fix(cobol): single-quote CALL/COPY, sequence number stripping, PERFORM keyword filtering

Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/afed41bd-98b4-48e8-a9e5-ebf0b97deaa8
Initial plan: review COBOL processor completeness
2026-03-24 17:10:16 +00:00 · 2026-03-24 16:59:25 +00:00 · 2026-03-24 16:48:12 +00:00 · 2026-03-24 16:10:29 +00:00 · 2026-03-24 15:41:00 +00:00 · 2026-03-24 15:20:26 +00:00
718 changed files with 33437 additions and 78721 deletions
@@ -1,21 +0,0 @@
---
-alwaysApply: true
---
-
-# GitNexus — Cursor project rules
-
-Last reviewed: 2026-03-24
-
-Canonical agent instructions: **[AGENTS.md](../AGENTS.md)** (GitNexus MCP rules, monorepo commands, Cursor Cloud notes). **[CLAUDE.md](../CLAUDE.md)** adds Claude Code-specific notes and points back to AGENTS.md for GitNexus.
-
-## Non-negotiables (always apply)
-
- NEVER edit a function/class/method without running `gitnexus_impact` first.
- NEVER rename symbols with find-and-replace — use `gitnexus_rename`.
- NEVER commit without running `gitnexus_detect_changes()`.
- NEVER ignore HIGH/CRITICAL risk warnings from impact analysis.
- NEVER run `npx gitnexus analyze` without `--embeddings` if `.gitnexus/meta.json` shows stored embeddings.
-
-Full rules: **[AGENTS.md](../AGENTS.md)** (`gitnexus:start` block, Cursor Cloud section).
-
-**Rule architecture:** Prefer this file plus optional `.cursor/rules/*.mdc` globs (YAML `globs` in frontmatter). Legacy `.cursorrules` is deprecated; content lives here.
@@ -1,12 +0,0 @@
---
-globs:
-  - "gitnexus/**"
-  - "gitnexus-web/**"
---
-
-# GitNexus build/test quick refs
-
- CLI (`gitnexus/`): `npm test`; `npm run test:integration`; `npx tsc --noEmit`.
- Web (`gitnexus-web/`): `npm test`; `npm run dev`; `npx tsc -b --noEmit`; `E2E=1 npx playwright test` (needs servers).
- `npm install` in `gitnexus/` runs `prepare` (tsc build) and `postinstall` (tree-sitter patches); needs `python3`, `make`, `g++`.
- LadybugDB locking tests may fail in containerized environments because of `/tmp` file locks (known issue, not a code bug).
@@ -1,14 +0,0 @@
---
-globs:
-  - "eval/**"
---
-
-# GitNexus eval harness (Python)
-
- **Run tests**: `cd eval && uv run pytest tests/`
- **Run with coverage**: `cd eval && uv run coverage run -m pytest tests/ && uv run coverage report`
- **Lint**: `cd eval && uv run ruff check .`
- **Run eval**: `cd eval && uv run python run_eval.py --config configs/<config>.yaml`
- Shared constants live in `eval/constants.py`; tool specs in `eval/tool_registry.py`.
- Error logging uses `utils/errors.py` — set `GITNEXUS_EVAL_DEBUG=1` for full tracebacks.
- Property-based tests use Hypothesis (`eval/tests/test_property_based.py`).
@@ -1,5 +1,5 @@
-# Deprecated for Cursor Agent Mode
+# AI Agent Rules

-Use **`.cursor/index.mdc`** (`alwaysApply: true`) for project rules. See [AGENTS.md](AGENTS.md).
+Follow .gitnexus/RULES.md for all project context and coding guidelines.

