dependencies": {
         "@braintree/sanitize-url": "^7.1.1",
-        "@iconify/utils": "^3.0.2",
-        "@mermaid-js/parser": "^1.1.0",
+        "@iconify/utils": "^3.0.1",
+        "@mermaid-js/parser": "^0.6.3",
         "@types/d3": "^7.4.3",
-        "@upsetjs/venn.js": "^2.0.0",
-        "cytoscape": "^3.33.1",
+        "cytoscape": "^3.29.3",
         "cytoscape-cose-bilkent": "^4.1.0",
         "cytoscape-fcose": "^2.2.0",
         "d3": "^7.9.0",
         "d3-sankey": "^0.12.3",
-        "dagre-d3-es": "7.0.14",
-        "dayjs": "^1.11.19",
-        "dompurify": "^3.3.1",
-        "katex": "^0.16.25",
+        "dagre-d3-es": "7.0.13",
+        "dayjs": "^1.11.18",
+        "dompurify": "^3.2.5",
+        "katex": "^0.16.22",
         "khroma": "^2.1.0",
-        "lodash-es": "^4.17.23",
-        "marked": "^16.3.0",
+        "lodash-es": "^4.17.21",
+        "marked": "^16.2.1",
         "roughjs": "^4.6.6",
         "stylis": "^4.3.6",
         "ts-dedent": "^2.2.0",
@@ -8083,13 +8317,10 @@
       }
     },
     "node_modules/proxy-from-env": {
-      "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-2.1.0.tgz",
-      "integrity": "sha512-cJ+oHTW1VAEa8cJslgmUZrc+sjRKgAKl3Zyse6+PV38hZe/V6Z14TbCuXcan9F9ghlz4QrFr2c92TNF82UkYHA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">=10"
-      }
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-1.1.0.tgz",
+      "integrity": "sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg==",
+      "license": "MIT"
     },
     "node_modules/punycode": {
       "version": "2.3.1",
@@ -8775,9 +9006,9 @@
       "license": "MIT"
     },
     "node_modules/tailwindcss": {
-      "version": "4.2.2",
-      "resolved": "https://registry.npmjs.org/tailwindcss/-/tailwindcss-4.2.2.tgz",
-      "integrity": "sha512-KWBIxs1Xb6NoLdMVqhbhgwZf2PGBpPEiwOqgI4pFIYbNTfBXiKYyWoTsXgBQ9WFg/OlhnvHaY+AEpW7wSmFo2Q==",
+      "version": "4.1.18",
+      "resolved": "https://registry.npmjs.org/tailwindcss/-/tailwindcss-4.1.18.tgz",
+      "integrity": "sha512-4+Z+0yiYyEtUVCScyfHCxOYP06L5Ne+JiHhY2IjR2KWMIWhJOYZKLSGZaP5HkZ8+bY0cxfzwDE5uOmzFXyIwxw==",
       "license": "MIT"
     },
     "node_modules/tapable": {
@@ -10039,9 +10270,9 @@
       "license": "MIT"
     },
     "node_modules/vscode-uri": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.1.0.tgz",
-      "integrity": "sha512-/BpdSx+yCQGnCvecbyXdxHDkuk55/G3xwnC0GqY4gmQ3j+A+g8kzzgB4Nk/SINjqn6+waqw3EgbVF2QKExkRxQ==",
+      "version": "3.0.8",
+      "resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.0.8.tgz",
+      "integrity": "sha512-AyFQ0EVmsOZOlAnxoFOGOq1SQDWAB7C6aqMGS23svWAllfOaxbuFvcT8D1i8z3Gyn8fraVeZNNmN6e9bxxXkKw==",
       "license": "MIT"
     },
     "node_modules/w3c-xmlserializer": {
@@ -10058,15 +10289,15 @@
       }
     },
     "node_modules/wait-on": {
-      "version": "9.0.5",
-      "resolved": "https://registry.npmjs.org/wait-on/-/wait-on-9.0.5.tgz",
-      "integrity": "sha512-qgnbHDfDTRIp73ANEJNRW/7kn8CrDUcvZz18xotJQku/P4saTGkbIzvnMZebPmVvVNUiRq1qWAPyqCH+W4H8KA==",
+      "version": "8.0.5",
+      "resolved": "https://registry.npmjs.org/wait-on/-/wait-on-8.0.5.tgz",
+      "integrity": "sha512-J3WlS0txVHkhLRb2FsmRg3dkMTCV1+M6Xra3Ho7HzZDHpE7DCOnoSoCJsZotrmW3uRMhvIJGSKUKrh/MeF4iag==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "axios": "^1.15.0",
-        "joi": "^18.1.2",
-        "lodash": "^4.18.1",
+        "axios": "^1.12.1",
+        "joi": "^18.0.1",
+        "lodash": "^4.17.21",
         "minimist": "^1.2.8",
         "rxjs": "^7.8.2"
       },
@@ -10074,7 +10305,7 @@
         "wait-on": "bin/wait-on"
       },
       "engines": {
-        "node": ">=20.0.0"
+        "node": ">=12.0.0"
       }
     },
     "node_modules/webidl-conversions": {

gitnexus-web/package.json

@@ -39,7 +39,7 @@
     "langchain": "^1.2.10",
     "lru-cache": "^11.2.4",
     "lucide-react": "^0.562.0",
-    "mermaid": "^11.14.0",
+    "mermaid": "^11.12.2",
     "mnemonist": "^0.39.0",
     "pandemonium": "^2.4.0",
     "react": "^18.3.1",
@@ -49,7 +49,7 @@
     "react-zoom-pan-pinch": "^3.7.0",
     "remark-gfm": "^4.0.1",
     "sigma": "^3.0.2",
-    "tailwindcss": "^4.2.2",
+    "tailwindcss": "^4.1.18",
     "uuid": "^13.0.0",
     "zod": "^3.25.76"
   },
@@ -67,11 +67,11 @@
     "@vercel/node": "^5.5.16",
     "@vitejs/plugin-react": "^5.1.0",
     "@vitest/coverage-v8": "^3.2.4",
-    "jsdom": "^29.0.2",
+    "jsdom": "^29.0.0",
     "tree-sitter-wasms": "^0.1.13",
     "typescript": "^5.4.5",
     "vite": "^5.2.0",
     "vitest": "^3.2.4",
-    "wait-on": "^9.0.5"
+    "wait-on": "^8.0.5"
   }
 }

gitnexus-web/vite.config.ts

@@ -16,7 +16,6 @@ export default defineConfig({
     alias: {
       '@': path.resolve(__dirname, './src'),
       '@shared': path.resolve(__dirname, '../shared'),
-      'gitnexus-shared': path.resolve(__dirname, '../gitnexus-shared/src/index.ts'),
       // Fix for Rollup failing to resolve this deep import from @langchain/anthropic
       '@anthropic-ai/sdk/lib/transform-json-schema': path.resolve(
         __dirname,

gitnexus/.npmignore

@@ -9,10 +9,6 @@ tsconfig.json
 .gitignore
 node_modules/
 
-# Vendor build artifacts (created during install, not shipped)
-vendor/**/node_modules
-vendor/**/build
-
 # Package lock (consumers use their own)
 package-lock.json
 

gitnexus/CHANGELOG.md

@@ -2,46 +2,6 @@
 
 All notable changes to GitNexus will be documented in this file.
 
-## [1.6.2] - 2026-04-18
-
-### Added
-
-- **Docker support** — containerized ingestion and MCP serving for reproducible runs on CI and container platforms (#848)
-- **Language-agnostic heritage extractor** — config+factory pattern for class-heritage extraction (EXTENDS / IMPLEMENTS), completing the extractor refactor alongside method/field/call/variable (#890)
-- **Language-agnostic call extractor** — config+factory pattern that collapses ~225 lines of inline parse-worker logic into declarative per-language configs (#877)
-- **Language-agnostic variable extractor** — structured metadata for `Const` / `Static` / `Variable` nodes via config+factory pattern (#878)
-- **AST-aware embedding chunking** — offset-based splitting preserves symbol boundaries, improving semantic search precision on large files (#889)
-- **HTTP consumer detection for jQuery and axios object-form** — `$.ajax` / `$.get` / `$.post` and `axios({ url, method })` now recognized as HTTP call sites (#887)
-
-### Fixed
-
-- **Python external dotted imports** — avoid spurious same-file matches when an import path like `foo.bar.baz` refers to a third-party module (#899)
-- **Worker warnings no longer terminate ingestion** — non-fatal parser warnings keep the pipeline running instead of aborting the run (#900, #261)
-- **Global-install upgrade `ENOTEMPTY`** — devendored `tree-sitter-proto` install lifecycle + preinstall cleanup so `npm i -g gitnexus@latest` succeeds on top of an older install (#843, #846)
-- **`env.cacheDir`** now defaults to a user-writable location, unblocking ingestion on systems where the install directory is read-only (#845)
-- **Content-hash staleness detection for embeddings** — zero-node rebuilds no longer skip vector-index creation, fixing semantic search after selective re-analysis (#831)
-- **`tree-sitter-c-sharp` version pin** — locked to 0.23.1 to avoid a breaking change in a transitive prerelease (#834)
-- **`release-drafter` v7 CI** — replaced the removed `disable-releaser` flag with `dry-run` so release-note drafts still work
-- **`npm arborist` crash from `tree-sitter-dart`** — switched the dependency URL format so `npm install` no longer crashes on clean installs
-- **Service-group `ManifestExtractor`** — `config.links` now wires the manifest extractor properly, restoring cross-link discovery that had silently dropped to zero
-
-### Changed
-
-- **SemanticModel wired as a first-class resolution input (SM-20)** — `call-processor`, `resolution-context`, `type-env`, and `heritage-map` now consult `table.model.*` directly; 37 internal call sites migrated off the SymbolTable wrapper (#885)
-- **Per-strategy `ImportSemantics` hooks** — `named` / `wildcard-transitive` / `wildcard-leaf` / `namespace` strategies split into composable hooks, replacing the monolithic conditional (Strategies 1–4 of #886)
-- **Class extraction configs moved to `configs/` subdirectory** — per-language class configs now co-locate with the other extractor configs, completing the extractor layer's directory convention (#879)
-- **CLI AI-context trimmed** — duplicated CLAUDE.md block removed from the shipped context, reducing token usage in LLM-consuming workflows (#904)
-- **LLM context files optimized** — AI-consumed documentation tuned for accuracy and token efficiency (#857)
-- **Workflow concurrency standardized** — all CI workflows adopt the consistent concurrency key pattern documented in CONTRIBUTING.md; release-note labeling automated (#837)
-- **E2E status-ready timeout raised** — 45s accommodates parallel-worker startup variance on CI (#908)
-
-### Chore / Dependencies
-
-- **tree-sitter 0.25 upgrade readiness** — daily Dependabot monitor for the upcoming major-version bump (#847)
-- Dependency bumps: `glob` 11.1.0 → 13.0.6 (#867), `commander` 12.1.0 → 14.0.3 (#868), `@huggingface/transformers` (#869), `@modelcontextprotocol/sdk` (#866), `lru-cache` 11.2.7 → 11.3.5 (#870), `mnemonist` 0.39.8 → 0.40.3 (#871), `@ladybugdb/core` (#873)
-- gitnexus-web dependency bumps: `mermaid` 11.12.2 → 11.14.0 (#860), `tailwindcss` (#861), `jsdom` 29.0.0 → 29.0.2 (#863), `wait-on` 8.0.5 → 9.0.5 (#859), `@vitest/coverage-v8` (#864)
-- GitHub Actions bumps: `actions/checkout` 4.3.1 → 6.0.2 (#842), `actions/upload-artifact` 4.6.2 → 7.0.1 (#838), `actions/setup-node` 4.4.0 → 6.3.0 (#841), `actions/cache` 5.0.4 → 5.0.5 (#840), `actions/github-script` 7.0.1 → 9.0.0 (#850), `dorny/paths-filter` 3.0.2 → 4.0.1 (#839), `amannn/action-semantic-pull-request` 6.1.1 (#853), `release-drafter/release-drafter` 6.0.0 → 7.2.0 (#852), `marocchino/sticky-pull-request-comment` 3.0.4 (#851), `softprops/action-gh-release` 2.5.0 → 3.0.0 (#849)
-
 ## [1.6.1] - 2026-04-13
 
 ### Added

gitnexus/Dockerfile.test

@@ -1,6 +1,6 @@
 FROM node:20-bookworm
 WORKDIR /app
-RUN apt-get -o Acquire::Check-Valid-Until=false -o Acquire::Check-Date=false update && apt-get install -y python3 make g++ && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y python3 make g++ && rm -rf /var/lib/apt/lists/*
 COPY . .
 RUN npm ci --ignore-scripts \
     && node scripts/patch-tree-sitter-swift.cjs \

gitnexus/README.md

@@ -234,29 +234,6 @@ Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setu
 - Node.js >= 18
 - Git repository (uses git for commit tracking)
 
-## Release candidates
-
-Stable releases publish to the default `latest` dist-tag. When a pull request
-with non-documentation changes merges into `main`, an automated workflow also
-publishes a prerelease build under the `rc` dist-tag, so early adopters can
-try in-flight fixes without waiting for the next stable cut. (Docs-only
-merges are skipped.)
-
-```bash
-# Try the latest release candidate (pre-stable — may change at any time)
-npm install -g gitnexus@rc
-# — or —
-npx gitnexus@rc analyze
-```
-
-Release-candidate versions follow the standard semver prerelease format
-`X.Y.Z-rc.N`, where `X.Y.Z` is the next stable target (bumped from the
-current `latest` by patch by default; `minor` or `major` when kicking off a
-bigger cycle) and `N` increments per published rc. Example sequence:
-`1.6.2-rc.1`, `1.6.2-rc.2`, …, then once `1.6.2` ships stable,
-`1.6.3-rc.1`. See the [Releases page](https://github.com/abhigyanpatwari/GitNexus/releases)
-for the full list; stable `latest` is unaffected.
-
 ## Troubleshooting
 