-This file is kept only as a breadcrumb for older workflows.
+This project uses GitNexus MCP for code intelligence. See .gitnexus/RULES.md for available tools and best practices.
@@ -1,5 +0,0 @@
-# Prettier initial formatting (2026-03-28)
-afcc3d1523f99c77ff67c4fd1af12334660113f6
-
-# ESLint unused import removal (2026-03-28)
-1491826bc8da5436d3b1eb092d9274f2c9f028a7
@@ -1,2 +0,0 @@
-* text=auto eol=lf
-.husky/* text eol=lf
@@ -1,86 +0,0 @@
-name: Bug report
-description: Report unexpected behavior or a regression
-labels: [bug]
-body:
-  - type: markdown
-    attributes:
-      value: |
-        **Goal:** capture enough context to reproduce and fix the issue quickly.
-        Use **one issue per bug**; split unrelated problems.
-
-  - type: dropdown
-    id: area
-    attributes:
-      label: Area
-      description: Where does the problem show up?
-      options:
-        - gitnexus (CLI / core / indexing / MCP server)
-        - gitnexus-web (browser UI / WASM / workers)
-        - CI / GitHub Actions
-        - Documentation / developer experience
-        - Other
-    validations:
-      required: true
-
-  - type: textarea
-    id: summary
-    attributes:
-      label: Summary
-      description: One sentence — what went wrong?
-    validations:
-      required: true
-
-  - type: textarea
-    id: context
-    attributes:
-      label: Context
-      description: What were you trying to do? Any relevant links, PRs, or commits?
-    validations:
-      required: false
-
-  - type: textarea
-    id: expected
-    attributes:
-      label: Expected behavior
-    validations:
-      required: true
-
-  - type: textarea
-    id: actual
-    attributes:
-      label: Actual behavior
-    validations:
-      required: true
-
-  - type: textarea
-    id: reproduce
-    attributes:
-      label: Steps to reproduce
-      description: Ordered steps, sample repo or minimal case, commands run.
-      placeholder: |
-        1. …
-        2. …
-        3. …
-    validations:
-      required: true
-
-  - type: textarea
-    id: environment
-    attributes:
-      label: Environment
-      description: OS, Node version, browser (if web), GitNexus version or commit SHA.
-      placeholder: |
-        - OS:
-        - Node:
-        - Browser (if applicable):
-        - Commit / version:
-    validations:
-      required: false
-
-  - type: textarea
-    id: logs
-    attributes:
-      label: Logs / screenshots
-      description: Paste errors, stack traces, or attach screenshots (redact secrets).
-    validations:
-      required: false
@@ -1 +0,0 @@
-blank_issues_enabled: true
@@ -1,74 +0,0 @@
-name: Feature request
-description: Propose a new capability or improvement
-labels: [enhancement]
-body:
-  - type: markdown
-    attributes:
-      value: |
-        **Goal:** describe the problem and desired outcome so maintainers can size and prioritize.
-        Prefer **small, shippable** requests; split large ideas into phases.
-
-  - type: dropdown
-    id: area
-    attributes:
-      label: Area
-      description: Primary part of the monorepo this relates to.
-      options:
-        - gitnexus (CLI / core / indexing / MCP server)
-        - gitnexus-web (browser UI / WASM / workers)
-        - CI / release / packaging
-        - Documentation / developer experience
-        - Other
-    validations:
-      required: true
-
-  - type: textarea
-    id: problem
-    attributes:
-      label: Problem or opportunity
-      description: What pain point or gap exists today?
-    validations:
-      required: true
-
-  - type: textarea
-    id: proposal
-    attributes:
-      label: Proposed solution
-      description: What should happen instead? User-visible behavior, APIs, or UX.
-    validations:
-      required: true
-
-  - type: textarea
-    id: alternatives
-    attributes:
-      label: Alternatives considered
-      description: Other approaches you considered and why this one is preferred.
-    validations:
-      required: false
-
-  - type: textarea
-    id: acceptance
-    attributes:
-      label: Acceptance criteria
-      description: Testable conditions for “done” (bullets or checkboxes in prose).
-      placeholder: |
-        - When … then …
-        - Documentation / tests updated where appropriate
-    validations:
-      required: false
-
-  - type: textarea
-    id: constraints
-    attributes:
-      label: Constraints
-      description: Compatibility, performance, security, or “must not change” boundaries.
-    validations:
-      required: false
-
-  - type: checkboxes
-    id: willing
-    attributes:
-      label: Contribution
-      options:
-        - label: I am willing to open a PR for this (may need design discussion first).
-          required: false
@@ -1,52 +0,0 @@
-## Summary
-
-<!-- One or two sentences: what does this PR change? -->
-
-## Motivation / context
-
-<!-- Why is this change needed? Link issues, ADRs, or prior discussion. -->
-
-## Areas touched
-
-<!-- Check all that apply -->
-
- [ ] `gitnexus/` (CLI / core / MCP server)
- [ ] `gitnexus-web/` (Vite / React UI)
- [ ] `.github/` (workflows, actions)
- [ ] `eval/` or other tooling
- [ ] Docs / agent config only (`AGENTS.md`, `CLAUDE.md`, `.cursor/`, `llms.txt`, etc.)
-
-## Scope & constraints
-
-**In scope**
-
- <!-- bullets -->
-
-**Explicitly out of scope / not done here**
-
- <!-- bullets — prevents reviewers assuming missing work is an oversight -->
-
-## Implementation notes
-
-<!-- Optional: design choices, tradeoffs, follow-ups -->
-
-## Testing & verification
-
-<!-- What you ran; paste commands. Omit sections that do not apply. -->
-
- [ ] `cd gitnexus && npm test`
- [ ] `cd gitnexus && npm run test:integration` *(if core/indexing/MCP paths changed)*
- [ ] `cd gitnexus && npx tsc --noEmit`
- [ ] `cd gitnexus-web && npm test` *(if web changed)*
- [ ] `cd gitnexus-web && npx tsc -b --noEmit` *(if web changed)*
- [ ] Manual / Playwright E2E *(note environment — see `gitnexus-web/e2e/`)*
-
-## Risk & rollout
-
-<!-- Breaking changes, migrations, index refresh (`npx gitnexus analyze`), release notes -->
-
-## Checklist
-
- [ ] PR body meets repo minimum length (workflow may label short descriptions)
- [ ] If `AGENTS.md` / overlays changed: headers, scope block, and changelog updated per project conventions
- [ ] No secrets, tokens, or machine-specific paths committed
@@ -1,21 +0,0 @@
-name: Setup GitNexus Web
-description: Setup Node.js 20, build gitnexus-shared, install web dependencies
-
-runs:
-  using: composite
-  steps:
-    - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-      with:
-        node-version: 20
-        cache: npm
-        cache-dependency-path: gitnexus-web/package-lock.json
-
-    - name: Build gitnexus-shared
-      run: npm install && npm run build
-      shell: bash
-      working-directory: gitnexus-shared
-
-    - name: Install web dependencies
-      run: npm ci
-      shell: bash
-      working-directory: gitnexus-web
@@ -16,11 +16,6 @@ runs:
        cache: npm
        cache-dependency-path: gitnexus/package-lock.json

-    - name: Build gitnexus-shared
-      run: npm install && npm run build
-      shell: bash
-      working-directory: gitnexus-shared
-
    - name: Install dependencies
      run: npm ci
      shell: bash
@@ -35,7 +35,7 @@ changelog:
        - dependencies
    - title: "\U0001F4DD Other Changes"
      labels:
-        - '*'
+        - "*"
      exclude:
        labels:
          - dependencies
@@ -28,7 +28,15 @@ jobs:
    steps:
      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4

-      - uses: ./.github/actions/setup-gitnexus-web
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus-web/package-lock.json
+
+      - name: Install frontend dependencies
+        run: npm ci
+        working-directory: gitnexus-web

      - name: Install Playwright browsers
        run: npx playwright install --with-deps chromium
@@ -4,32 +4,6 @@ on:
  workflow_call:

 jobs:
-  format:
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-        with:
-          node-version: 20
-          cache: npm
-          cache-dependency-path: package-lock.json
-      - run: npm ci
-      - run: npx prettier --check .
-
-  lint:
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-        with:
-          node-version: 20
-          cache: npm
-          cache-dependency-path: package-lock.json
-      - run: npm ci
-      - run: npx eslint .
-
  typecheck:
    runs-on: ubuntu-latest
    timeout-minutes: 10
@@ -44,6 +18,12 @@ jobs:
    timeout-minutes: 10
    steps:
      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: ./.github/actions/setup-gitnexus-web
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus-web/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus-web
      - run: npx tsc -b --noEmit
        working-directory: gitnexus-web
@@ -6,12 +6,12 @@ name: CI Report

 on:
  workflow_run:
-    workflows: ['CI']
+    workflows: ["CI"]
    types: [completed]

 permissions:
-  actions: read # needed to list/download workflow run artifacts
-  contents: read # needed for sparse checkout of vitest.config.ts
+  actions: read        # needed to list/download workflow run artifacts
+  contents: read       # needed for sparse checkout of vitest.config.ts
  pull-requests: write # needed to post sticky PR comment

 jobs:
@@ -28,7 +28,6 @@ jobs:
          --coverage.reportOnFailure=true
        working-directory: gitnexus

-      # gitnexus-shared already built by setup-gitnexus action above
      - name: Install gitnexus-web dependencies
        run: npm ci
        working-directory: gitnexus-web
@@ -53,7 +53,7 @@ jobs:
      pull-requests: write
      issues: write
      id-token: write
-      actions: read # required for Claude to read CI results on PRs
+      actions: read         # required for Claude to read CI results on PRs
    steps:
      # For PR-related triggers, resolve the fork repo so we can checkout correctly.
      - name: Resolve PR context
@@ -30,10 +30,6 @@ jobs:
          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
-
      - run: npm ci
        working-directory: gitnexus

@@ -67,22 +63,7 @@ jobs:
        env:
          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}

-      - name: Extract release notes from CHANGELOG
-        id: changelog
-        shell: bash
-        run: |
-          VERSION="${GITHUB_REF#refs/tags/v}"
-          NOTES=$(awk "/^## \\[$VERSION\\]/{found=1; next} /^## \\[/{if(found) exit} found" gitnexus/CHANGELOG.md)
-          if [ -z "$NOTES" ]; then
-            echo "::warning::No CHANGELOG entry found for v$VERSION, falling back to auto-generated notes"
-            echo "fallback=true" >> "$GITHUB_OUTPUT"
-          else
-            echo "$NOTES" > /tmp/release-notes.md
-            echo "fallback=false" >> "$GITHUB_OUTPUT"
-          fi
-
      - name: Create GitHub Release
        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' }}
+          generate_release_notes: true
@@ -93,6 +93,4 @@ GitNexus.sln

 .history/

-.swarm/
-
-local_docs/
+.swarm/
@@ -1,26 +1,33 @@
 #!/usr/bin/env bash
-# Pre-commit hook: format staged files + typecheck.
-# Tests run in CI (ci-tests.yml), not here.
+# Pre-commit hook (husky): typecheck + unit tests for both packages.
+# Mirrors CI checks from ci-quality.yml and ci-tests.yml.
 # Skip with: git commit --no-verify
+#
+# CI coverage:
+#   quality / typecheck      → tsc --noEmit in gitnexus/
+#   quality / typecheck-web  → tsc -b --noEmit in gitnexus-web/
+#   tests / ubuntu+coverage  → vitest run in gitnexus/ (all projects)
+#   e2e / chromium           → playwright (requires servers — skipped)

 ROOT="$(git rev-parse --show-toplevel)"

-# 1. Format staged files with prettier via lint-staged
-echo "pre-commit: formatting staged files..."
-"$ROOT/node_modules/.bin/lint-staged" || exit 1
-
-# 2. Typecheck changed packages
 WEB_CHANGED=$(git diff --cached --name-only -- 'gitnexus-web/' | head -1)
 CLI_CHANGED=$(git diff --cached --name-only -- 'gitnexus/' | head -1)

 if [ -n "$WEB_CHANGED" ]; then
  echo "pre-commit: typechecking gitnexus-web (tsc -b)..."
-  cd "$ROOT/gitnexus-web" && ./node_modules/.bin/tsc -b --noEmit || exit 1
+  cd "$ROOT/gitnexus-web" && npx tsc -b --noEmit
+
+  echo "pre-commit: running gitnexus-web unit tests..."
+  npx vitest run --reporter=dot
 fi

 if [ -n "$CLI_CHANGED" ]; then
  echo "pre-commit: typechecking gitnexus..."
-  cd "$ROOT/gitnexus" && ./node_modules/.bin/tsc --noEmit || exit 1
+  cd "$ROOT/gitnexus" && npx tsc --noEmit
+
+  echo "pre-commit: running gitnexus unit tests (default project)..."
+  npx vitest run --project default --reporter=dot
 fi

 echo "pre-commit: all checks passed"
@@ -1,16 +0,0 @@
-dist/
-coverage/
-gitnexus/vendor/
-gitnexus/test/fixtures/
-gitnexus-web/playwright-report/
-gitnexus-web/test-results/
-*.d.ts
-*.snap
-*.wasm
-*.md
-.gitnexus/
-.vercel/
-.claude-flow/
-.swarm/
-assets/
-repomix-output*
@@ -1,10 +0,0 @@
-{
-  "semi": true,
-  "singleQuote": true,
-  "trailingComma": "all",
-  "printWidth": 100,
-  "tabWidth": 2,
-  "endOfLine": "lf",
-  "plugins": ["prettier-plugin-tailwindcss"],
-  "tailwindStylesheet": "./gitnexus-web/src/index.css"
-}
@@ -1,69 +1,7 @@
-<!-- version: 1.2.0 -->
-<!--
-  Metadata: version, last reviewed, scope, model policy, reference docs, changelog.
-  Last updated: 2026-03-22
-->
-
-Last reviewed: 2026-03-24
-
-**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
-
-| | |
-|--|--|
-| **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:** 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)
-
-Long sessions dilute instructions. 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 (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
-
-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 (Cursor / standards)
-
-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 Documentation
-
- **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 |
-|------|---------|--------|
-| 2026-03-24 | 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

-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.
+This project is indexed by GitNexus as **GitNexus** (2487 symbols, 6056 relationships, 188 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.