 ### `Cannot destructure property 'package' of 'node.target' as it is null`

gitnexus/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.3-rc.18",
+  "version": "1.6.1",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",
@@ -46,32 +46,32 @@
     "test:integration": "vitest run test/integration",
     "test:watch": "vitest",
     "test:coverage": "vitest run --coverage",
-    "postinstall": "node scripts/patch-tree-sitter-swift.cjs && node scripts/build-tree-sitter-proto.cjs",
+    "postinstall": "node scripts/patch-tree-sitter-swift.cjs",
     "prepare": "node scripts/build.js",
     "prepack": "node scripts/build.js"
   },
   "dependencies": {
-    "@huggingface/transformers": "^4.1.0",
+    "@huggingface/transformers": "^3.0.0",
     "@ladybugdb/core": "^0.15.2",
     "@modelcontextprotocol/sdk": "^1.0.0",
     "@scarf/scarf": "^1.4.0",
     "cli-progress": "^3.12.0",
-    "commander": "^14.0.3",
+    "commander": "^12.0.0",
     "cors": "^2.8.5",
     "express": "^4.19.2",
-    "glob": "^13.0.6",
+    "glob": "^11.0.0",
     "graphology": "^0.25.4",
     "graphology-indices": "^0.17.0",
     "graphology-utils": "^2.3.0",
     "ignore": "^7.0.5",
     "js-yaml": "^4.1.1",
     "lru-cache": "^11.0.0",
-    "mnemonist": "^0.40.3",
+    "mnemonist": "^0.39.0",
     "onnxruntime-node": "^1.24.0",
     "pandemonium": "^2.4.0",
     "tree-sitter": "^0.21.1",
     "tree-sitter-c": "0.23.2",
-    "tree-sitter-c-sharp": "0.23.1",
+    "tree-sitter-c-sharp": "^0.23.1",
     "tree-sitter-cpp": "^0.23.4",
     "tree-sitter-go": "^0.23.0",
     "tree-sitter-java": "^0.23.5",
@@ -84,8 +84,6 @@
     "uuid": "^13.0.0"
   },
   "optionalDependencies": {
-    "node-addon-api": "^8.0.0",
-    "node-gyp-build": "^4.8.0",
     "tree-sitter-dart": "git+https://github.com/UserNobody14/tree-sitter-dart.git#80e23c07b64494f7e21090bb3450223ef0b192f4",
     "tree-sitter-kotlin": "^0.3.8",
     "tree-sitter-proto": "file:./vendor/tree-sitter-proto",

gitnexus/scripts/build-tree-sitter-proto.cjs

@@ -1,82 +0,0 @@
-#!/usr/bin/env node
-/**
- * Build tree-sitter-proto native binding.
- *
- * Why this script exists:
- *   tree-sitter-proto is vendored under gitnexus/vendor/tree-sitter-proto/
- *   and declared as a `file:` optionalDependency. Previously, the vendored
- *   package had its own `dependencies` and `install` script, which caused
- *   npm to create `vendor/tree-sitter-proto/node_modules/` and
- *   `vendor/tree-sitter-proto/build/` during install. Those directories
- *   blocked `rmdir` on global-install upgrade, producing:
- *
- *     ENOTEMPTY: directory not empty, rmdir
- *       '.../gitnexus/vendor/tree-sitter-proto/node_modules/node-addon-api'
- *
- *   (See https://github.com/abhigyanpatwari/GitNexus/issues/836.)
- *
- *   We stripped `dependencies` and the `install` script from the vendored
- *   package.json, hoisted `node-addon-api` and `node-gyp-build` into
- *   gitnexus's own optionalDependencies, and moved native compilation here.
- *
- * What this does:
- *   Runs `npx node-gyp rebuild` inside `node_modules/tree-sitter-proto/`
- *   (which npm creates as a copy of vendor/tree-sitter-proto/ when
- *   resolving the file: dep). Build output lands in
- *   `node_modules/tree-sitter-proto/build/Release/tree_sitter_proto_binding.node`
- *   — under npm-managed territory, safe on upgrade.
- *
- *   Mirrors scripts/patch-tree-sitter-swift.cjs. Best-effort: if any
- *   precondition fails (optional dep absent, no toolchain, --ignore-scripts),
- *   warn and exit 0 so gitnexus install still succeeds.
- */
-const fs = require('fs');
-const path = require('path');
-const { execSync } = require('child_process');
-
-const protoDir = path.join(__dirname, '..', 'node_modules', 'tree-sitter-proto');
-const bindingGyp = path.join(protoDir, 'binding.gyp');
-const bindingNode = path.join(protoDir, 'build', 'Release', 'tree_sitter_proto_binding.node');
-
-try {
-  if (!fs.existsSync(bindingGyp)) {
-    // tree-sitter-proto is an optionalDependency; absent when install
-    // skipped optional deps or the file: dep was not resolved.
-    process.exit(0);
-  }
-
-  // Skip if the native binding already exists (idempotent re-run).
-  if (fs.existsSync(bindingNode)) {
-    process.exit(0);
-  }
-
-  // Pre-flight: the hoisted build deps must be resolvable.
-  try {
-    require.resolve('node-addon-api');
-    require.resolve('node-gyp-build');
-  } catch (resolveErr) {
-    console.warn(
-      '[tree-sitter-proto] Skipping build: hoisted build deps not resolvable (%s).',
-      resolveErr.message,
-    );
-    console.warn(
-      '[tree-sitter-proto] Proto parsing will be unavailable. Install without --no-optional and with scripts enabled to build.',
-    );
-    process.exit(0);
-  }
-
-  console.log('[tree-sitter-proto] Building native binding...');
-  execSync('npx node-gyp rebuild', {
-    cwd: protoDir,
-    stdio: 'pipe',
-    timeout: 180000,
-  });
-  console.log('[tree-sitter-proto] Native binding built successfully');
-} catch (err) {
-  console.warn('[tree-sitter-proto] Could not build native binding:', err.message);
-  console.warn(
-    '[tree-sitter-proto] Proto (.proto) parsing will be unavailable. Non-proto gitnexus functionality is unaffected.',
-  );
-  // Exit 0: optionalDependency failures must not fail the gitnexus install.
-  process.exit(0);
-}

gitnexus/shadow-parity-dashboard/index.html

@@ -1,291 +0,0 @@
-<!doctype html>
-<html lang="en">
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width,initial-scale=1" />
-    <title>GitNexus — Shadow Parity Dashboard</title>
-    <!--
-      Static dashboard for the RFC #909 shadow-mode parity report.
-
-      Reads `latest.json` from this directory and renders a per-language
-      parity table. Zero build step, zero runtime dependencies — a
-      single file that any browser or file:// context can open.
-
-      Usage:
-          # from repo root, after a shadow-mode run
-          cp .gitnexus/shadow-parity/latest.json gitnexus/shadow-parity-dashboard/
-          open gitnexus/shadow-parity-dashboard/index.html
-
-      CI artifact wiring (follow-up): the CI job publishes a snapshot
-      of this directory + latest.json as a downloadable bundle per run.
-    -->
-    <style>
-      :root {
-        color-scheme: light dark;
-        --fg: #1f2937;
-        --fg-muted: #6b7280;
-        --bg: #ffffff;
-        --bg-muted: #f9fafb;
-        --border: #e5e7eb;
-        --good: #16a34a;
-        --warn: #d97706;
-        --bad: #dc2626;
-        --primary-tag-legacy: #7c3aed;
-        --primary-tag-registry: #0ea5e9;
-      }
-      @media (prefers-color-scheme: dark) {
-        :root {
-          --fg: #e5e7eb;
-          --fg-muted: #9ca3af;
-          --bg: #111827;
-          --bg-muted: #1f2937;
-          --border: #374151;
-        }
-      }
-      html,
-      body {
-        margin: 0;
-        padding: 0;
-        background: var(--bg);
-        color: var(--fg);
-        font:
-          14px/1.45 system-ui,
-          -apple-system,
-          sans-serif;
-      }
-      main {
-        max-width: 1200px;
-        margin: 0 auto;
-        padding: 24px 16px;
-      }
-      h1 {
-        font-size: 20px;
-        margin: 0 0 4px;
-      }
-      .meta {
-        color: var(--fg-muted);
-        font-size: 12px;
-        margin-bottom: 20px;
-      }
-      .cards {
-        display: grid;
-        grid-template-columns: repeat(auto-fit, minmax(180px, 1fr));
-        gap: 10px;
-        margin-bottom: 20px;
-      }
-      .card {
-        border: 1px solid var(--border);
-        border-radius: 6px;
-        padding: 10px 12px;
-        background: var(--bg-muted);
-      }
-      .card .k {
-        color: var(--fg-muted);
-        font-size: 11px;
-        text-transform: uppercase;
-        letter-spacing: 0.04em;
-      }
-      .card .v {
-        font-size: 20px;
-        font-weight: 600;
-      }
-      table {
-        width: 100%;
-        border-collapse: collapse;
-        font-variant-numeric: tabular-nums;
-      }
-      th,
-      td {
-        padding: 6px 10px;
-        text-align: right;
-        border-bottom: 1px solid var(--border);
-      }
-      th:first-child,
-      td:first-child {
-        text-align: left;
-      }
-      thead th {
-        font-weight: 600;
-        color: var(--fg-muted);
-        font-size: 12px;
-        background: var(--bg-muted);
-      }
-      tbody tr:hover {
-        background: var(--bg-muted);
-      }
-      .parity {
-        font-weight: 600;
-      }
-      .parity.good {
-        color: var(--good);
-      }
-      .parity.warn {
-        color: var(--warn);
-      }
-      .parity.bad {
-        color: var(--bad);
-      }
-      .tag {
-        display: inline-block;
-        padding: 1px 6px;
-        border-radius: 10px;
-        font-size: 10px;
-        margin-left: 6px;
-        color: white;
-      }
-      .tag.legacy {
-        background: var(--primary-tag-legacy);
-      }
-      .tag.registry {
-        background: var(--primary-tag-registry);
-      }
-      .empty {
-        padding: 40px;
-        text-align: center;
-        color: var(--fg-muted);
-      }
-      code {
-        font-family: ui-monospace, SFMono-Regular, Menlo, monospace;
-        background: var(--bg-muted);
-        padding: 1px 4px;
-        border-radius: 3px;
-      }
-    </style>
-  </head>
-  <body>
-    <main>
-      <h1>Shadow Parity — RFC #909</h1>
-      <div class="meta" id="meta">loading <code>latest.json</code>…</div>
-      <div class="cards" id="cards"></div>
-      <table id="per-language">
-        <thead>
-          <tr>
-            <th>Language</th>
-            <th>Total</th>
-            <th>Agree</th>
-            <th>Only legacy</th>
-            <th>Only new</th>
-            <th>Disagree</th>
-            <th>Both empty</th>
-            <th>Parity</th>
-          </tr>
-        </thead>
-        <tbody></tbody>
-      </table>
-      <div id="empty" class="empty" style="display: none">
-        No records yet. Enable <code>GITNEXUS_SHADOW_MODE=1</code> and run ingestion to populate.
-      </div>
-    </main>
-    <script>
-      /* global fetch, document */
-      (async function () {
-        const tbody = document.querySelector('#per-language tbody');
-        const cards = document.getElementById('cards');
-        const meta = document.getElementById('meta');
-        const empty = document.getElementById('empty');
-        const table = document.getElementById('per-language');
-
-        let payload;
-        try {
-          const r = await fetch('./latest.json', { cache: 'no-store' });
-          if (!r.ok) throw new Error('HTTP ' + r.status);
-          payload = await r.json();
-        } catch (err) {
-          meta.textContent = 'Failed to load latest.json: ' + err.message;
-          table.style.display = 'none';
-          empty.style.display = 'block';
-          return;
-        }
-
-        const primary = payload.primaryByLanguage || {};
-        const report = payload.report || {};
-        const perLang = report.perLanguage || [];
-        const overall = report.overall || {};
-
-        meta.textContent =
-          'Run ' +
-          payload.runId +
-          ' — generated ' +
-          payload.generatedAt +
-          ' (schema v' +
-          payload.schemaVersion +
-          ')';
-
-        // Overall summary cards.
-        cards.innerHTML = '';
-        const overallParity = overall.parity !== undefined ? overall.parity : 0;
-        cards.appendChild(makeCard('Total calls', overall.totalCalls ?? 0));
-        cards.appendChild(makeCard('Both agree', overall.bothAgree ?? 0));
-        cards.appendChild(makeCard('Disagree', overall.bothDisagree ?? 0));
-        cards.appendChild(makeCard('Overall parity', formatPct(overallParity)));
-
-        if (!perLang.length) {
-          table.style.display = 'none';
-          empty.style.display = 'block';
-          return;
-        }
-
-        for (const row of perLang) {
-          const tr = document.createElement('tr');
-          const primaryTag = primary[row.language];
-          const tag = primaryTag
-            ? '<span class="tag ' + primaryTag + '">primary: ' + primaryTag + '</span>'
-            : '';
-          const parityClass = parityClassFor(row.parity);
-          tr.innerHTML =
-            '<td>' +
-            escape(row.language) +
-            tag +
-            '</td>' +
-            '<td>' +
-            row.totalCalls +
-            '</td>' +
-            '<td>' +
-            row.bothAgree +
-            '</td>' +
-            '<td>' +
-            row.onlyLegacy +
-            '</td>' +
-            '<td>' +
-            row.onlyNew +
-            '</td>' +
-            '<td>' +
-            row.bothDisagree +
-            '</td>' +
-            '<td>' +
-            row.bothEmpty +
-            '</td>' +
-            '<td class="parity ' +
-            parityClass +
-            '">' +
-            formatPct(row.parity) +
-            '</td>';
-          tbody.appendChild(tr);
-        }
-
-        function makeCard(k, v) {
-          const div = document.createElement('div');
-          div.className = 'card';
-          div.innerHTML =
-            '<div class="k">' + escape(k) + '</div><div class="v">' + escape(String(v)) + '</div>';
-          return div;
-        }
-        function formatPct(x) {
-          if (typeof x !== 'number' || !isFinite(x)) return '—';
-          return (x * 100).toFixed(1) + '%';
-        }
-        function parityClassFor(x) {
-          if (typeof x !== 'number') return '';
-          if (x >= 0.95) return 'good';
-          if (x >= 0.8) return 'warn';
-          return 'bad';
-        }
-        function escape(s) {
-          return String(s).replace(/[&<>"']/g, function (c) {
-            return { '&': '&amp;', '<': '&lt;', '>': '&gt;', '"': '&quot;', "'": '&#39;' }[c];
-          });
-        }
-      })();
-    </script>
-  </body>
-</html>

gitnexus/src/cli/ai-context.ts

@@ -101,6 +101,19 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 - When exploring unfamiliar code, use \`gitnexus_query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
 - When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`gitnexus_context({name: "symbolName"})\`.
 
+## When Debugging
+
+1. \`gitnexus_query({query: "<error or symptom>"})\` — find execution flows related to the issue
+2. \`gitnexus_context({name: "<suspect function>"})\` — see all callers, callees, and process participation
+3. \`READ gitnexus://repo/${projectName}/process/{processName}\` — trace the full execution flow step by step
+4. For regressions: \`gitnexus_detect_changes({scope: "compare", base_ref: "main"})\` — see what your branch changed
+
+## When Refactoring
+
+- **Renaming**: MUST use \`gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})\` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with \`dry_run: false\`.
+- **Extracting/Splitting**: MUST run \`gitnexus_context({name: "target"})\` to see all incoming/outgoing refs, then \`gitnexus_impact({target: "target", direction: "upstream"})\` to find all external callers before moving code.
+- After any refactor: run \`gitnexus_detect_changes({scope: "all"})\` to verify only expected files changed.
+
 ## Never Do
 
 - NEVER edit a function, class, or method without first running \`gitnexus_impact\` on it.
@@ -108,6 +121,25 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 - NEVER rename symbols with find-and-replace — use \`gitnexus_rename\` which understands the call graph.
 - NEVER commit changes without running \`gitnexus_detect_changes()\` to check affected scope.
 