@@ -161,44 +99,3 @@ To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.
 | Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |

 <!-- gitnexus:end -->
-
-## Cursor Cloud specific instructions
-
-### Repository structure
-
-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
-
- **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/`)**
- **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/`)**
- **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`
-
-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). 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.
@@ -1,98 +0,0 @@
-# Architecture — GitNexus
-
-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/` | 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** (`gitnexus analyze`)  
-   - Entry: `gitnexus/src/cli/analyze.ts` → `runPipelineFromRepo` in `gitnexus/src/core/ingestion/pipeline.ts`.  
-   - Walks the git working tree, parses supported languages via **Tree-sitter**, resolves imports/calls/inheritance, detects **communities** and **processes** (execution flows), and builds an in-memory **knowledge graph** (`gitnexus/src/core/graph/`).  
-   - 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 & 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 & 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**  
-   - `gitnexus/src/mcp/staleness.ts` compares indexed `lastCommit` to `HEAD` and surfaces hints when the graph is behind git.
-
-## MCP tools (summary)
-
-| Tool | Purpose |
-|------|---------|
-| `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
-
-| 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, processors, resolvers, type-extractors). |
-| 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/`. |
-
-## Known limitations
-
-### Overloaded method resolution
-
-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`.
-
-**Remaining limitation — same-arity overloads:** When two overloads share the
-same parameter count but differ only in types (e.g. `save(int)` vs
-`save(String)`), they still share a node ID. This is rare in practice; a future
-enhancement may add type-hash disambiguation for languages with reliable type
-extraction (see issue #574).
-
-**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).
-
-**Confidence tiering** for `METHOD_IMPLEMENTS` edges:
-
-| 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 expectations for **this** repo when indexed by GitNexus.
@@ -10,19 +10,6 @@ All notable changes to GitNexus will be documented in this file.
 - Added automatic cleanup of stale KuzuDB index files
 - LadybugDB v0.15 requires explicit VECTOR extension loading for semantic search

-## [1.5.3] - 2026-04-01
-
-### Added
-
- **TypeScript/JavaScript MethodExtractor config** — shared extraction config covering abstract methods, visibility modifiers, async/override keywords, decorators, rest/optional/destructured parameters, and return types (#588) — @compound-ai
-
-### Fixed
-
- **Azure OpenAI compatibility** — use `max_completion_tokens` instead of deprecated `max_tokens` (newer models reject `max_tokens`); skip `temperature` for Azure provider (some models reject non-default values) (#618)
- **Simplified Azure interactive setup** — 3 prompts (endpoint, deployment, key) instead of 7 (#618)
- **Wiki HTML viewer script injection** — escape `</script>` in embedded JSON so LLM-generated markdown no longer breaks the viewer (#618)
- Ensure import rewrites survive npm publish lifecycle
-
 ## [1.4.0] - 2026-03-13

 ### Added
@@ -1,60 +1,7 @@
-<!-- version: 1.2.0 -->
-<!--
-  Metadata: version, last reviewed, scope, model policy, reference docs, changelog.
-  Last updated: 2026-03-22
-->
-
-Last reviewed: 2026-03-24
-
-**Project:** GitNexus · **Environment:** dev · **Maintainer:** repository maintainers (see GitHub)
-
-Follow **AGENTS.md** for the canonical rules; this file adds Claude Code–specific deltas. Cursor-specific notes live only in `AGENTS.md`.
-
-## Scope
-
-See the **Scope** table in [AGENTS.md](AGENTS.md) for read/write/execute/off-limits boundaries. Cursor-specific workflow notes also live only in AGENTS.md.
-
-## Model Configuration
-
- **Primary:** Pin per **Claude Code** / Anthropic org policy (explicit model id). Do not rely on an unversioned `latest` alias for governed workflows.
- **Fallback:** As configured in Claude Code (organization default or user override).
- **Notes:** The GitNexus CLI analyzer does not call an LLM.
-
-## Execution Sequence (complex tasks)
-
-Same discipline as [AGENTS.md](AGENTS.md): before large multi-step work, state which **AGENTS.md** / **GUARDRAILS.md** rules apply, current **Scope**, and planned validation commands (`npm test`, `tsc`, etc.). When pausing, summarize progress in the chat or a **local** scratch file (do not add `HANDOFF.md` to the repo), then `/clear` and resume with that summary.
-
-## Claude Code hooks
-
-Prefer **PreToolUse** hooks for hard gates (e.g. tests before `git_commit`). Adapt hook commands to `gitnexus/` npm scripts.
-
-## Context budget
-
-If always-on instructions grow, load deep conventions via conditional reads (e.g. *“When writing new code, read STANDARDS.md”*) instead of pasting long blocks here. In Cursor, prefer `.cursor/index.mdc` plus optional `.cursor/rules/*.mdc` globs (see [AGENTS.md](AGENTS.md) § Context budget).
-
-## Reference Documentation
-
- **This repository:** [AGENTS.md](AGENTS.md) (Cursor + monorepo notes), [ARCHITECTURE.md](ARCHITECTURE.md), [CONTRIBUTING.md](CONTRIBUTING.md), [GUARDRAILS.md](GUARDRAILS.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
-
-| Date | Version | Change |
-|------|---------|--------|
-| 2026-03-24 | 1.2.0 | Removed duplicated gitnexus:start block and scope table; replaced with pointers to AGENTS.md. |
-| 2026-03-23 | 1.1.0 | Updated agent instructions to match AGENTS.md. |
-| 2026-03-22 | 1.0.0 | Added structured header and changelog. |
-
---
-
-## GitNexus rules
-
-GitNexus MCP rules are in the `<!-- gitnexus:start -->` … `<!-- 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.
+This project is indexed by GitNexus as **GitNexus** (2487 symbols, 6056 relationships, 188 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.