+## Tools Quick Reference
+
+| Tool | When to use | Command |
+|------|-------------|---------|
+| \`query\` | Find code by concept | \`gitnexus_query({query: "auth validation"})\` |
+| \`context\` | 360-degree view of one symbol | \`gitnexus_context({name: "validateUser"})\` |
+| \`impact\` | Blast radius before editing | \`gitnexus_impact({target: "X", direction: "upstream"})\` |
+| \`detect_changes\` | Pre-commit scope check | \`gitnexus_detect_changes({scope: "staged"})\` |
+| \`rename\` | Safe multi-file rename | \`gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})\` |
+| \`cypher\` | Custom graph queries | \`gitnexus_cypher({query: "MATCH ..."})\` |
+
+## Impact Risk Levels
+
+| Depth | Meaning | Action |
+|-------|---------|--------|
+| d=1 | WILL BREAK — direct callers/importers | MUST update these |
+| d=2 | LIKELY AFFECTED — indirect deps | Should test |
+| d=3 | MAY NEED TESTING — transitive | Test if critical path |
+
 ## Resources
 
 | Resource | Use for |
@@ -117,6 +149,32 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 | \`gitnexus://repo/${projectName}/processes\` | All execution flows |
 | \`gitnexus://repo/${projectName}/process/{name}\` | Step-by-step execution trace |
 
+## Self-Check Before Finishing
+
+Before completing any code modification task, verify:
+1. \`gitnexus_impact\` was run for all modified symbols
+2. No HIGH/CRITICAL risk warnings were ignored
+3. \`gitnexus_detect_changes()\` confirms changes match expected scope
+4. All d=1 (WILL BREAK) dependents were updated
+
+## Keeping the Index Fresh
+
+After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
+
+\`\`\`bash
+npx gitnexus analyze
+\`\`\`
+
+If the index previously included embeddings, preserve them by adding \`--embeddings\`:
+
+\`\`\`bash
+npx gitnexus analyze --embeddings
+\`\`\`
+
+To check whether embeddings exist, inspect \`.gitnexus/meta.json\` — the \`stats.embeddings\` field shows the count (0 means no embeddings). **Running analyze without \`--embeddings\` will delete any previously generated embeddings.**
+
+> Claude Code users: A PostToolUse hook handles this automatically after \`git commit\` and \`git merge\`.
+
 ${
   groupNames && groupNames.length > 0
     ? `## Cross-Repo Groups

gitnexus/src/cli/analyze.ts

@@ -13,11 +13,7 @@ import { execFileSync } from 'child_process';
 import v8 from 'v8';
 import cliProgress from 'cli-progress';
 import { closeLbug } from '../core/lbug/lbug-adapter.js';
-import {
-  getStoragePaths,
-  getGlobalRegistryPath,
-  RegistryNameCollisionError,
-} from '../storage/repo-manager.js';
+import { getStoragePaths, getGlobalRegistryPath } from '../storage/repo-manager.js';
 import { getGitRoot, hasGitDir } from '../storage/git.js';
 import { runFullAnalysis } from '../core/run-analyze.js';
 import fs from 'fs/promises';
@@ -63,21 +59,6 @@ export interface AnalyzeOptions {
   noStats?: boolean;
   /** Index the folder even when no .git directory is present. */
   skipGit?: boolean;
-  /**
-   * Override the default basename-derived registry `name` with a
-   * user-supplied alias (#829). Disambiguates repos whose paths share a
-   * basename. Persisted — subsequent re-analyses of the same path without
-   * `--name` preserve the alias.
-   */
-  name?: string;
-  /**
-   * Allow registration even when another path already uses the same
-   * `--name` alias (#829). Intentionally a distinct flag from `--force`
-   * because the user may want to coexist under the same name WITHOUT
-   * paying the cost of a pipeline re-index. Maps to registerRepo's
-   * `allowDuplicateName` option end-to-end.
-   */
-  allowDuplicateName?: boolean;
 }
 
 export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOptions) => {
@@ -166,11 +147,9 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
   const origLog = console.log.bind(console);
   const origWarn = console.warn.bind(console);
   const origError = console.error.bind(console);
-  let barCurrentValue = 0;
   const barLog = (...args: any[]) => {
     process.stdout.write('\x1b[2K\r');
     origLog(args.map((a) => (typeof a === 'string' ? a : String(a))).join(' '));
-    bar.update(barCurrentValue);
   };
   console.log = barLog;
   console.warn = barLog;
@@ -181,7 +160,6 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
   let phaseStart = Date.now();
 
   const updateBar = (value: number, phaseLabel: string) => {
-    barCurrentValue = value;
     if (phaseLabel !== lastPhaseLabel) {
       lastPhaseLabel = phaseLabel;
       phaseStart = Date.now();
@@ -205,20 +183,11 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
     const result = await runFullAnalysis(
       repoPath,
       {
-        // Pipeline re-index — OR'd with --skills because skill generation
-        // needs a fresh pipelineResult. Has no bearing on the registry
-        // collision guard (see allowDuplicateName below).
         force: options?.force || options?.skills,
         embeddings: options?.embeddings,
         skipGit: options?.skipGit,
         skipAgentsMd: options?.skipAgentsMd,
         noStats: options?.noStats,
-        registryName: options?.name,
-        // Registry-collision bypass — its own CLI flag, intentionally NOT
-        // overloading --force. A user who hits the collision guard should
-        // be able to accept the duplicate name without also paying the
-        // cost of a full pipeline re-index. See #829 review round 2.
-        allowDuplicateName: options?.allowDuplicateName,
       },
       {
         onProgress: (_phase, percent, message) => {
@@ -326,22 +295,6 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
     bar.stop();
 
     const msg = err.message || String(err);
-
-    // Registry name-collision from --name (#829) — surface as an
-    // actionable error rather than a generic stack-trace.
-    if (err instanceof RegistryNameCollisionError) {
-      console.error(`\n  Registry name collision:\n`);
-      console.error(`    "${err.registryName}" is already used by "${err.existingPath}".\n`);
-      console.error(`  Options:`);
-      console.error(`    • Pick a different alias:  gitnexus analyze --name <alias>`);
-      console.error(
-        `    • Allow the duplicate:     gitnexus analyze --allow-duplicate-name  (leaves "-r ${err.registryName}" ambiguous)`,
-      );
-      console.error('');
-      process.exitCode = 1;
-      return;
-    }
-
     console.error(`\n  Analysis failed: ${msg}\n`);
 
     // Provide helpful guidance for known failure modes

gitnexus/src/cli/index.ts

@@ -28,16 +28,6 @@ program
   .option('--skip-agents-md', 'Skip updating the gitnexus section in AGENTS.md and CLAUDE.md')
   .option('--no-stats', 'Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md')
   .option('--skip-git', 'Index a folder without requiring a .git directory')
-  .option(
-    '--name <alias>',
-    'Register this repo under a custom name in ~/.gitnexus/registry.json ' +
-      '(disambiguates repos whose paths share a basename, e.g. two different .../app folders)',
-  )
-  .option(
-    '--allow-duplicate-name',
-    'Register this repo even if another path already uses the same --name alias. ' +
-      'Leaves `-r <name>` ambiguous for the two paths; use -r <path> to disambiguate.',
-  )
   .option('-v, --verbose', 'Enable verbose ingestion warnings (default: false)')
   .addHelpText(
     'after',

gitnexus/src/cli/list.ts

@@ -17,23 +17,12 @@ export const listCommand = async () => {
 
   console.log(`\n  Indexed Repositories (${entries.length})\n`);
 
-  // Count occurrences of each name so colliding entries can be
-  // disambiguated in the header (#829). Unique-name entries render
-  // identically to pre-#829 output; only collisions gain a suffix.
-  const nameCounts = new Map<string, number>();
-  for (const e of entries) {
-    const key = e.name.toLowerCase();
-    nameCounts.set(key, (nameCounts.get(key) ?? 0) + 1);
-  }
-
   for (const entry of entries) {
     const indexedDate = new Date(entry.indexedAt).toLocaleString();
     const stats = entry.stats || {};
     const commitShort = entry.lastCommit?.slice(0, 7) || 'unknown';
-    const hasCollision = (nameCounts.get(entry.name.toLowerCase()) ?? 0) > 1;
-    const header = hasCollision ? `${entry.name}  (${entry.path})` : entry.name;
 
-    console.log(`  ${header}`);
+    console.log(`  ${entry.name}`);
     console.log(`    Path:    ${entry.path}`);
     console.log(`    Indexed: ${indexedDate}`);
     console.log(`    Commit:  ${commitShort}`);

gitnexus/src/core/embeddings/ast-utils.ts

@@ -1,112 +0,0 @@
-/**
- * Shared AST utilities for the embedding pipeline.
- * Centralizes parser caching and tree-sitter node lookups
- * used by both chunker.ts and structural-extractor.ts.
- */
-
-import { getLanguageFromFilename } from 'gitnexus-shared';
-import {
-  createParserForLanguage,
-  isLanguageAvailable,
-  resolveLanguageKey,
-} from '../tree-sitter/parser-loader.js';
-
-const parserCache = new Map<string, any>();
-
-/**
- * Ensure parser is initialized and language is loaded, then parse content.
- * Returns null if language is unavailable or parsing fails.
- */
-export const ensureAndParse = async (content: string, filePath: string): Promise<any | null> => {
-  const language = getLanguageFromFilename(filePath);
-  if (!language) return null;
-  if (!isLanguageAvailable(language)) return null;
-
-  const parserKey = resolveLanguageKey(language, filePath);
-  let parserInstance = parserCache.get(parserKey);
-  if (!parserInstance) {
-    parserInstance = await createParserForLanguage(language, filePath);
-    parserCache.set(parserKey, parserInstance);
-  }
-
-  return parserInstance.parse(content);
-};
-
-const FUNCTION_LIKE_TYPES = new Set([
-  'function_declaration',
-  'function_definition',
-  'method_declaration',
-  'method_definition',
-  'function_item',
-  'function_signature_item',
-  'arrow_function',
-  'function_expression',
-  'generator_function_declaration',
-  'generator_function',
-  'async_function_declaration',
-  'async_arrow_function',
-  'constructor_declaration',
-  'constructor_definition',
-  'compact_constructor_declaration',
-  'short_function_declaration',
-  'proc_declaration',
-  'func_literal',
-  'local_function_statement',
-  'anonymous_function',
-  'lambda_literal',
-  'init_declaration',
-  'deinit_declaration',
-]);
-
-/**
- * Find the first function/method-like declaration in a snippet AST.
- * Used by the chunker when parsing node.content where absolute line
- * numbers don't apply.
- */
-export const findFunctionNode = (root: any): any | null => {
-  if (FUNCTION_LIKE_TYPES.has(root.type)) return root;
-
-  for (let i = 0; i < root.namedChildCount; i++) {
-    const child = root.namedChild(i);
-    if (!child) continue;
-    if (FUNCTION_LIKE_TYPES.has(child.type)) return child;
-    const found = findFunctionNode(child);
-    if (found) return found;
-  }
-
-  return null;
-};
-
-/**
- * Find the first class/struct/interface/enum-like declaration in an AST.
- * Used when parsing node.content (a snippet, not a full file) where
- * absolute line numbers don't apply.
- */
-export const findDeclarationNode = (root: any): any | null => {
-  const CLASS_LIKE_TYPES = new Set([
-    'class_declaration',
-    'class_definition',
-    'struct_declaration',
-    'struct_item',
-    'interface_declaration',
-    'interface_definition',
-    'enum_declaration',
-    'enum_item',
-    'type_declaration', // Go: type X struct
-    'declaration', // Go: type X struct
-    'object_declaration', // Kotlin: object
-    'impl_item', // Rust: impl
-  ]);
-
-  if (CLASS_LIKE_TYPES.has(root.type)) return root;
-
-  for (let i = 0; i < root.namedChildCount; i++) {
-    const child = root.namedChild(i);
-    if (!child) continue;
-    if (CLASS_LIKE_TYPES.has(child.type)) return child;
-    const found = findDeclarationNode(child);
-    if (found) return found;
-  }
-
-  return null;
-};

gitnexus/src/core/embeddings/character-chunk.ts

@@ -1,63 +0,0 @@
-/**
- * Character-based sliding window chunking (pure, no tree-sitter dependency)
- */
-
-import { buildLineIndex, resolveChunkLines } from './line-index.js';
-
-export interface Chunk {
-  text: string;
-  chunkIndex: number;
-  startOffset: number;
-  endOffset: number;
-  startLine: number;
-  endLine: number;
-}
-
-export const characterChunk = (
-  content: string,
-  startLine: number,
-  endLine: number,
-  chunkSize: number = 1200,
-  overlap: number = 120,
-): Chunk[] => {
-  if (content.length <= chunkSize) {
-    return [
-      {
-        text: content,
-        chunkIndex: 0,
-        startOffset: 0,
-        endOffset: content.length,
-        startLine,
-        endLine,
-      },
-    ];
-  }
-
-  const chunks: Chunk[] = [];
-  let offset = 0;
-  const lineOffsets = buildLineIndex(content);
-
-  while (offset < content.length) {
-    const end = Math.min(offset + chunkSize, content.length);
-    const chunkText = content.slice(offset, end);
-    const lineRange = resolveChunkLines(lineOffsets, offset, end, startLine);
-
-    chunks.push({
-      text: chunkText,
-      chunkIndex: chunks.length,
-      startOffset: offset,
-      endOffset: end,
-      startLine: lineRange.startLine,
-      endLine: lineRange.endLine,
-    });
-
-    offset = end - overlap;
-    if (offset >= content.length) break;
-    if (end >= content.length) break;
-    if (offset <= (chunks.length > 1 ? end - chunkSize : 0)) {
-      offset = end;
-    }
-  }
-
-  return chunks;
-};

gitnexus/src/core/embeddings/chunker.ts

@@ -1,363 +0,0 @@
-/**
- * Chunker Module
- *
- * Splits code nodes into chunks for embedding.
- * - Function/Method: AST-aware chunking by statement boundaries
- * - Other types: character-based sliding window fallback
- * - Short content (≤ chunkSize): no chunking
- */
-
-export { type Chunk, characterChunk } from './character-chunk.js';
-
-import { characterChunk } from './character-chunk.js';
-import type { Chunk } from './character-chunk.js';
-import { ensureAndParse, findDeclarationNode, findFunctionNode } from './ast-utils.js';
-import { buildLineIndex, resolveChunkLines } from './line-index.js';
-
-/**
- * Main chunkNode function: dispatches by label
- */
-export const chunkNode = async (
-  label: string,
-  content: string,
-  filePath: string,
-  startLine: number,
-  endLine: number,
-  chunkSize: number = 1200,
-  overlap: number = 120,
-): Promise<Chunk[]> => {
-  // Content fits in one chunk — no splitting needed
-  if (content.length <= chunkSize) {
-    return [
-      {
-        text: content,
-        chunkIndex: 0,
-        startOffset: 0,
-        endOffset: content.length,
-        startLine,
-        endLine,
-      },
-    ];
-  }
-
-  // Only function-like labels get AST chunking
-  if (label === 'Function' || label === 'Method' || label === 'Constructor') {
-    try {
-      const astChunks = await astChunk(content, filePath, startLine, endLine, chunkSize, overlap);
-      if (astChunks.length > 0) return astChunks;
-    } catch {
-      // AST parsing failed — fall through to character fallback
-    }
-  }
-
-  if (label === 'Class' || label === 'Interface') {
-    try {
-      const declarationChunks = await declarationChunk(
-        label,
-        content,
-        filePath,
-        startLine,
-        endLine,
-        chunkSize,
-        overlap,
-      );
-      if (declarationChunks.length > 0) return declarationChunks;
-    } catch {
-      // AST parsing failed — fall through to character fallback
-    }
-  }
-
-  // Character-based fallback for everything else
-  return characterChunk(content, startLine, endLine, chunkSize, overlap);
-};
-
-/**
- * AST-based chunking for Function/Method
- * Parse snippet content, locate the function declaration node,
- * split body by statement boundaries.
- */
-const astChunk = async (
-  content: string,
-  filePath: string,
-  startLine: number,
-  endLine: number,
-  chunkSize: number,
-  overlap: number,
-): Promise<Chunk[]> => {
-  const tree = await ensureAndParse(content, filePath);
-  if (!tree) return [];
-
-  const root = tree.rootNode;
-  const lineOffsets = buildLineIndex(content);
-
-  // Find the function/method declaration in the snippet AST.
-  // tree-sitter parses node.content (a snippet), so rows are relative (0-based).
-  const targetNode = findFunctionNode(root);
-  if (!targetNode) return [];
-
-  // Get the body (statements) via childForFieldName('body')
-  const bodyNode = targetNode.childForFieldName('body');
-  if (!bodyNode) return [];
-
-  // Extract individual statements
-  const statements: Array<{ startIndex: number; endIndex: number }> = [];
-  for (let i = 0; i < bodyNode.namedChildCount; i++) {
-    const child = bodyNode.namedChild(i);
-    if (!child) continue;
-    statements.push({
-      startIndex: child.startIndex,
-      endIndex: child.endIndex,
-    });
-  }
-
-  if (statements.length === 0) return [];
-
-  return chunkByUnits(
-    content,
-    lineOffsets,
-    startLine,
-    chunkSize,
-    overlap,
-    statements,
-    targetNode.startIndex,
-    targetNode.endIndex,
-    true,
-    true,
-  );
-};
-
-const DECLARATION_BODY_NODE_TYPES = new Set([
-  'class_body',
-  'object_type',
-  'declaration_list',
-  'interface_body',
-]);
-
-const FIELD_LIKE_MEMBER_TYPES = new Set([
-  'field_definition',
-  'public_field_definition',
-  'property_definition',
-  'property_signature',
-  'variable_declarator',
-  'lexical_declaration',
-  'pair',
-  'enum_assignment',
-]);
-
-const declarationChunk = async (
-  label: 'Class' | 'Interface',
-  content: string,
-  filePath: string,
-  startLine: number,
-  endLine: number,
-  chunkSize: number,
-  overlap: number,
-): Promise<Chunk[]> => {
-  const tree = await ensureAndParse(content, filePath);
-  if (!tree) return [];
-
-  const targetNode = findDeclarationNode(tree.rootNode);
-  if (!targetNode) return [];
-
-  const bodyNode = getDeclarationBodyNode(targetNode);
-  if (!bodyNode) return [];
-
-  const members = collectDeclarationUnits(bodyNode, label);
-  if (members.length === 0) return [];
-
-  return chunkByUnits(
-    content,
-    buildLineIndex(content),
-    startLine,
-    chunkSize,
-    overlap,
-    members,
-    targetNode.startIndex,
-    targetNode.endIndex,
-    false,
-    false,
-  );
-};
-
-const buildChunk = (
-  content: string,
-  lineOffsets: Int32Array,
-  chunkIndex: number,
-  startOffset: number,
-  endOffset: number,
-  baseStartLine: number,
-): Chunk => {
-  const lineRange = resolveChunkLines(lineOffsets, startOffset, endOffset, baseStartLine);
-  return {
-    text: content.slice(startOffset, endOffset),
-    chunkIndex,
-    startOffset,
-    endOffset,
-    startLine: lineRange.startLine,
-    endLine: lineRange.endLine,
-  };
-};
-
-const chunkByUnits = (
-  content: string,
-  lineOffsets: Int32Array,
-  baseStartLine: number,
-  chunkSize: number,
-  overlap: number,
-  units: Array<{ startIndex: number; endIndex: number }>,
-  containerStartOffset: number,
-  containerEndOffset: number,
-  includeContainerPrefixOnFirstChunk: boolean,
-  includeContainerSuffixOnLastChunk: boolean,
-): Chunk[] => {
-  const chunks: Chunk[] = [];
-  let chunkStartUnitIdx = 0;
-
-  while (chunkStartUnitIdx < units.length) {
-    const chunkStartOffset =
-      chunkStartUnitIdx === 0 && includeContainerPrefixOnFirstChunk
-        ? containerStartOffset
-        : units[chunkStartUnitIdx].startIndex;
-
-    let chunkEndUnitIdx = chunkStartUnitIdx;
-    let candidateEndOffset =
-      chunkEndUnitIdx === units.length - 1 && includeContainerSuffixOnLastChunk
-        ? containerEndOffset
-        : units[chunkEndUnitIdx].endIndex;
-
-    while (chunkEndUnitIdx + 1 < units.length) {
-      const nextEndOffset =
-        chunkEndUnitIdx + 1 === units.length - 1 && includeContainerSuffixOnLastChunk
-          ? containerEndOffset
-          : units[chunkEndUnitIdx + 1].endIndex;
-      if (nextEndOffset - chunkStartOffset > chunkSize) break;
-      chunkEndUnitIdx += 1;
-      candidateEndOffset = nextEndOffset;
-    }
-
-    if (candidateEndOffset - chunkStartOffset > chunkSize) {
-      const oversizedUnit = units[chunkStartUnitIdx];
-      const oversizedLineRange = resolveChunkLines(
-        lineOffsets,
-        oversizedUnit.startIndex,
-        oversizedUnit.endIndex,
-        baseStartLine,
-      );
-      const oversizedChunks = characterChunk(
-        content.slice(oversizedUnit.startIndex, oversizedUnit.endIndex),
-        oversizedLineRange.startLine,
-        oversizedLineRange.endLine,
-        chunkSize,
-        overlap,
-      ).map((chunk, offsetIdx) => ({
-        ...chunk,
-        chunkIndex: chunks.length + offsetIdx,
-        startOffset: chunk.startOffset + oversizedUnit.startIndex,
-        endOffset: chunk.endOffset + oversizedUnit.startIndex,
-      }));
-      chunks.push(...oversizedChunks);
-      chunkStartUnitIdx += 1;
-      continue;
-    }
-
-    chunks.push(
-      buildChunk(
-        content,
-        lineOffsets,
-        chunks.length,
-        chunkStartOffset,
-        candidateEndOffset,
-        baseStartLine,
-      ),
-    );
-
-    if (chunkEndUnitIdx === units.length - 1) {
-      break;
-    }
-
-    const nextChunkStartUnitIdx = findOverlapStartIndex(
-      units,
-      chunkStartUnitIdx,
-      chunkEndUnitIdx,
-      overlap,
-    );
-    if (nextChunkStartUnitIdx <= chunkStartUnitIdx) {
-      chunkStartUnitIdx = chunkEndUnitIdx + 1;
-    } else {
-      chunkStartUnitIdx = nextChunkStartUnitIdx;
-    }
-  }
-
-  return chunks;
-};
-
-const findOverlapStartIndex = (
-  statements: Array<{ startIndex: number; endIndex: number }>,
-  chunkStartStmtIdx: number,
-  chunkEndStmtIdx: number,
-  overlapSize: number,
-): number => {
-  if (overlapSize <= 0) return chunkEndStmtIdx + 1;
-
-  let overlapStartIdx = chunkEndStmtIdx;
-  while (overlapStartIdx > chunkStartStmtIdx) {
-    const overlapLength =
-      statements[chunkEndStmtIdx].endIndex - statements[overlapStartIdx - 1].startIndex;
-    if (overlapLength > overlapSize) break;
-    overlapStartIdx -= 1;
-  }
-
-  return overlapStartIdx;
-};
-
-const getDeclarationBodyNode = (node: any): any | null => {
-  const bodyNode = node.childForFieldName?.('body');
-  if (bodyNode) return bodyNode;
-
-  for (let i = 0; i < node.namedChildCount; i++) {
-    const child = node.namedChild(i);
-    if (!child) continue;
-    if (DECLARATION_BODY_NODE_TYPES.has(child.type)) return child;
-  }
-
-  return null;
-};
-
-const collectDeclarationUnits = (
-  bodyNode: any,
-  label: 'Class' | 'Interface',
-): Array<{ startIndex: number; endIndex: number }> => {
-  const members: Array<{ startIndex: number; endIndex: number; groupable: boolean }> = [];
-
-  for (let i = 0; i < bodyNode.namedChildCount; i++) {
-    const child = bodyNode.namedChild(i);
-    if (!child) continue;
-    members.push({
-      startIndex: child.startIndex,
-      endIndex: child.endIndex,
-      groupable: label === 'Class' && FIELD_LIKE_MEMBER_TYPES.has(child.type),
-    });
-  }
-
-  if (members.length === 0) return [];
-
-  const grouped: Array<{ startIndex: number; endIndex: number }> = [];
-  let current = members[0];
-
-  for (let i = 1; i < members.length; i++) {
-    const next = members[i];
-    if (current.groupable && next.groupable) {
-      current = {
-        startIndex: current.startIndex,
-        endIndex: next.endIndex,
-        groupable: true,
-      };
-      continue;
-    }
-    grouped.push({ startIndex: current.startIndex, endIndex: current.endIndex });
-    current = next;
-  }
-
-  grouped.push({ startIndex: current.startIndex, endIndex: current.endIndex });
-  return grouped;
-};

gitnexus/src/core/embeddings/embedder.ts

@@ -157,11 +157,6 @@ export const initEmbedder = async (
     try {
       // Configure transformers.js environment
       env.allowLocalModels = false;
-      // Default cache to user-writable location. transformers.js defaults to
-      // ./node_modules/.cache inside its own install dir, which is unwritable
-      // when gitnexus is installed globally (e.g. /usr/lib/node_modules/).
-      // Respect HF_HOME if set, otherwise fall back to ~/.cache/huggingface.
-      env.cacheDir = process.env.HF_HOME ?? `${process.env.HOME}/.cache/huggingface`;
 
       const isDev = process.env.NODE_ENV === 'development';
       if (isDev) {

gitnexus/src/core/embeddings/embedding-pipeline.ts

@@ -3,13 +3,12 @@
  *
  * Orchestrates the background embedding process:
  * 1. Query embeddable nodes from LadybugDB
- * 2. Generate text representations with enriched metadata
- * 3. Chunk long nodes, batch embed
- * 4. Update LadybugDB with chunk-aware embeddings
+ * 2. Generate text representations
+ * 3. Batch embed using transformers.js
+ * 4. Update LadybugDB with embeddings
  * 5. Create vector index for semantic search
  */
 
-import { createHash } from 'crypto';
 import {
   initEmbedder,
   embedBatch,
@@ -17,54 +16,19 @@ import {
   embeddingToArray,
   isEmbedderReady,
 } from './embedder.js';
-import { generateEmbeddingText } from './text-generator.js';
-import { chunkNode, characterChunk } from './chunker.js';
-import { extractStructuralNames } from './structural-extractor.js';
+import { generateBatchEmbeddingTexts } from './text-generator.js';
 import {
   type EmbeddingProgress,
   type EmbeddingConfig,
   type EmbeddableNode,
   type SemanticSearchResult,
   type ModelProgress,
-  type EmbeddingContext,
   DEFAULT_EMBEDDING_CONFIG,
   EMBEDDABLE_LABELS,
-  isShortLabel,
-  LABELS_WITH_EXPORTED,
-  STRUCTURAL_LABELS,
-  collectBestChunks,
 } from './types.js';
-import {
-  EMBEDDING_TABLE_NAME,
-  EMBEDDING_INDEX_NAME,
-  CREATE_VECTOR_INDEX_QUERY,
-  STALE_HASH_SENTINEL,
-} from '../lbug/schema.js';
-import { loadVectorExtension } from '../lbug/lbug-adapter.js';
 
 const isDev = process.env.NODE_ENV === 'development';
 
-/**
- * Compute a stable content fingerprint for an embeddable node.
- * Used to detect when the underlying text has changed so stale vectors
- * can be replaced (DELETE-then-INSERT, the Kuzu-sanctioned pattern for
- * vector-indexed rows).
- */
-export const contentHashForNode = (
-  node: EmbeddableNode,
-  config: Partial<EmbeddingConfig> = {},
-): string => {
-  // Hash must be deterministic across runs, so exclude methodNames/fieldNames
-  // which are populated during the batch loop via AST extraction.
-  // Using only node.content ensures the hash stays stable.
-  const text = generateEmbeddingText(
-    { ...node, methodNames: undefined, fieldNames: undefined },
-    node.content,
-    config,
-  );
-  return createHash('sha1').update(text).digest('hex');
-};
-
 /**
  * Progress callback type
  */
@@ -72,50 +36,37 @@ export type EmbeddingProgressCallback = (progress: EmbeddingProgress) => void;
 
 /**
  * Query all embeddable nodes from LadybugDB
- * Uses table-specific queries for different label types
+ * Uses table-specific queries (File has different schema than code elements)
  */
 const queryEmbeddableNodes = async (
   executeQuery: (cypher: string) => Promise<any[]>,
 ): Promise<EmbeddableNode[]> => {
   const allNodes: EmbeddableNode[] = [];
 
+  // Query each embeddable table with table-specific columns
   for (const label of EMBEDDABLE_LABELS) {
     try {
       let query: string;
 
-      if (label === 'Method') {
-        // Method has parameterCount and returnType
+      if (label === 'File') {
+        // File nodes don't have startLine/endLine
         query = `
-          MATCH (n:Method)
-          RETURN n.id AS id, n.name AS name, 'Method' AS label,
-                 n.filePath AS filePath, n.content AS content,
-                 n.startLine AS startLine, n.endLine AS endLine,
-                 n.isExported AS isExported, n.description AS description,
-                 n.parameterCount AS parameterCount, n.returnType AS returnType
-        `;
-      } else if (LABELS_WITH_EXPORTED.has(label)) {
-        // Function, Class, Interface have isExported and description
-        query = `
-          MATCH (n:\`${label}\`)
-          RETURN n.id AS id, n.name AS name, '${label}' AS label,
-                 n.filePath AS filePath, n.content AS content,
-                 n.startLine AS startLine, n.endLine AS endLine,
-                 n.isExported AS isExported, n.description AS description
+          MATCH (n:File)
+          RETURN n.id AS id, n.name AS name, 'File' AS label, 
+                 n.filePath AS filePath, n.content AS content
         `;
       } else {
-        // Multi-language tables (Struct, Enum, etc.) — have description but no isExported
+        // Code elements have startLine/endLine
         query = `
-          MATCH (n:\`${label}\`)
-          RETURN n.id AS id, n.name AS name, '${label}' AS label,
+          MATCH (n:${label})
+          RETURN n.id AS id, n.name AS name, '${label}' AS label, 
                  n.filePath AS filePath, n.content AS content,
-                 n.startLine AS startLine, n.endLine AS endLine,
-                 n.description AS description
+                 n.startLine AS startLine, n.endLine AS endLine
         `;
       }
 
       const rows = await executeQuery(query);
       for (const row of rows) {
-        const hasExportedColumn = label === 'Method' || LABELS_WITH_EXPORTED.has(label);
         allNodes.push({
           id: row.id ?? row[0],
           name: row.name ?? row[1],
@@ -124,17 +75,10 @@ const queryEmbeddableNodes = async (
           content: row.content ?? row[4] ?? '',
           startLine: row.startLine ?? row[5],
           endLine: row.endLine ?? row[6],
-          isExported: hasExportedColumn ? (row.isExported ?? row[7]) : undefined,
-          description: row.description ?? (hasExportedColumn ? row[8] : row[7]),
-          ...(label === 'Method'
-            ? {
-                parameterCount: row.parameterCount ?? row[9],
-                returnType: row.returnType ?? row[10],
-              }
-            : {}),
         });
       }
     } catch (error) {
+      // Table might not exist or be empty, continue
       if (isDev) {
         console.warn(`Query for ${label} nodes failed:`, error);
       }
@@ -145,52 +89,52 @@ const queryEmbeddableNodes = async (
 };
 