@@ -1,50 +0,0 @@
-# Contributing to GitNexus
-
-How to propose changes, run checks locally, and open pull requests.
-
-## License
-
-This project uses the [PolyForm Noncommercial License 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/). By contributing, you agree your contributions are licensed under the same terms unless stated otherwise.
-
-## Where to discuss
-
- **Issues & feature ideas:** use [GitHub Issues](https://github.com/abhigyanpatwari/GitNexus/issues) for the upstream repo, or your fork’s tracker if you work from a fork.
- **Community:** see the Discord link in the root [README.md](README.md).
-
-## Development setup
-
-1. Clone the repository.
-2. **CLI / MCP package:** `cd gitnexus && npm install && npm run build`
-3. **Web UI (if needed):** `cd gitnexus-web && npm install`
-4. Run tests as described in [TESTING.md](TESTING.md).
-
-## Branch and pull requests
-
- Use short-lived branches off the default branch of the repo you are targeting.
- 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.
-
-## 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` — 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.
-
-## 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.
@@ -1,88 +0,0 @@
-# Guardrails — GitNexus (repo + agents)
-
-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 (typical agent session)
-
-When automating changes in this repository, treat scope as **least privilege**:
-
- **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, `.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)
-
-Use this format: **Trigger → Instruction → Reason**.  
-Append new Signs here when the same mistake repeats (e.g. CI broken twice the same way).
-
-### Sign: Stale graph after edits
-
- **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.
-
-### Sign: Embeddings vanished after analyze
-
- **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.
-
-### Sign: MCP lists no repos
-
- **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.
-
-### Sign: Wrong repo in multi-repo setups
-
- **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.
-
-### Sign: LadybugDB lock / “database busy”
-
- **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; 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.
-
---
-
-## Escalation
-
-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”).  
- 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.
@@ -1,27 +0,0 @@
-# Migration Guide
-
-## OVERRIDES → METHOD_OVERRIDES (PR #642)
-
-The `OVERRIDES` relationship type has been renamed to `METHOD_OVERRIDES` for
-consistency with the new `METHOD_IMPLEMENTS` edge type.
-
-### Do I need to migrate?
-
-**No.** Backward compatibility is handled automatically at runtime:
-
- `local-backend.ts` dual-reads both `OVERRIDES` and `METHOD_OVERRIDES` in all
-  impact-analysis and context queries. Existing stored graphs with `OVERRIDES`
-  edges continue to return correct results without any manual intervention.
- The `REL_TYPES` array in `schema-constants.ts` includes both names so Cypher
-  queries that reference either will work.
-
-### What happens on re-index?
-
-Running `npx gitnexus analyze` on a repository produces `METHOD_OVERRIDES`
-edges going forward. The old `OVERRIDES` edges are replaced as part of the
-normal full re-index.
-
-### When will the legacy alias be removed?
-
-The `OVERRIDES` compat alias will remain until a future major version. Removal
-will be announced in this file and in the changelog before it happens.
@@ -19,8 +19,6 @@
    <img src="https://img.shields.io/badge/License-PolyForm%20Noncommercial-blue.svg" alt="License: PolyForm Noncommercial"/>
  </a>

-  <p><strong>Enterprise (SaaS & Self-hosted)</strong> - <a href="https://akonlabs.com">akonlabs.com</a></p>
-
 </div>

 **Building nervous system for agent context.**
@@ -61,36 +59,6 @@ https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72

 ---

-## Enterprise
-
-GitNexus is available as an **enterprise offering** - either as a fully managed **SaaS** or a **self-hosted** deployment. Also available for **commercial use** of the OSS version with proper licensing.
-
-Enterprise includes:
- **PR Review** - automated blast radius analysis on pull requests
- **Auto-updating Code Wiki** - always up-to-date documentation (Code Wiki is also available in OSS)
- **Auto-reindexing** - knowledge graph stays fresh automatically
- **Multi-repo support** - unified graph across repositories
- **OCaml support** - additional language coverage
- **Priority feature/language support** - request new languages or features
-
-**Upcoming:**
- Auto regression forensics
- End-to-end test generation
-
-👉 Learn more at [akonlabs.com](https://akonlabs.com)
-
-💬 For commercial licensing or enterprise inquiries, ping us on [Discord](https://discord.gg/AAsRVT6fGb) or drop an email at founders@akonlabs.com
-
---
-
-## Development
-
- [ARCHITECTURE.md](ARCHITECTURE.md) — packages, index → graph → MCP flow, where to change code
- [RUNBOOK.md](RUNBOOK.md) — analyze, embeddings, stale index, MCP recovery, CI snippets
- [GUARDRAILS.md](GUARDRAILS.md) — safety rules and operational “Signs” for contributors and agents
- [CONTRIBUTING.md](CONTRIBUTING.md) — license, setup, commits, and pull requests
- [TESTING.md](TESTING.md) — test commands for `gitnexus` and `gitnexus-web`
-
 ## CLI + MCP (recommended)

 The CLI indexes your repository and runs an MCP server that gives AI agents deep codebase awareness.
@@ -171,8 +139,8 @@ codex mcp add gitnexus -- npx -y gitnexus@latest mcp
 {
  "mcp": {
    "gitnexus": {
-      "type": "local",
-      "command": ["gitnexus", "mcp"]
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
 }
@@ -189,14 +157,13 @@ args = ["-y", "gitnexus@latest", "mcp"]
 ### CLI Commands

 ```bash
-gitnexus setup                   # Configure MCP for your editors (one-time)
-gitnexus analyze [path]          # Index a repository (or update stale index)
-gitnexus analyze --force         # Force full re-index
-gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
+gitnexus setup                    # Configure MCP for your editors (one-time)
+gitnexus analyze [path]           # Index a repository (or update stale index)
+gitnexus analyze --force          # Force full re-index
+gitnexus analyze --skills         # Generate repo-specific skill files from detected communities
 gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
-gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
-gitnexus analyze --embeddings    # Enable embedding generation (slower, better search)
-gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
+gitnexus analyze --embeddings     # Enable embedding generation (slower, better search)
+gitnexus analyze --verbose        # Log skipped files when parsers are unavailable
 gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
 gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
 gitnexus list                    # List all indexed repositories
@@ -206,21 +173,11 @@ gitnexus clean --all --force     # Delete all indexes
 gitnexus wiki [path]             # Generate repository wiki from knowledge graph
 gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
 gitnexus wiki --base-url <url>   # Wiki with custom LLM API base URL
-
-# Repository groups (multi-repo / monorepo service tracking)
-gitnexus group create <name>     # Create a repository group
-gitnexus group add <name> <repo> # Add a repo to a group
-gitnexus group remove <name> <repo> # Remove a repo from a group
-gitnexus group list [name]       # List groups, or show one group's config
-gitnexus group sync <name>       # Extract contracts and match across repos/services
-gitnexus group contracts <name>  # Inspect extracted contracts and cross-links
-gitnexus group query <name> <q>  # Search execution flows across all repos in a group
-gitnexus group status <name>     # Check staleness of repos in a group
 ```

 ### What Your AI Agent Gets

-**16 tools** exposed via MCP (11 per-repo + 5 group):
+**7 tools** exposed via MCP:

 | Tool               | What It Does                                                      | `repo` Param |
 | ------------------ | ----------------------------------------------------------------- | -------------- |
@@ -231,11 +188,6 @@ gitnexus group status <name>     # Check staleness of repos in a group
 | `detect_changes` | Git-diff impact — maps changed lines to affected processes       | Optional       |
 | `rename`         | Multi-file coordinated rename with graph + text search            | Optional       |
 | `cypher`         | Raw Cypher graph queries                                          | Optional       |
-| `group_list`     | List configured repository groups                                 | —             |
-| `group_sync`     | Extract contracts and match across repos/services                 | —             |
-| `group_contracts`| Inspect extracted contracts and cross-links                       | —             |
-| `group_query`    | Search execution flows across all repos in a group                | —             |
-| `group_status`   | Check staleness of repos in a group                               | —             |

 > When only one repo is indexed, the `repo` parameter is optional. With multiple repos, specify which one: `query({query: "auth", repo: "my-app"})`.