 /**
- * Batch INSERT chunk-aware embeddings into CodeEmbedding table
+ * Batch INSERT embeddings into separate CodeEmbedding table
+ * Using a separate lightweight table avoids copy-on-write overhead
+ * that occurs when UPDATEing nodes with large content fields
  */
-export const batchInsertEmbeddings = async (
+const batchInsertEmbeddings = async (
   executeWithReusedStatement: (
     cypher: string,
     paramsList: Array<Record<string, any>>,
   ) => Promise<void>,
-  updates: Array<{
-    nodeId: string;
-    chunkIndex: number;
-    startLine: number;
-    endLine: number;
-    embedding: number[];
-    contentHash?: string;
-  }>,
+  updates: Array<{ id: string; embedding: number[] }>,
 ): Promise<void> => {
-  const cypher = `CREATE (e:${EMBEDDING_TABLE_NAME} {id: $id, nodeId: $nodeId, chunkIndex: $chunkIndex, startLine: $startLine, endLine: $endLine, embedding: $embedding, contentHash: $contentHash})`;
-  const paramsList = updates.map((u) => ({
-    id: `${u.nodeId}:${u.chunkIndex}`,
-    nodeId: u.nodeId,
-    chunkIndex: u.chunkIndex,
-    startLine: u.startLine,
-    endLine: u.endLine,
-    embedding: u.embedding,
-    contentHash: u.contentHash ?? STALE_HASH_SENTINEL,
-  }));
+  // MERGE instead of CREATE — idempotent, handles concurrent analyzes and partial prior runs
+  const cypher = `MERGE (e:CodeEmbedding {nodeId: $nodeId}) SET e.embedding = $embedding`;
+  const paramsList = updates.map((u) => ({ nodeId: u.id, embedding: u.embedding }));
   await executeWithReusedStatement(cypher, paramsList);
 };
 
 /**
  * Create the vector index for semantic search
-
- * Now indexes the separate CodeEmbedding table.
- * Delegates extension loading to lbug-adapter's loadVectorExtension(),
- * which owns the VECTOR extension lifecycle and state tracking.
-
+ * Now indexes the separate CodeEmbedding table
  */
+let vectorExtensionLoaded = false;
+
 const createVectorIndex = async (
   executeQuery: (cypher: string) => Promise<any[]>,
 ): Promise<void> => {
-  // Delegate to the adapter which tracks loaded state and handles DB reconnect resets
-  await loadVectorExtension();
+  // LadybugDB v0.15+ requires explicit VECTOR extension loading (once per session)
+  if (!vectorExtensionLoaded) {
+    try {
+      await executeQuery('INSTALL VECTOR');
+      await executeQuery('LOAD EXTENSION VECTOR');
+      vectorExtensionLoaded = true;
+    } catch {
+      // Extension may already be loaded — CREATE_VECTOR_INDEX will fail clearly if not
+      vectorExtensionLoaded = true;
+    }
+  }
+
+  const cypher = `
+    CALL CREATE_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 'embedding', metric := 'cosine')
+  `;
 
   try {
-    await executeQuery(CREATE_VECTOR_INDEX_QUERY);
+    await executeQuery(cypher);
   } catch (error) {
+    // Index might already exist
     if (isDev) {
       console.warn('Vector index creation warning:', error);
     }
@@ -205,11 +149,6 @@ const createVectorIndex = async (
  * @param onProgress - Callback for progress updates
  * @param config - Optional configuration override
  * @param skipNodeIds - Optional set of node IDs that already have embeddings (incremental mode)
- * @param context - Optional repo/server context for metadata enrichment
- * @param existingEmbeddings - Optional map of nodeId → contentHash for incremental mode.
- *        Nodes whose hash matches are skipped; nodes with a changed hash are DELETE'd
- *        and re-embedded; nodes not in the map are embedded fresh.
-
  */
 export const runEmbeddingPipeline = async (
   executeQuery: (cypher: string) => Promise<any[]>,
@@ -220,8 +159,6 @@ export const runEmbeddingPipeline = async (
   onProgress: EmbeddingProgressCallback,
   config: Partial<EmbeddingConfig> = {},
   skipNodeIds?: Set<string>,
-  context?: EmbeddingContext,
-  existingEmbeddings?: Map<string, string>,
 ): Promise<void> => {
   const finalConfig = { ...DEFAULT_EMBEDDING_CONFIG, ...config };
 
@@ -257,65 +194,13 @@ export const runEmbeddingPipeline = async (
     // Phase 2: Query embeddable nodes
     let nodes = await queryEmbeddableNodes(executeQuery);
 
-    // Apply context metadata
-    if (context?.repoName) {
-      for (const node of nodes) {
-        node.repoName = context.repoName;
-        node.serverName = context.serverName;
-      }
-    }
-
-    // Incremental mode: compare content hashes, delete stale rows, skip fresh ones.
-    // Computed hashes for stale nodes are cached so batchInsertEmbeddings can reuse them
-    // (avoids double computation).
-    const computedStaleHashes = new Map<string, string>();
-    if (existingEmbeddings && existingEmbeddings.size > 0) {
+    // Incremental mode: filter out nodes that already have embeddings
+    if (skipNodeIds && skipNodeIds.size > 0) {
       const beforeCount = nodes.length;
-      const staleNodeIds: string[] = [];
-      nodes = nodes.filter((n) => {
-        const existingHash = existingEmbeddings.get(n.id);
-        if (existingHash === undefined) {
-          // New node — needs embedding
-          return true;
-        }
-        const currentHash = contentHashForNode(n, finalConfig);
-        if (currentHash !== existingHash) {
-          // Content changed — cache hash for reuse during insert, mark for DELETE + re-embed
-          computedStaleHashes.set(n.id, currentHash);
-          staleNodeIds.push(n.id);
-          return true;
-        }
-        // Hash matches — skip (fresh); no need to cache hash for skipped nodes
-        return false;
-      });
-
-      // DELETE stale embedding rows so they can be re-inserted
-      // (Kuzu forbids SET on vector-indexed properties; DELETE-then-INSERT is the sanctioned pattern)
-      if (staleNodeIds.length > 0) {
-        if (isDev) {
-          console.log(`🔄 Deleting ${staleNodeIds.length} stale embedding rows for re-embed`);
-        }
-        try {
-          await executeWithReusedStatement(
-            `MATCH (e:${EMBEDDING_TABLE_NAME} {nodeId: $nodeId}) DELETE e`,
-            staleNodeIds.map((nodeId) => ({ nodeId })),
-          );
-        } catch (err) {
-          // "does not exist" = rows already gone — safe to proceed.
-          // All other errors risk vector-index corruption (Kuzu requires DELETE-before-INSERT
-          // for vector-indexed properties) — propagate so the pipeline aborts cleanly.
-          const msg = err instanceof Error ? err.message : String(err);
-          if (!msg.includes('does not exist')) {
-            throw new Error(
-              `[embed] Failed to delete stale embedding rows — aborting to prevent vector-index corruption: ${msg}`,
-            );
-          }
-        }
-      }
-
+      nodes = nodes.filter((n) => !skipNodeIds.has(n.id));
       if (isDev) {
         console.log(
-          `📦 Incremental embeddings: ${beforeCount} total, ${existingEmbeddings.size} cached, ${staleNodeIds.length} stale, ${nodes.length} to embed`,
+          `📦 Incremental embeddings: ${beforeCount} total, ${skipNodeIds.size} cached, ${nodes.length} to embed`,
         );
       }
     }
@@ -327,11 +212,6 @@ export const runEmbeddingPipeline = async (
     }
 
     if (totalNodes === 0) {
-      // Ensure the vector index exists even when no new nodes need embedding.
-      // A prior crash or first-time incremental run may have left CodeEmbedding
-      // rows without ever reaching index creation.
-      await createVectorIndex(executeQuery);
-
       onProgress({
         phase: 'ready',
         percent: 100,
@@ -341,12 +221,10 @@ export const runEmbeddingPipeline = async (
       return;
     }
 
-    // Phase 3: Chunk + embed nodes
+    // Phase 3: Batch embed nodes
     const batchSize = finalConfig.batchSize;
-    const chunkSize = finalConfig.chunkSize;
-    const overlap = finalConfig.overlap;
+    const totalBatches = Math.ceil(totalNodes / batchSize);
     let processedNodes = 0;
-    let totalChunks = 0;
 
     onProgress({
       phase: 'embedding',
@@ -354,116 +232,39 @@ export const runEmbeddingPipeline = async (
       nodesProcessed: 0,
       totalNodes,
       currentBatch: 0,
-      totalBatches: Math.ceil(totalNodes / batchSize),
+      totalBatches,
     });
 
-    // Process in batches of nodes
-    for (let batchIndex = 0; batchIndex < totalNodes; batchIndex += batchSize) {
-      const batch = nodes.slice(batchIndex, batchIndex + batchSize);
+    for (let batchIndex = 0; batchIndex < totalBatches; batchIndex++) {
+      const start = batchIndex * batchSize;
+      const end = Math.min(start + batchSize, totalNodes);
+      const batch = nodes.slice(start, end);
 
-      // Chunk each node and generate text
-      const allTexts: string[] = [];
-      const allUpdates: Array<{
-        nodeId: string;
-        chunkIndex: number;
-        startLine: number;
-        endLine: number;
-        contentHash: string;
-      }> = [];
+      // Generate texts for this batch
+      const texts = generateBatchEmbeddingTexts(batch, finalConfig);
 
-      for (const node of batch) {
-        const isShort = isShortLabel(node.label);
-        const startLine = node.startLine ?? 0;
-        const endLine = node.endLine ?? 0;
+      // Embed the batch
+      const embeddings = await embedBatch(texts);
 
-        // Extract structural names for class-like nodes via AST extractors
-        if (!isShort && STRUCTURAL_LABELS.has(node.label)) {
-          try {
-            const names = await extractStructuralNames(node.content, node.filePath);
-            node.methodNames = names.methodNames;
-            node.fieldNames = names.fieldNames;
-          } catch {
-            // AST extraction failed — names stay undefined, text-generator handles gracefully
-          }
-        }
+      // Update LadybugDB with embeddings
+      const updates = batch.map((node, i) => ({
+        id: node.id,
+        embedding: embeddingToArray(embeddings[i]),
+      }));
 
-        // Compute content hash once per node (re-use cached value for stale nodes)
-        const hash = computedStaleHashes.get(node.id) ?? contentHashForNode(node, finalConfig);
-
-        let chunks: Array<{ text: string; chunkIndex: number; startLine: number; endLine: number }>;
-        if (isShort) {
-          chunks = [{ text: node.content, chunkIndex: 0, startLine, endLine }];
-        } else {
-          try {
-            chunks = await chunkNode(
-              node.label,
-              node.content,
-              node.filePath,
-              startLine,
-              endLine,
-              chunkSize,
-              overlap,
-            );
-          } catch (chunkErr) {
-            if (isDev) {
-              console.warn(
-                `⚠️ AST chunking failed for ${node.label} "${node.name}" (${node.filePath}), falling back to character-based chunking:`,
-                chunkErr,
-              );
-            }
-            chunks = characterChunk(node.content, startLine, endLine, chunkSize, overlap);
-          }
-        }
-
-        for (const chunk of chunks) {
-          const text = generateEmbeddingText(node, chunk.text, finalConfig);
-          allTexts.push(text);
-          allUpdates.push({
-            nodeId: node.id,
-            chunkIndex: chunk.chunkIndex,
-            startLine: chunk.startLine,
-            endLine: chunk.endLine,
-            contentHash: hash,
-          });
-        }
-      }
-
-      // Embed chunk texts in sub-batches to control memory
-      const EMBED_SUB_BATCH = 8;
-      for (let si = 0; si < allTexts.length; si += EMBED_SUB_BATCH) {
-        const subTexts = allTexts.slice(si, si + EMBED_SUB_BATCH);
-        const subUpdates = allUpdates.slice(si, si + EMBED_SUB_BATCH);
-
-        let embeddings: Float32Array[];
-        try {
-          embeddings = await embedBatch(subTexts);
-        } catch (embedErr) {
-          console.error(
-            `❌ embedBatch failed for ${subTexts.length} texts (first: "${subTexts[0]?.substring(0, 80)}..."):`,
-            embedErr,
-          );
-          throw embedErr;
-        }
-
-        const dbUpdates = subUpdates.map((u, i) => ({
-          ...u,
-          embedding: embeddingToArray(embeddings[i]),
-        }));
-
-        await batchInsertEmbeddings(executeWithReusedStatement, dbUpdates);
-      }
+      await batchInsertEmbeddings(executeWithReusedStatement, updates);
 
       processedNodes += batch.length;
-      totalChunks += allUpdates.length;
 
+      // Report progress (20-90% for embedding phase)
       const embeddingProgress = 20 + (processedNodes / totalNodes) * 70;
       onProgress({
         phase: 'embedding',
         percent: Math.round(embeddingProgress),
         nodesProcessed: processedNodes,
         totalNodes,
-        currentBatch: Math.floor(batchIndex / batchSize) + 1,
-        totalBatches: Math.ceil(totalNodes / batchSize),
+        currentBatch: batchIndex + 1,
+        totalBatches,
       });
     }
 
@@ -481,6 +282,7 @@ export const runEmbeddingPipeline = async (
 
     await createVectorIndex(executeQuery);
 
+    // Complete
     onProgress({
       phase: 'ready',
       percent: 100,
@@ -489,9 +291,7 @@ export const runEmbeddingPipeline = async (
     });
 
     if (isDev) {
-      console.log(
-        `✅ Embedding pipeline complete! (${totalChunks} chunks from ${totalNodes} nodes)`,
-      );
+      console.log('✅ Embedding pipeline complete!');
     }
   } catch (error) {
     const errorMessage = error instanceof Error ? error.message : 'Unknown error';
@@ -511,7 +311,15 @@ export const runEmbeddingPipeline = async (
 };
 
 /**
- * Perform semantic search using the vector index with chunk deduplication
+ * Perform semantic search using the vector index
+ *
+ * Uses CodeEmbedding table and queries each node table to get metadata
+ *
+ * @param executeQuery - Function to execute Cypher queries
+ * @param query - Search query text
+ * @param k - Number of results to return (default: 10)
+ * @param maxDistance - Maximum distance threshold (default: 0.5)
+ * @returns Array of search results ordered by relevance
  */
 export const semanticSearch = async (
   executeQuery: (cypher: string) => Promise<any[]>,
@@ -523,46 +331,37 @@ export const semanticSearch = async (
     throw new Error('Embedding model not initialized. Run embedding pipeline first.');
   }
 
+  // Embed the query
   const queryEmbedding = await embedText(query);
   const queryVec = embeddingToArray(queryEmbedding);
   const queryVecStr = `[${queryVec.join(',')}]`;
 
-  const bestChunks = await collectBestChunks(k, async (fetchLimit) => {
-    const vectorQuery = `
-      CALL QUERY_VECTOR_INDEX('${EMBEDDING_TABLE_NAME}', '${EMBEDDING_INDEX_NAME}',
-        CAST(${queryVecStr} AS FLOAT[${queryVec.length}]), ${fetchLimit})
-      YIELD node AS emb, distance
-      WITH emb, distance
-      WHERE distance < ${maxDistance}
-      RETURN emb.nodeId AS nodeId, emb.chunkIndex AS chunkIndex,
-             emb.startLine AS startLine, emb.endLine AS endLine, distance
-      ORDER BY distance
-    `;
+  // Query the vector index on CodeEmbedding to get nodeIds and distances
+  const vectorQuery = `
+    CALL QUERY_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 
+      CAST(${queryVecStr} AS FLOAT[${queryVec.length}]), ${k})
+    YIELD node AS emb, distance
+    WITH emb, distance
+    WHERE distance < ${maxDistance}
+    RETURN emb.nodeId AS nodeId, distance
+    ORDER BY distance
+  `;
 
-    const embResults = await executeQuery(vectorQuery);
-    return embResults.map((row) => ({
-      nodeId: row.nodeId ?? row[0],
-      chunkIndex: row.chunkIndex ?? row[1] ?? 0,
-      startLine: row.startLine ?? row[2] ?? 0,
-      endLine: row.endLine ?? row[3] ?? 0,
-      distance: row.distance ?? row[4],
-    }));
-  });
+  const embResults = await executeQuery(vectorQuery);
 
-  if (bestChunks.size === 0) {
+  if (embResults.length === 0) {
     return [];
   }
 
   // Group results by label for batched metadata queries
-  const byLabel = new Map<
-    string,
-    Array<{ nodeId: string; distance: number } & Record<string, any>>
-  >();
-  for (const [nodeId, chunk] of Array.from(bestChunks.entries()).slice(0, k)) {
+  const byLabel = new Map<string, Array<{ nodeId: string; distance: number }>>();
+  for (const embRow of embResults) {
+    const nodeId = embRow.nodeId ?? embRow[0];
+    const distance = embRow.distance ?? embRow[1];
     const labelEndIdx = nodeId.indexOf(':');
     const label = labelEndIdx > 0 ? nodeId.substring(0, labelEndIdx) : 'Unknown';
     if (!byLabel.has(label)) byLabel.set(label, []);
-    byLabel.get(label)!.push({ nodeId, ...chunk });
+    byLabel.get(label)!.push({ nodeId, distance });
   }
 
   // Batch-fetch metadata per label
@@ -571,11 +370,19 @@ export const semanticSearch = async (
   for (const [label, items] of byLabel) {
     const idList = items.map((i) => `'${i.nodeId.replace(/'/g, "''")}'`).join(', ');
     try {
-      const nodeQuery = `
-        MATCH (n:\`${label}\`) WHERE n.id IN [${idList}]
-        RETURN n.id AS id, n.name AS name, n.filePath AS filePath,
-               n.startLine AS startLine, n.endLine AS endLine
-      `;
+      let nodeQuery: string;
+      if (label === 'File') {
+        nodeQuery = `
+          MATCH (n:File) WHERE n.id IN [${idList}]
+          RETURN n.id AS id, n.name AS name, n.filePath AS filePath
+        `;
+      } else {
+        nodeQuery = `
+          MATCH (n:${label}) WHERE n.id IN [${idList}]
+          RETURN n.id AS id, n.name AS name, n.filePath AS filePath,
+                 n.startLine AS startLine, n.endLine AS endLine
+        `;
+      }
       const nodeRows = await executeQuery(nodeQuery);
       const rowMap = new Map<string, any>();
       for (const row of nodeRows) {
@@ -591,8 +398,8 @@ export const semanticSearch = async (
             label,
             filePath: nodeRow.filePath ?? nodeRow[2] ?? '',
             distance: item.distance,
-            startLine: item.startLine,
-            endLine: item.endLine,
+            startLine: label !== 'File' ? (nodeRow.startLine ?? nodeRow[3]) : undefined,
+            endLine: label !== 'File' ? (nodeRow.endLine ?? nodeRow[4]) : undefined,
           });
         }
       }
@@ -601,6 +408,7 @@ export const semanticSearch = async (
     }
   }
 
+  // Re-sort by distance since batch queries may have mixed order
   results.sort((a, b) => a.distance - b.distance);
 
   return results;
@@ -608,6 +416,16 @@ export const semanticSearch = async (
 
 /**
  * Semantic search with graph expansion (flattened results)
+ *
+ * Note: With multi-table schema, graph traversal is simplified.
+ * Returns semantic matches with their metadata.
+ * For full graph traversal, use execute_vector_cypher tool directly.
+ *
+ * @param executeQuery - Function to execute Cypher queries
+ * @param query - Search query text
+ * @param k - Number of initial semantic matches (default: 5)
+ * @param _hops - Unused (kept for API compatibility).
+ * @returns Semantic matches with metadata
  */
 export const semanticSearchWithContext = async (
   executeQuery: (cypher: string) => Promise<any[]>,
@@ -615,6 +433,8 @@ export const semanticSearchWithContext = async (
   k: number = 5,
   _hops: number = 1,
 ): Promise<any[]> => {
+  // For multi-table schema, just return semantic search results
+  // Graph traversal is complex with separate tables - use execute_vector_cypher instead
   const results = await semanticSearch(executeQuery, query, k, 0.5);
 
   return results.map((r) => ({

gitnexus/src/core/embeddings/line-index.ts

@@ -1,50 +0,0 @@
-export interface ResolvedLineRange {
-  startLine: number;
-  endLine: number;
-}
-
-export const buildLineIndex = (content: string): Int32Array => {
-  const offsets: number[] = [0];
-  for (let i = 0; i < content.length; i++) {
-    if (content.charCodeAt(i) === 10) offsets.push(i + 1);
-  }
-  return new Int32Array(offsets);
-};
-
-const clampOffset = (lineOffsets: Int32Array, charOffset: number): number => {
-  if (lineOffsets.length === 0) return 0;
-  const maxOffset = lineOffsets[lineOffsets.length - 1];
-  if (charOffset < 0) return 0;
-  if (charOffset > maxOffset) return maxOffset;
-  return charOffset;
-};
-
-export const lineFromOffset = (lineOffsets: Int32Array, charOffset: number): number => {
-  if (lineOffsets.length === 0) return 0;
-
-  const clamped = clampOffset(lineOffsets, charOffset);
-  let lo = 0;
-  let hi = lineOffsets.length - 1;
-  while (lo < hi) {
-    const mid = (lo + hi + 1) >> 1;
-    if (lineOffsets[mid] <= clamped) lo = mid;
-    else hi = mid - 1;
-  }
-  return lo;
-};
-
-export const resolveChunkLines = (
-  lineOffsets: Int32Array,
-  startOffset: number,
-  endOffset: number,
-  baseStartLine: number,
-): ResolvedLineRange => {
-  const relativeStartLine = lineFromOffset(lineOffsets, startOffset);
-  const effectiveEndOffset = endOffset > startOffset ? endOffset - 1 : startOffset;
-  const relativeEndLine = lineFromOffset(lineOffsets, effectiveEndOffset);
-
-  return {
-    startLine: baseStartLine + relativeStartLine,
-    endLine: baseStartLine + relativeEndLine,
-  };
-};

gitnexus/src/core/embeddings/server-mapping.ts

@@ -1,37 +0,0 @@
-/**
- * Server Mapping Configuration
- *
- * Reads ~/.gitnexus/server-mapping.json to map repo names to service names.
- * Used in embedding text to enrich metadata with microservice context.
- */
-
-import fs from 'fs/promises';
-import path from 'path';
-import os from 'os';
-
-const MAPPING_FILE = path.join(os.homedir(), '.gitnexus', 'server-mapping.json');
-
-let cachedMapping: Record<string, string> | null = null;
-
-/**
- * Read the server mapping file and return the serverName for a given repoName.
- * Returns undefined if no mapping exists.
- */
-export const readServerMapping = async (repoName: string): Promise<string | undefined> => {
-  try {
-    if (!cachedMapping) {
-      const raw = await fs.readFile(MAPPING_FILE, 'utf-8');
-      cachedMapping = JSON.parse(raw);
-    }
-    return cachedMapping[repoName];
-  } catch {
-    return undefined;
-  }
-};
-
-/**
- * Clear the cached mapping (useful for testing or after file changes)
- */
-export const clearServerMappingCache = (): void => {
-  cachedMapping = null;
-};

gitnexus/src/core/embeddings/structural-extractor.ts

@@ -1,89 +0,0 @@
-/**
- * Structural Extractor Module
- *
- * Reuses ingestion pipeline's AST-based MethodExtractor / FieldExtractor
- * to extract method and field names for embedding text generation.
- */
-
-import { getProviderForFile } from '../ingestion/languages/index.js';
-import type { MethodExtractorContext, ExtractedMethods } from '../ingestion/method-types.js';
-import type { FieldExtractorContext, ExtractedFields } from '../ingestion/field-types.js';
-import type { LanguageProvider } from '../ingestion/language-provider.js';
-import { buildTypeEnv } from '../ingestion/type-env.js';
-import { SupportedLanguages } from 'gitnexus-shared';
-import { ensureAndParse, findDeclarationNode } from './ast-utils.js';
-
-export interface StructuralNames {
-  methodNames: string[];
-  fieldNames: string[];
-}
-
-const NOOP_SYMBOL_TABLE = {
-  lookupExactAll: () => [],
-  lookupExact: () => undefined,
-  lookupExactFull: () => undefined,
-} as any;
-
-/**
- * Extract method and field names from a class/struct/interface node
- * using the ingestion pipeline's AST extractors.
- */
-export const extractStructuralNames = async (
-  content: string,
-  filePath: string,
-): Promise<StructuralNames> => {
-  const provider = getProviderForFile(filePath);
-  if (!provider) return { methodNames: [], fieldNames: [] };
-
-  const tree = await ensureAndParse(content, filePath);
-  if (!tree) return { methodNames: [], fieldNames: [] };
-
-  // Parse node.content (a snippet) — find declaration directly, not by range
-  const classNode = findDeclarationNode(tree.rootNode);
-  if (!classNode) return { methodNames: [], fieldNames: [] };
-
-  const language = provider.id;
-
-  const methodNames = extractMethodNames(classNode, provider, filePath, language);
-  const fieldNames = extractFieldNames(classNode, provider, tree, filePath, language);
-
-  return { methodNames, fieldNames };
-};
-
-function extractMethodNames(
-  classNode: any,
-  provider: LanguageProvider,
-  filePath: string,
-  language: SupportedLanguages,
-): string[] {
-  if (!provider.methodExtractor) return [];
-
-  const context: MethodExtractorContext = { filePath, language };
-  const result: ExtractedMethods | null = provider.methodExtractor.extract(classNode, context);
-  if (!result?.methods?.length) return [];
-
-  return result.methods.map((m) => m.name);
-}
-
-function extractFieldNames(
-  classNode: any,
-  provider: LanguageProvider,
-  tree: any,
-  filePath: string,
-  language: SupportedLanguages,
-): string[] {
-  if (!provider.fieldExtractor) return [];
-
-  const typeEnv = buildTypeEnv(tree, language);
-
-  const context: FieldExtractorContext = {
-    typeEnv,
-    symbolTable: NOOP_SYMBOL_TABLE,
-    filePath,
-    language,
-  };
-  const result: ExtractedFields | null = provider.fieldExtractor.extract(classNode, context);
-  if (!result?.fields?.length) return [];
-
-  return result.fields.map((f) => f.name);
-}

gitnexus/src/core/embeddings/text-generator.ts

@@ -1,253 +1,206 @@
 /**
  * Text Generator Module
  *
- * Generates enriched embedding text from code nodes with metadata.
- * Supports chunkable labels (Function/Method with AST chunking),
- * Class-specific structural text, and short-node direct embed.
- *
- * Method/field names for Class nodes are extracted by the ingestion
- * pipeline's AST extractors and passed via node.methodNames/node.fieldNames.
+ * Pure functions to generate embedding text from code nodes.
+ * Combines node metadata with code snippets for semantic matching.
  */
 
 import type { EmbeddableNode, EmbeddingConfig } from './types.js';
-import { DEFAULT_EMBEDDING_CONFIG, isShortLabel } from './types.js';
+import { DEFAULT_EMBEDDING_CONFIG } from './types.js';
 
 /**
- * Truncate description to max length at sentence/word boundary
+ * Extract the filename from a file path
  */
-const truncateDescription = (text: string, maxLength: number): string => {
-  if (text.length <= maxLength) return text;
+const getFileName = (filePath: string): string => {
+  const parts = filePath.split('/');
+  return parts[parts.length - 1] || filePath;
+};
 
-  const truncated = text.slice(0, maxLength);
+/**
+ * Extract the directory path from a file path
+ */
+const getDirectory = (filePath: string): string => {
+  const parts = filePath.split('/');
+  parts.pop();
+  return parts.join('/') || '';
+};
 
-  // Try sentence boundary (. ! ?)
-  const sentenceEnd = Math.max(
-    truncated.lastIndexOf('. '),
-    truncated.lastIndexOf('! '),
-    truncated.lastIndexOf('? '),
-  );
-  if (sentenceEnd > maxLength * 0.5) {
-    return truncated.slice(0, sentenceEnd + 1);
+/**
+ * Truncate content to max length, preserving word boundaries
+ */
+const truncateContent = (content: string, maxLength: number): string => {
+  if (content.length <= maxLength) {
+    return content;
   }
 
-  // Try word boundary
+  // Find last space before maxLength to avoid cutting words
+  const truncated = content.slice(0, maxLength);
   const lastSpace = truncated.lastIndexOf(' ');
-  if (lastSpace > maxLength * 0.5) {
-    return truncated.slice(0, lastSpace);
+
+  if (lastSpace > maxLength * 0.8) {
+    return truncated.slice(0, lastSpace) + '...';
   }
 
-  return truncated;
+  return truncated + '...';
 };
 
 /**
  * Clean code content for embedding
+ * Removes excessive whitespace while preserving structure
  */
 const cleanContent = (content: string): string => {
-  return content
-    .replace(/\r\n/g, '\n')
-    .replace(/\n{3,}/g, '\n\n')
-    .split('\n')
-    .map((line) => line.trimEnd())
-    .join('\n')
-    .trim();
+  return (
+    content
+      // Normalize line endings
+      .replace(/\r\n/g, '\n')
+      // Remove excessive blank lines (more than 2)
+      .replace(/\n{3,}/g, '\n\n')
+      // Trim each line
+      .split('\n')
+      .map((line) => line.trimEnd())
+      .join('\n')
+      .trim()
+  );
 };
 
 /**
- * Build metadata header for a node
+ * Generate embedding text for a Function node
  */
-const buildMetadataHeader = (node: EmbeddableNode, config: Partial<EmbeddingConfig>): string => {
-  const parts: string[] = [];
+const generateFunctionText = (node: EmbeddableNode, maxSnippetLength: number): string => {
+  const parts: string[] = [`Function: ${node.name}`, `File: ${getFileName(node.filePath)}`];
 
-  // Label + name
-  parts.push(`${node.label}: ${node.name}`);
-
-  // Repo name
-  if (node.repoName) {
-    parts.push(`Repo: ${node.repoName}`);
+  const dir = getDirectory(node.filePath);
+  if (dir) {
+    parts.push(`Directory: ${dir}`);
   }
 
-  // Server name (optional)
-  if (node.serverName) {
-    parts.push(`Server: ${node.serverName}`);
-  }
-
-  // Full file path
-  parts.push(`Path: ${node.filePath}`);
-
-  // Export status
-  if (node.isExported !== undefined) {
-    parts.push(`Export: ${node.isExported}`);
-  }
-
-  // Description (truncated)
-  if (node.description) {
-    const maxLen = config.maxDescriptionLength ?? DEFAULT_EMBEDDING_CONFIG.maxDescriptionLength;
-    const truncated = truncateDescription(node.description, maxLen);
-    if (truncated) {
-      parts.push(truncated);
-    }
+  if (node.content) {
+    const cleanedContent = cleanContent(node.content);
+    const snippet = truncateContent(cleanedContent, maxSnippetLength);
+    parts.push('', snippet);
   }
 
   return parts.join('\n');
 };
 