@@ -331,8 +283,8 @@ Or run locally:

 ```bash
 git clone https://github.com/abhigyanpatwari/gitnexus.git
-cd gitnexus/gitnexus-shared && npm install && npm run build
-cd ../gitnexus-web && npm install
+cd gitnexus/gitnexus-web
+npm install
 npm run dev
 ```

@@ -415,7 +367,6 @@ GitNexus builds a complete knowledge graph of your codebase through a multi-phas
 | Swift | — | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
 | C | — | — | ✓ | — | ✓ | ✓ | — | ✓ | ✓ |
 | C++ | — | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| Dart | ✓ | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |

 **Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics

@@ -580,7 +531,7 @@ The wiki generator reads the indexed graph structure, groups files into modules
 - [X] Constructor-Inferred Type Resolution, `self`/`this` Receiver Mapping
 - [X] Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
 - [X] Process-Grouped Search, 360-Degree Context, Claude Code Hooks
- [X] Multi-Repo MCP, Zero-Config Setup, 14 Language Support
+- [X] Multi-Repo MCP, Zero-Config Setup, 13 Language Support
 - [X] Community Detection, Process Detection, Confidence Scoring
 - [X] Hybrid Search, Vector Index

@@ -1,163 +0,0 @@
-# Runbook — GitNexus
-
-Short, copy-paste operations for **local development**, **MCP**, and **CI**. Commands assume a Unix shell; on Windows use Git Bash or equivalent paths.
-
-## Prerequisites
-
- **Node.js** ≥ 20 (`gitnexus-web/package.json` `engines`).  
- **Git** (analyze requires a git repository).  
- From repo root, install and build the CLI package:
-
-```bash
-cd gitnexus
-npm install
-npm run build
-```
-
-Use `npx gitnexus …` from any path after global/published install, or `node dist/cli/index.js …` when developing from `gitnexus/` with a local build.
-
---
-
-## Index out of date / “stale” tools
-
-**Symptom:** MCP or resources warn the index is behind `HEAD`, or results don’t reflect recent commits.
-
-**Fix (from the target repo root):**
-
-```bash
-npx gitnexus analyze
-```
-
-**Force full rebuild** (same commit but suspect corruption or changed ignore rules):
-
-```bash
-npx gitnexus analyze --force
-```
-
-**Check status:**
-
-```bash
-npx gitnexus status
-```
-
-**List what MCP knows about:**
-
-```bash
-npx gitnexus list
-```
-
---
-
-## Embeddings
-
-**First time with vectors** (slower, more disk/RAM):
-
-```bash
-npx gitnexus analyze --embeddings
-```
-
-**Important:** If you already had embeddings, **always** pass `--embeddings` on later analyzes, or they can be dropped. See `stats.embeddings` in `.gitnexus/meta.json` (0 means none).
-
-**Large repos:** Analyze may skip or limit embedding work when node counts are very high; watch CLI output.
-
---
-
-## MCP: no repos / empty tools
-
-**Symptom:** `GitNexus: No indexed repos yet` on stderr when starting MCP.
-
-**Fix:** In each project you want indexed:
-
-```bash
-cd /path/to/repo
-npx gitnexus analyze
-```
-
-Restart the editor MCP session if needed. The server **refreshes the registry lazily**; new analyzes are picked up without necessarily reinstalling MCP.
-
-**Symptom:** Wrong repo when multiple are indexed — pass `repo` on tools or use `list_repos` first.
-
---
-
-## Clean slate (corrupt or huge `.gitnexus`)
-
-**Current repo only** (prompts for confirmation):
-
-```bash
-npx gitnexus clean
-```
-
-**Skip confirmation:**
-
-```bash
-npx gitnexus clean --force
-```
-
-**All registered repos:**
-
-```bash
-npx gitnexus clean --all --force
-```
-
-Then re-run `npx gitnexus analyze` (and `--embeddings` if you need vectors).
-
---
-
-## Local bridge for the web UI
-
-```bash
-cd gitnexus
-npx gitnexus serve
-# default http://127.0.0.1:4747 — see serve --help for port/host
-```
-
-Use when the browser UI should talk to **local** indexed repos instead of WASM-only mode.
-
---
-
-## CLI equivalents of MCP tools
-
-Useful for debugging without an editor:
-
-```bash
-cd gitnexus
-npx gitnexus query "authentication flow" --repo MyRepo
-npx gitnexus context SomeSymbol --repo MyRepo
-npx gitnexus impact SomeSymbol --direction upstream --repo MyRepo
-npx gitnexus cypher "MATCH (n) RETURN count(n) LIMIT 1" --repo MyRepo
-```
-
---
-
-## CI failures (contributors)
-
-Orchestrator: `.github/workflows/ci.yml`.
-
-| Job | Typical local repro |
-|-----|---------------------|
-| **quality** | `cd gitnexus && npx tsc --noEmit` |
-| **unit-tests** | `cd gitnexus && npx vitest run test/unit` |
-| **integration** | `cd gitnexus && npx vitest run test/integration` (see workflow matrix for groups) |
-| **e2e** | Triggered when `gitnexus-web/` changes; `cd gitnexus-web && E2E=1 npx playwright test` (requires `gitnexus serve` + `npm run dev`) |
-
-**Note:** Pushes that touch only certain markdown paths may be skipped by `paths-ignore` in CI — see workflow file for exact patterns.
-
---
-
-## Memory / analyze crashes
-
-Analyze re-execs Node with a **large old-space heap** when needed (`analyze.ts`). If you still OOM on huge repos, close other processes, avoid `--embeddings` for a first pass, or analyze a smaller path if supported by your workflow.
-
---
-
-## LadybugDB / lock errors
-
-Only one process should open a repo’s `.gitnexus/lbug` store at a time. If MCP and a second `analyze` run conflict, stop one process, then retry `analyze` or restart MCP.
-
---
-
-## Where to dig deeper
-
- Architecture overview: [ARCHITECTURE.md](ARCHITECTURE.md)  
- Agent safety rules: [GUARDRAILS.md](GUARDRAILS.md)  
- Tests: [TESTING.md](TESTING.md)
@@ -1,95 +0,0 @@
-# Testing — GitNexus
-
-How we structure tests and which commands to run locally and in CI.
-
-## Packages
-
-| Package        | Path           | Runner   | Notes                          |
-| -------------- | -------------- | -------- | ------------------------------ |
-| CLI + MCP core | `gitnexus/`    | Vitest   | Primary test surface in CI     |
-| Web UI         | `gitnexus-web/`| Vitest   | Unit/component tests           |
-| Web UI E2E     | `gitnexus-web/`| Playwright | Run when changing UI flows   |
-
-## Commands (local)
-
-From repository root, unless noted:
-
-**`gitnexus` (CLI / library)**
-
-```bash
-cd gitnexus
-npm install
-npm run build
-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)
-```
-
-**`gitnexus-web`**
-
-```bash
-cd gitnexus-web
-npm install
-npm test                    # unit tests (vitest)
-npx tsc -b --noEmit         # typecheck (matches CI)
-npm run test:coverage
-npm run test:e2e            # Playwright (requires gitnexus serve + npm run dev)
-```
-
-## Pre-commit hook
-
-A husky pre-commit hook (`.husky/pre-commit`) runs automatically on every `git commit`:
-
- **`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).
-
-## Test categories
-
- **Unit** — Pure logic, parsers, graph/query helpers; fast; no network.
- **Integration** — Real combinations (filesystem, MCP wiring, larger pipelines) as already organized under `gitnexus/test/integration`.
- **Eval-style / golden sets** — For agent- or classification-style behavior, keep labeled inputs and expected outputs (JSON or table-driven tests) and run them in CI when relevant.
- **E2E (web)** — Critical user paths only; prefer `data-testid` attributes for stable selectors. Tests run against real backend (`gitnexus serve`) and Vite dev server.
-
-## Performance metrics (targets)
-
-Set targets to match team expectations, then tune to this repo’s CI reality:
-
-| Metric              | Target (initial) | Notes                                      |
-| ------------------- | ---------------- | ------------------------------------------ |
-| Unit coverage       | Align with CI    | CI runs Vitest with coverage in `gitnexus` |
-| Unit wall time      | Fast PR feedback | Use `vitest run test/unit` for tight loop  |
-| Integration duration| &lt; few minutes | Guard heavy tests with env flags if needed |
-
-## Regression testing
-
-Re-run the full relevant suite when:
-
- Prompt or agent-behavior documentation changes (if tests encode behavior)
- Model or embedding-related code paths change
- Graph schema, query contracts, or MCP tool shapes change
- Dependencies with parsing or runtime impact upgrade
-
-## CI integration
-
-GitHub Actions (`.github/workflows/ci.yml`) orchestrate:
-
- **`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
-
-Local checks before pushing:
-
-```bash
-cd gitnexus && npx tsc --noEmit && npm test
-cd ../gitnexus-web && npx tsc -b --noEmit && npm test
-```
-
-Or rely on the pre-commit hook which runs these automatically for staged files.
-
-## User acceptance / beta (optional)
-
-For staged releases or UI betas: deploy to a staging environment, collect structured feedback, watch errors and latency, then iterate before a wider release.
@@ -84,17 +84,13 @@ sequenceDiagram
    end
 ```

-The return type `CopyExpansionResult` contains `expandedContent` and `copyResolutions`. The `expansionDepth` field has been removed from the return type (it was unused by callers).
-
-COPY statement line numbers in `CopyResolution` are 1-based (consistent with the preprocessor's line numbering). The splice operation that replaces COPY lines with expanded content adjusts for 0-based array indexing internally.
-
 ## Cycle Detection

 Circular COPY references (e.g., copybook A includes copybook B which includes copybook A) are detected and handled:

 1. Each expansion chain maintains a `visited` set of resolved copybook paths
 2. If a copybook path is already in the visited set, the expansion is skipped
-3. A `warnedCircular` set (internal to `expandCopies()`, not a parameter) deduplicates warning messages within a single file expansion
+3. A `warnedCircular` set (shared across all files in a chunk) deduplicates warning messages

 Known circular copybooks in PROJECT-NAME: `ANAZI`, `ANDIP`, `QDIPE` (self-referential includes).

@@ -102,10 +98,6 @@ Known circular copybooks in PROJECT-NAME: `ANAZI`, `ANDIP`, `QDIPE` (self-refere

 Nested COPY expansion is limited to **10 levels** (`DEFAULT_MAX_DEPTH`). If a COPY chain exceeds this depth, a warning is logged and the remaining COPY statements are left unexpanded.

-## Max Total Expansions
-
-A breadth amplification guard caps the total number of COPY expansions across all branches within a single file to **500** (`MAX_TOTAL_EXPANSIONS`). This prevents exponential blowup from diamond-shaped COPY graphs where N copybooks each include N other copybooks. Once the limit is reached, further COPY statements in that file are left unexpanded and a single warning is logged.
-
 ## REPLACING Application Detail

 The REPLACING engine works by scanning all COBOL identifiers (matching `\b[A-Z][A-Z0-9-]*\b`) in the copybook content and applying each replacement rule:
@@ -147,10 +139,6 @@ The expansion runs **per chunk**, after file content is read but before dispatch
 3. Only programs (not copybooks themselves) undergo expansion
 4. The expanded content replaces the original content in-place before worker dispatch

-## Inline Comment Handling
-
-The copy expander's `stripInlineComment()` helper is quote-aware: pipe characters (`|`) inside single- or double-quoted strings are preserved. This matches the same quote-aware logic used by the preprocessor.
-
 ## Source Files

 - `gitnexus/src/core/ingestion/cobol-copy-expander.ts` -- `expandCopies()`, `parseReplacingClause()`, `applyReplacing()`
@@ -100,12 +100,10 @@ Tables are extracted from SQL clauses:
 | Clause Pattern | Example |
 |----------------|---------|
 | `FROM <table>` | `SELECT * FROM EMPLOYEES` |
-| `INSERT INTO <table>` | `INSERT INTO EMPLOYEES` |
+| `INTO <table>` | `INSERT INTO EMPLOYEES` |
 | `UPDATE <table>` | `UPDATE EMPLOYEES SET ...` |
 | `JOIN <table>` | `LEFT JOIN DEPARTMENTS ON ...` |

-Note: The `INTO` pattern is restricted to `INSERT INTO` to avoid false positives from `FETCH ... INTO :host-var` and `SELECT ... INTO :host-var` statements, where `INTO` introduces host variables rather than table names.
-
 ### Cursor Detection

 ```cobol
@@ -244,66 +242,21 @@ The USING clause identifies parameters received by the program from its caller.