-const generateCodeBodyText = (
-  node: EmbeddableNode,
-  codeBody: string,
-  config: Partial<EmbeddingConfig>,
-): string => {
-  const header = buildMetadataHeader(node, config);
-  const cleaned = cleanContent(codeBody);
-  return `${header}\n\n${cleaned}`;
-};
-
 /**
- * Generate embedding text for Class nodes
- * Signature + properties + method name list only (no method bodies)
- * Method/field names come from AST extractors via node.methodNames/node.fieldNames.
+ * Generate embedding text for a Class node
  */
-const generateClassText = (
-  node: EmbeddableNode,
-  codeBody: string,
-  config: Partial<EmbeddingConfig>,
-): string => {
-  return generateStructuralTypeText(node, codeBody, config);
-};
+const generateClassText = (node: EmbeddableNode, maxSnippetLength: number): string => {
+  const parts: string[] = [`Class: ${node.name}`, `File: ${getFileName(node.filePath)}`];
 
-const generateStructuralTypeText = (
-  node: EmbeddableNode,
-  codeBody: string,
-  config: Partial<EmbeddingConfig>,
-): string => {
-  const header = buildMetadataHeader(node, config);
-  const parts: string[] = [header];
-
-  if (node.methodNames?.length) {
-    parts.push(`Methods: ${node.methodNames.join(', ')}`);
-  }
-  if (node.fieldNames?.length) {
-    parts.push(`Properties: ${node.fieldNames.join(', ')}`);
+  const dir = getDirectory(node.filePath);
+  if (dir) {
+    parts.push(`Directory: ${dir}`);
   }
 
-  const declarationOnly = extractDeclarationOnly(cleanContent(node.content));
-  if (declarationOnly) {
-    parts.push('', declarationOnly);
-  }
-
-  const cleanedChunk = cleanContent(codeBody);
-  if (cleanedChunk && cleanedChunk !== cleanContent(node.content)) {
-    parts.push('', cleanedChunk);
+  if (node.content) {
+    const cleanedContent = cleanContent(node.content);
+    const snippet = truncateContent(cleanedContent, maxSnippetLength);
+    parts.push('', snippet);
   }
 
   return parts.join('\n');
 };
 
-const DECL_START_RE =
-  /^(?:(?:export|pub|data|abstract)\s+)*(?:type\s+\w+\s+struct|(?:class|struct|enum|interface)\s)/;
-
 /**
- * Extract class/interface/struct declaration lines, skipping method bodies.
- * - Brace-based languages: detects method signatures (lines with `(` and `{`)
- *   and skips until depth returns to class body level.
- * - Non-brace languages (Python/Ruby): returns empty string (patterns handle extraction).
+ * Generate embedding text for a Method node
  */
-export const extractDeclarationOnly = (content: string): string => {
-  const lines = content.split('\n');
-  const declLines: string[] = [];
-  let depth = 0;
-  let started = false;
-  let classDepth = 0;
-  let skipDepth = 0;
+const generateMethodText = (node: EmbeddableNode, maxSnippetLength: number): string => {
+  const parts: string[] = [`Method: ${node.name}`, `File: ${getFileName(node.filePath)}`];
 
-  for (const [idx, line] of lines.entries()) {
-    const trimmed = line.trim();
-
-    if (!started) {
-      if (DECL_START_RE.test(trimmed)) {
-        // Non-brace language check: current line or next 3 lines must have `{`
-        const nextLines = lines.slice(idx + 1, idx + 4);
-        if (!trimmed.includes('{') && !nextLines.some((l) => l.includes('{'))) {
-          return '';
-        }
-        started = true;
-        declLines.push(trimmed);
-        for (const ch of trimmed) {
-          if (ch === '{') depth++;
-          else if (ch === '}') depth--;
-        }
-        if (depth > 0) classDepth = depth;
-      }
-      continue;
-    }
-
-    // Always update depth (even when skipping)
-    const opens = (trimmed.match(/{/g) || []).length;
-    const closes = (trimmed.match(/}/g) || []).length;
-    const prevDepth = depth;
-    depth += opens - closes;
-
-    if (skipDepth > 0) {
-      if (depth <= classDepth) {
-        skipDepth = 0;
-        // Closing brace of class
-        if (depth <= 0) {
-          declLines.push(trimmed);
-          break;
-        }
-      }
-      continue;
-    }
-
-    // Detect method signature: line has both `(` and `{` and goes deeper than class body
-    const hasParens = trimmed.includes('(');
-    const hasOpenBrace = opens > 0;
-    if (hasParens && hasOpenBrace && prevDepth + opens > classDepth) {
-      if (opens === closes && trimmed.endsWith(';')) {
-        // Property with function/object initializer like `config = { timeout: 5000 };` — keep
-        declLines.push(trimmed);
-      }
-      // else: single-line or multi-line method — skip entirely
-      if (opens !== closes) {
-        skipDepth = classDepth;
-      }
-      continue;
-    }
-
-    declLines.push(trimmed);
-
-    if (depth <= 0 && declLines.length > 1) break;
+  const dir = getDirectory(node.filePath);
+  if (dir) {
+    parts.push(`Directory: ${dir}`);
   }
 
-  return declLines.join('\n').trim();
+  if (node.content) {
+    const cleanedContent = cleanContent(node.content);
+    const snippet = truncateContent(cleanedContent, maxSnippetLength);
+    parts.push('', snippet);
+  }
+
+  return parts.join('\n');
+};
+
+/**
+ * Generate embedding text for an Interface node
+ */
+const generateInterfaceText = (node: EmbeddableNode, maxSnippetLength: number): string => {
+  const parts: string[] = [`Interface: ${node.name}`, `File: ${getFileName(node.filePath)}`];
+
+  const dir = getDirectory(node.filePath);
+  if (dir) {
+    parts.push(`Directory: ${dir}`);
+  }
+
+  if (node.content) {
+    const cleanedContent = cleanContent(node.content);
+    const snippet = truncateContent(cleanedContent, maxSnippetLength);
+    parts.push('', snippet);
+  }
+
+  return parts.join('\n');
+};
+
+/**
+ * Generate embedding text for a File node
+ * Uses file name and first N characters of content
+ */
+const generateFileText = (node: EmbeddableNode, maxSnippetLength: number): string => {
+  const parts: string[] = [`File: ${node.name}`, `Path: ${node.filePath}`];
+
+  if (node.content) {
+    const cleanedContent = cleanContent(node.content);
+    // For files, use a shorter snippet since they can be very long
+    const snippet = truncateContent(cleanedContent, Math.min(maxSnippetLength, 300));
+    parts.push('', snippet);
+  }
+
+  return parts.join('\n');
 };
 
 /**
  * Generate embedding text for any embeddable node
  * Dispatches to the appropriate generator based on node label
+ *
+ * @param node - The node to generate text for
+ * @param config - Optional configuration for max snippet length
+ * @returns Text suitable for embedding
  */
 export const generateEmbeddingText = (
   node: EmbeddableNode,
-  codeBody: string,
   config: Partial<EmbeddingConfig> = {},
 ): string => {
-  if (isShortLabel(node.label)) {
-    const header = buildMetadataHeader(node, config);
-    const cleaned = cleanContent(node.content);
-    return `${header}\n\n${cleaned}`;
-  }
+  const maxSnippetLength = config.maxSnippetLength ?? DEFAULT_EMBEDDING_CONFIG.maxSnippetLength;
 
-  if (node.label === 'Class') {
-    return generateClassText(node, codeBody, config);
+  switch (node.label) {
+    case 'Function':
+      return generateFunctionText(node, maxSnippetLength);
+    case 'Class':
+      return generateClassText(node, maxSnippetLength);
+    case 'Method':
+      return generateMethodText(node, maxSnippetLength);
+    case 'Interface':
+      return generateInterfaceText(node, maxSnippetLength);
+    case 'File':
+      return generateFileText(node, maxSnippetLength);
+    default:
+      // Fallback for any other embeddable type
+      return `${node.label}: ${node.name}\nPath: ${node.filePath}`;
   }
-
-  if (node.label === 'Interface') {
-    return generateStructuralTypeText(node, codeBody, config);
-  }
-
-  return generateCodeBodyText(node, codeBody, config);
 };
 
 /**
- * Export truncation helper for testing
+ * Generate embedding texts for a batch of nodes
+ *
+ * @param nodes - Array of nodes to generate text for
+ * @param config - Optional configuration
+ * @returns Array of texts in the same order as input nodes
  */
-export { truncateDescription };
+export const generateBatchEmbeddingTexts = (
+  nodes: EmbeddableNode[],
+  config: Partial<EmbeddingConfig> = {},
+): string[] => {
+  return nodes.map((node) => generateEmbeddingText(node, config));
+};

gitnexus/src/core/embeddings/types.ts

@@ -5,40 +5,10 @@
  */
 
 /**
- * Node labels that need chunking (have code body, potentially long)
+ * Node labels that should be embedded for semantic search
+ * These are code elements that benefit from semantic matching
  */
-export const CHUNKABLE_LABELS = [
-  'Function',
-  'Method',
-  'Constructor',
-  'Class',
-  'Interface',
-  'Struct',
-  'Enum',
-  'Trait',
-  'Impl',
-  'Macro',
-  'Namespace',
-] as const;
-
-/**
- * Node labels that are short (no chunking needed, embed directly)
- */
-export const SHORT_LABELS = [
-  'TypeAlias',
-  'Typedef',
-  'Const',
-  'Property',
-  'Record',
-  'Union',
-  'Static',
-  'Variable',
-] as const;
-
-/**
- * All embeddable labels (union of CHUNKABLE + SHORT)
- */
-export const EMBEDDABLE_LABELS = [...CHUNKABLE_LABELS, ...SHORT_LABELS] as const;
+export const EMBEDDABLE_LABELS = ['Function', 'Class', 'Method', 'Interface', 'File'] as const;
 
 export type EmbeddableLabel = (typeof EMBEDDABLE_LABELS)[number];
 
@@ -48,39 +18,6 @@ export type EmbeddableLabel = (typeof EMBEDDABLE_LABELS)[number];
 export const isEmbeddableLabel = (label: string): label is EmbeddableLabel =>
   EMBEDDABLE_LABELS.includes(label as EmbeddableLabel);
 
-/**
- * Check if a label needs chunking
- */
-export const isChunkableLabel = (label: string): boolean =>
-  (CHUNKABLE_LABELS as readonly string[]).includes(label);
-
-/**
- * Check if a label is a short type (no chunking)
- */
-export const isShortLabel = (label: string): boolean =>
-  (SHORT_LABELS as readonly string[]).includes(label);
-
-/**
- * Node labels that have structural names (methods/fields) extractable via AST
- */
-export const STRUCTURAL_LABELS: ReadonlySet<string> = new Set([
-  'Class',
-  'Struct',
-  'Interface',
-  'Enum',
-]);
-
-/**
- * Node labels that have isExported column in their schema
- */
-export const LABELS_WITH_EXPORTED = new Set([
-  'Function',
-  'Class',
-  'Interface',
-  'Method',
-  'CodeElement',
-]) as ReadonlySet<string>;
-
 /**
  * Embedding pipeline phases
  */
@@ -120,12 +57,6 @@ export interface EmbeddingConfig {
   device: 'auto' | 'dml' | 'cuda' | 'cpu' | 'wasm';
   /** Maximum characters of code snippet to include */
   maxSnippetLength: number;
-  /** Maximum code chunk size in characters (for chunking long code) */
-  chunkSize: number;
-  /** Overlap between chunks in characters */
-  overlap: number;
-  /** Maximum description length in characters */
-  maxDescriptionLength: number;
 }
 
 /**
@@ -139,9 +70,6 @@ export const DEFAULT_EMBEDDING_CONFIG: EmbeddingConfig = {
   dimensions: 384,
   device: 'auto',
   maxSnippetLength: 500,
-  chunkSize: 1200,
-  overlap: 120,
-  maxDescriptionLength: 150,
 };
 
 /**
@@ -168,34 +96,6 @@ export interface EmbeddableNode {
   content: string;
   startLine?: number;
   endLine?: number;
-  isExported?: boolean;
-  description?: string;
-  parameterCount?: number;
-  returnType?: string;
-  repoName?: string;
-  serverName?: string;
-  methodNames?: string[];
-  fieldNames?: string[];
-}
-
-/**
- * Cached embedding entry restored from LadybugDB before a graph rebuild
- */
-export interface CachedEmbedding {
-  nodeId: string;
-  chunkIndex: number;
-  startLine: number;
-  endLine: number;
-  embedding: number[];
-  contentHash?: string;
-}
-
-/**
- * Context info for embedding pipeline (repo/server metadata enrichment)
- */
-export interface EmbeddingContext {
-  repoName?: string;
-  serverName?: string;
 }
 
 /**
@@ -208,75 +108,3 @@ export interface ModelProgress {
   loaded?: number;
   total?: number;
 }
-
-export interface ChunkSearchRow {
-  nodeId: string;
-  chunkIndex: number;
-  startLine: number;
-  endLine: number;
-  distance: number;
-}
-
-export interface BestChunkMatch {
-  chunkIndex: number;
-  startLine: number;
-  endLine: number;
-  distance: number;
-}
-
-/**
- * Deduplicate vector search chunk results by nodeId,
- * keeping the chunk with smallest distance for each node.
- */
-export const dedupBestChunks = (
-  rows: ChunkSearchRow[],
-  limit?: number,
-): Map<string, BestChunkMatch> => {
-  const best = new Map<string, BestChunkMatch>();
-  for (const row of rows) {
-    const existing = best.get(row.nodeId);
-    if (!existing || row.distance < existing.distance) {
-      best.set(row.nodeId, {
-        chunkIndex: row.chunkIndex,
-        startLine: row.startLine,
-        endLine: row.endLine,
-        distance: row.distance,
-      });
-    }
-    if (limit !== undefined && best.size >= limit) break;
-  }
-  return best;
-};
-
-const DEFAULT_FETCH_MULTIPLIER = 4;
-const DEFAULT_FETCH_BUFFER = 8;
-const DEFAULT_MAX_FETCH = 200;
-
-/**
- * Fetch vector-search chunks until we have enough unique nodeIds
- * or can tell the result set is exhausted.
- */
-export const collectBestChunks = async (
-  limit: number,
-  fetchRows: (fetchLimit: number) => Promise<ChunkSearchRow[]>,
-  maxFetch: number = DEFAULT_MAX_FETCH,
-): Promise<Map<string, BestChunkMatch>> => {
-  if (limit <= 0) return new Map();
-
-  let fetchLimit = Math.max(limit * DEFAULT_FETCH_MULTIPLIER, limit + DEFAULT_FETCH_BUFFER);
-  let previousFetchLimit = 0;
-
-  while (fetchLimit > previousFetchLimit) {
-    const rows = await fetchRows(fetchLimit);
-    const bestChunks = dedupBestChunks(rows, limit);
-
-    if (bestChunks.size >= limit || rows.length < fetchLimit) {
-      return bestChunks;
-    }
-
-    previousFetchLimit = fetchLimit;
-    fetchLimit = fetchLimit >= maxFetch ? fetchLimit * 2 : Math.min(maxFetch, fetchLimit * 2);
-  }
-
-  return new Map();
-};

gitnexus/src/core/group/extractors/http-patterns/node.ts

@@ -17,9 +17,6 @@ import type { HttpDetection, HttpLanguagePlugin } from './types.js';
  *   - Express `router.get(...)` / `app.post(...)` providers
  *   - `fetch(url)` / `fetch(url, { method: 'POST' })` consumers
  *   - `axios.get(url)` / `axios.delete(url)` consumers
- *   - `axios({ method, url })` object-form consumers
- *   - jQuery `$.get(url)` / `$.post(url, ...)` shorthand consumers
- *   - jQuery `$.ajax({ url, method | type })` consumers
  *
  * Because the JavaScript and TypeScript tree-sitter grammars share
  * node type names for every construct we query, pattern sources are
@@ -106,48 +103,6 @@ const AXIOS_SPEC: PatternSpec<Record<string, never>> = {
   `,
 };
 
-// ─── Consumer: jQuery shorthand $.get(url) / $.post(url, ...) ────────
-// `$` is a valid JS identifier, so tree-sitter parses `$.get(...)` as a
-// call_expression whose function is a member_expression on identifier `$`.
-const JQUERY_SHORTHAND_SPEC: PatternSpec<Record<string, never>> = {
-  meta: {},
-  query: `
-    (call_expression
-      function: (member_expression
-        object: (identifier) @obj (#eq? @obj "$")
-        property: (property_identifier) @http_method (#match? @http_method "^(get|post)$"))
-      arguments: (arguments . [(string) (template_string)] @path))
-  `,
-};
-
-// ─── Consumer: jQuery $.ajax({ url, method|type }) ───────────────────
-// The query captures the options object only; key/value pairs are read
-// programmatically via `readStringProp` below, which tolerates any key
-// order and accepts either `method:` or `type:` (jQuery supports both).
-const JQUERY_AJAX_SPEC: PatternSpec<Record<string, never>> = {
-  meta: {},
-  query: `
-    (call_expression
-      function: (member_expression
-        object: (identifier) @obj (#eq? @obj "$")
-        property: (property_identifier) @fn (#eq? @fn "ajax"))
-      arguments: (arguments (object) @options))
-  `,
-};
-
-// ─── Consumer: axios({ method, url }) object form ────────────────────
-// Distinct from AXIOS_SPEC above because the call target is an identifier
-// (`axios`) rather than a member expression (`axios.get`). As with the
-// jQuery ajax form, option keys are resolved programmatically.
-const AXIOS_OBJECT_SPEC: PatternSpec<Record<string, never>> = {
-  meta: {},
-  query: `
-    (call_expression
-      function: (identifier) @fn (#eq? @fn "axios")
-      arguments: (arguments (object) @options))
-  `,
-};
-
 interface NodePatternBundle {
   controller: CompiledPatterns<Record<string, never>>;
   methodDecorator: CompiledPatterns<Record<string, never>>;
@@ -155,9 +110,6 @@ interface NodePatternBundle {
   fetchNoOptions: CompiledPatterns<Record<string, never>>;
   fetchWithOptions: CompiledPatterns<Record<string, never>>;
   axios: CompiledPatterns<Record<string, never>>;
-  jqueryShorthand: CompiledPatterns<Record<string, never>>;
-  jqueryAjax: CompiledPatterns<Record<string, never>>;
-  axiosObject: CompiledPatterns<Record<string, never>>;
 }
 
 function compileBundle(language: unknown, name: string): NodePatternBundle {
@@ -174,9 +126,6 @@ function compileBundle(language: unknown, name: string): NodePatternBundle {
     fetchNoOptions: mk(FETCH_NO_OPTIONS_SPEC, 'fetch-no-options'),
     fetchWithOptions: mk(FETCH_WITH_OPTIONS_SPEC, 'fetch-with-options'),
     axios: mk(AXIOS_SPEC, 'axios'),
-    jqueryShorthand: mk(JQUERY_SHORTHAND_SPEC, 'jquery-shorthand'),
-    jqueryAjax: mk(JQUERY_AJAX_SPEC, 'jquery-ajax'),
-    axiosObject: mk(AXIOS_OBJECT_SPEC, 'axios-object'),
   };
 }
 
@@ -211,28 +160,6 @@ function joinPath(prefix: string, sub: string): string {
   return `/${cleanPrefix}/${cleanSub}`;
 }
 
-/**
- * Walk `pair` children of an `object` literal and return the unquoted
- * string/template_string value for the first pair whose key matches one
- * of `keyNames`. Returns null when no matching pair is present or the
- * value is not a string literal. Used by the jQuery ajax / axios object
- * consumers to resolve `url` / `method` / `type` keys in any order.
- */
-function readStringProp(objectNode: Parser.SyntaxNode, keyNames: readonly string[]): string | null {
-  for (let i = 0; i < objectNode.namedChildCount; i++) {
-    const pair = objectNode.namedChild(i);
-    if (!pair || pair.type !== 'pair') continue;
-    const keyNode = pair.childForFieldName('key');
-    const valueNode = pair.childForFieldName('value');
-    if (!keyNode || !valueNode) continue;
-    if (!keyNames.includes(keyNode.text)) continue;
-    if (valueNode.type !== 'string' && valueNode.type !== 'template_string') continue;
-    const lit = unquoteLiteral(valueNode.text);
-    if (lit !== null) return lit;
-  }
-  return null;
-}
-
 /**
  * For a standalone `decorator` node (child of class_body / program),
  * find the related `class_declaration` node that it decorates. In
@@ -424,62 +351,6 @@ function scanBundle(bundle: NodePatternBundle, tree: Parser.Tree): HttpDetection
     });
   }
 
-  // Consumer: jQuery shorthand $.get(url) / $.post(url, ...)
-  for (const match of runCompiledPatterns(bundle.jqueryShorthand, tree)) {
-    const methodNode = match.captures.http_method;
-    const pathNode = match.captures.path;
-    if (!methodNode || !pathNode) continue;
-    const path = unquoteLiteral(pathNode.text);
-    if (path === null) continue;
-    out.push({
-      role: 'consumer',
-      framework: 'jquery',
-      method: methodNode.text.toUpperCase(),
-      path,
-      name: null,
-      confidence: 0.7,
-    });
-  }
-
-  // Consumer: jQuery $.ajax({ url, method|type }). jQuery accepts either
-  // `method:` or `type:`; both default to GET when absent.
-  for (const match of runCompiledPatterns(bundle.jqueryAjax, tree)) {
-    const optionsNode = match.captures.options;
-    if (!optionsNode) continue;
-    const path = readStringProp(optionsNode, ['url']);
-    if (path === null) continue;
-    const rawMethod = readStringProp(optionsNode, ['method', 'type']);
-    const method = (rawMethod ?? 'GET').toUpperCase();
-    out.push({
-      role: 'consumer',
-      framework: 'jquery',
-      method,
-      path,
-      name: null,
-      confidence: 0.7,
-    });
-  }
-
-  // Consumer: axios({ method, url }) object form. Structurally distinct
-  // from axios.<verb>(url) (identifier vs member_expression call), so no
-  // dedup against the member-form loop above is required.
-  for (const match of runCompiledPatterns(bundle.axiosObject, tree)) {
-    const optionsNode = match.captures.options;
-    if (!optionsNode) continue;
-    const path = readStringProp(optionsNode, ['url']);
-    if (path === null) continue;
-    const rawMethod = readStringProp(optionsNode, ['method']);
-    const method = (rawMethod ?? 'GET').toUpperCase();
-    out.push({
-      role: 'consumer',
-      framework: 'axios',
-      method,
-      path,
-      name: null,
-      confidence: 0.7,
-    });
-  }
-
   return out;
 }
 

gitnexus/src/core/group/extractors/manifest-extractor.ts

@@ -79,50 +79,17 @@ export class ManifestExtractor {
     links: GroupManifestLink[],
     dbExecutors?: Map<string, CypherExecutor>,
   ): Promise<ManifestExtractResult> {
-    // Resolve all (repo, link) pairs in parallel. The previous sequential
-    // await-per-link produced 2N round-trips; parallel resolution uses the
-    // per-repo executor pool directly and scales linearly with manifest size.
-    //
-    // Memoization: a manifest can list the same contract multiple times
-    // (e.g. a consumer and provider declaration, or cross-referenced groups).
-    // Key on (repo, type, contract) — the canonical input to the Cypher
-    // query — so duplicate links resolve to one DB hit.
-    type ResolvedSymbol = { filePath: string; name: string; uid: string } | null;
-    const resolveCache = new Map<string, Promise<ResolvedSymbol>>();
-    const resolveOnce = (repo: string, link: GroupManifestLink): Promise<ResolvedSymbol> => {
-      const key = `${repo}\u0000${link.type}\u0000${link.contract}`;
-      let pending = resolveCache.get(key);
-      if (!pending) {
-        pending = this.resolveSymbol(repo, link, dbExecutors);
-        resolveCache.set(key, pending);
-      }
-      return pending;
-    };
-
-    const perLink = await Promise.all(
-      links.map(async (link) => {
-        const contractId = this.buildContractId(link.type, link.contract);
-        const providerRepo = link.role === 'provider' ? link.from : link.to;
-        const consumerRepo = link.role === 'provider' ? link.to : link.from;
-        const [providerSymbol, consumerSymbol] = await Promise.all([
-          resolveOnce(providerRepo, link),
-          resolveOnce(consumerRepo, link),
-        ]);
-        return { link, contractId, providerRepo, consumerRepo, providerSymbol, consumerSymbol };
-      }),
-    );
-
     const contracts: StoredContract[] = [];
     const crossLinks: CrossLink[] = [];
 
-    for (const {
-      link,
-      contractId,
-      providerRepo,
-      consumerRepo,
-      providerSymbol,
-      consumerSymbol,
-    } of perLink) {
+    for (const link of links) {
+      const contractId = this.buildContractId(link.type, link.contract);
+
+      const providerRepo = link.role === 'provider' ? link.from : link.to;
+      const consumerRepo = link.role === 'provider' ? link.to : link.from;
+
+      const providerSymbol = await this.resolveSymbol(providerRepo, link, dbExecutors);
+      const consumerSymbol = await this.resolveSymbol(consumerRepo, link, dbExecutors);
       const providerRef = providerSymbol || { filePath: '', name: link.contract };
       const consumerRef = consumerSymbol || { filePath: '', name: link.contract };
       // When the resolver finds a real graph symbol we keep its uid, otherwise

gitnexus/src/core/group/sync.ts

@@ -7,7 +7,6 @@ import type { GroupConfig, RepoHandle, RepoSnapshot, StoredContract, CrossLink }
 import { HttpRouteExtractor } from './extractors/http-route-extractor.js';
 import { GrpcExtractor } from './extractors/grpc-extractor.js';
 import { TopicExtractor } from './extractors/topic-extractor.js';
-import { ManifestExtractor } from './extractors/manifest-extractor.js';
 import { runExactMatch } from './matching.js';
 import { detectServiceBoundaries, assignService } from './service-boundary-detector.js';
 import type { CypherExecutor } from './contract-extractor.js';
@@ -61,28 +60,10 @@ function defaultResolveHandle(allEntries: RegistryEntry[]) {
   };
 }
 
-/**
- * Dedupe cross-links that point from the same consumer endpoint to the same
- * provider endpoint for the same contract. Preserves first-seen order so the
- * caller controls precedence (e.g., pass manifest links first).
- */
-function dedupeCrossLinks(links: CrossLink[]): CrossLink[] {
-  const seen = new Set<string>();
-  const out: CrossLink[] = [];
-  for (const link of links) {
-    const key = `${link.from.repo}::${link.from.symbolUid}|${link.to.repo}::${link.to.symbolUid}|${link.type}|${link.contractId}`;
-    if (seen.has(key)) continue;
-    seen.add(key);
-    out.push(link);
-  }
-  return out;
-}
-
 export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promise<SyncResult> {
   const missingRepos: string[] = [];
   const repoSnapshots: Record<string, RepoSnapshot> = {};
   let autoContracts: StoredContract[] = [];
-  let manifestCrossLinks: CrossLink[] = [];
   let dbExecutors: Map<string, CypherExecutor> | undefined;
 
   const eo = opts?.extractorOverride;
@@ -177,44 +158,8 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
     }
   }
 
-  // Process manifest links declared in group.yaml.
-  // ManifestExtractor is fully implemented but was never wired into this
-  // pipeline — config.links were parsed and validated but silently dropped.
-  // Placed after the DB try/finally: resolveSymbol falls back to synthetic
-  // UIDs when dbExecutors is undefined or a pool is closed, so cross-links
-  // are always generated regardless of whether real DB executors are available.
-  if (config.links.length > 0) {
-    // Warn about dangling links that reference repos not declared in config.repos.
-    // They still generate cross-links via synthetic UIDs (determinism is preserved),
-    // but the operator probably meant something that now silently does nothing useful.
-    const knownRepos = new Set(Object.keys(config.repos));
-    for (const link of config.links) {
-      const dangling = [link.from, link.to].filter((r) => !knownRepos.has(r));
-      if (dangling.length > 0) {
-        console.warn(
-          `[group/sync] manifest link ${link.type}:${link.contract} references repos not in config.repos: ${dangling.join(', ')} — cross-links will use synthetic UIDs`,
-        );
-      }
-    }
-
-    const manifestEx = new ManifestExtractor();
-    const manifestResult = await manifestEx.extractFromManifest(config.links, dbExecutors);
-    autoContracts.push(...manifestResult.contracts);
-    manifestCrossLinks = manifestResult.crossLinks;
-    if (opts?.verbose) {
-      console.log(
-        `  manifest: ${manifestCrossLinks.length} cross-links from ${config.links.length} declared links`,
-      );
-    }
-  }
-
   const { matched, unmatched } = runExactMatch(autoContracts);
-
-  // Dedupe cross-links. Manifest contracts participate in runExactMatch, so a
-  // manifest-declared link can also emit a matchType:'exact' CrossLink with the
-  // same endpoints. Prefer the manifest version — it reflects operator intent
-  // and carries matchType:'manifest' which downstream consumers may rely on.
-  const crossLinks = dedupeCrossLinks([...manifestCrossLinks, ...matched]);
+  const crossLinks: CrossLink[] = matched;
   const allContracts: StoredContract[] = autoContracts;
 
   const registry: ContractRegistry = {

gitnexus/src/core/ingestion/call-extractors/configs/c-cpp.ts

@@ -1,12 +0,0 @@
-// gitnexus/src/core/ingestion/call-extractors/configs/c-cpp.ts
-
-import { SupportedLanguages } from 'gitnexus-shared';
-import type { CallExtractionConfig } from '../../call-types.js';
-
-export const cCallConfig: CallExtractionConfig = {
-  language: SupportedLanguages.C,
-};
-
-export const cppCallConfig: CallExtractionConfig = {
-  language: SupportedLanguages.CPlusPlus,
-};

gitnexus/src/core/ingestion/call-extractors/configs/csharp.ts

@@ -1,9 +0,0 @@
-// gitnexus/src/core/ingestion/call-extractors/configs/csharp.ts
-
-import { SupportedLanguages } from 'gitnexus-shared';
-import type { CallExtractionConfig } from '../../call-types.js';
-
-export const csharpCallConfig: CallExtractionConfig = {
-  language: SupportedLanguages.CSharp,
-  typeAsReceiverHeuristic: true,
-};

gitnexus/src/core/ingestion/call-extractors/configs/dart.ts

@@ -1,8 +0,0 @@
-// gitnexus/src/core/ingestion/call-extractors/configs/dart.ts
-
-import { SupportedLanguages } from 'gitnexus-shared';
-import type { CallExtractionConfig } from '../../call-types.js';
-
-export const dartCallConfig: CallExtractionConfig = {
-  language: SupportedLanguages.Dart,
-};