 ## MOVE Statements

-MOVE statements produce `ACCESSES` edges in the graph:
+MOVE statements are extracted but currently only stored in the regex results (not emitted as graph edges):

 ```cobol
       MOVE WK-NAME TO OUT-NAME.
       MOVE CORRESPONDING WK-INPUT TO WK-OUTPUT.
-       MOVE CORR WK-IN TO WK-OUT.
 ```

 ### Extraction Details

 - Source and target identifiers are captured
- `CORRESPONDING` and its abbreviation `CORR` are both recognized (bulk field-by-field move)
+- `CORRESPONDING` keyword is tracked (bulk field-by-field move)
 - Figurative constants (SPACES, ZEROS, LOW-VALUES, HIGH-VALUES, QUOTES, ALL) are skipped
 - The enclosing paragraph (`caller`) is tracked for context

-### MOVE CORRESPONDING / CORR Edge Reasons
-
-MOVE CORRESPONDING (and CORR) produces distinct edge reasons to differentiate from simple MOVE:
-
-| Edge | Reason (simple MOVE) | Reason (CORRESPONDING/CORR) |
-|------|---------------------|-----------------------------|
-| Read (source) | `cobol-move-read` | `cobol-move-corresponding-read` |
-| Write (target) | `cobol-move-write` | `cobol-move-corresponding-write` |
-
-This distinction allows queries to find bulk field-by-field moves separately from simple variable assignments.
-
-## GO TO DEPENDING ON
-
-The `GO TO` statement with multiple targets and a `DEPENDING ON` clause is a computed branch:
-
-```cobol
-       GO TO PARA-1 PARA-2 PARA-3
-           DEPENDING ON WK-SELECTOR.
-```
-
-All target paragraph names are extracted and emitted as separate `gotos` entries. Each target produces a `CALLS` edge in the graph (same semantics as PERFORM). The `DEPENDING ON` variable is not currently tracked as a data-flow dependency.
-
-## SORT INPUT/OUTPUT PROCEDURE
-
-SORT and MERGE statements can specify procedural entry points instead of file-based I/O:
-
-```cobol
-       SORT SORT-FILE ON ASCENDING KEY SORT-KEY
-           INPUT PROCEDURE IS PREPARE-INPUT
-           OUTPUT PROCEDURE IS FORMAT-OUTPUT.
-```
-
-`INPUT PROCEDURE IS` and `OUTPUT PROCEDURE IS` targets are extracted as control-flow targets (same as PERFORM). They produce `performs` entries and corresponding `CALLS` edges in the graph.
-
-## Fixed-Format Literal Continuation
-
-In fixed-format COBOL, string literals can span multiple lines using the continuation indicator (`-` in column 7). When a continuation line starts with a quote character, the extractor joins it with the predecessor by removing the trailing quote from the previous line and the opening quote from the continuation:
-
-```
-Line N:          MOVE "THIS IS A LONG STRI
-Line N+1 (cont): -    "NG VALUE" TO WK-FIELD.
-Merged:          MOVE "THIS IS A LONG STRING VALUE" TO WK-FIELD.
-```
-
-The trailing `"` on line N and the opening `"` on line N+1 are both removed, producing a seamless literal. If no matching quote is found on the predecessor line, the continuation is appended as-is.
+DATA_FLOW edges from MOVE statements are reserved for a future release.

 ## Source Files

@@ -45,31 +45,6 @@ GITNEXUS_COBOL_DIRS=s,c,wfproc GITNEXUS_VERBOSE=1 node --max-old-space-size=8192
  /path/to/gitnexus/dist/cli/index.js analyze --force
 ```

-## Open-Source Benchmarks
-
-### CardDemo (AWS)
-
-| Metric | Value |
-| ------ | ----- |
-| Graph nodes | 12,323 |
-| Graph edges | 8,893 |
-| Total time | 7.4s |
-
-### ACAS
-
-| Metric | Value |
-| ------ | ----- |
-| Graph nodes | 14,016 |
-| Graph edges | 15,452 |
-| Total time | 9.3s |
-
-### Micro-Benchmark (Single-File Extraction)
-
-| Metric | Value |
-| ------ | ----- |
-| Per-iteration | 0.65ms |
-| Throughput | ~382K lines/sec |
-
 ## Worker Pool Tuning

 ### Sub-Batch Size
@@ -134,10 +109,6 @@ To increase the cap for specific needs, modify the `MAX_DATA_ITEMS_PER_FILE` con

 ## Memory Management

-### COPY Expansion Breadth Guard
-
-A per-file `MAX_TOTAL_EXPANSIONS = 500` limit prevents exponential blowup from diamond-shaped COPY graphs (e.g., N copybooks each containing N COPY statements). Once the limit is reached, further COPY statements in that file are left unexpanded. See [copy-expansion.md](copy-expansion.md) for details.
-
 ### COPY Expansion Memory

 All copybook content is loaded upfront into a Map before chunk processing begins. For PROJECT-NAME:
@@ -71,13 +71,11 @@ Indicator col 7
                        buffer as new pending logical line
 ```

-After all lines are processed, the final pending line is flushed, along with any accumulated SELECT statement, SORT/MERGE accumulator, and any open EXEC block (truncated file without `END-EXEC`).
+After all lines are processed, the final pending line is flushed, along with any accumulated SELECT statement.

 ### Inline Comment Stripping

-Enterprise COBOL (particularly Italian dialect) uses the pipe character `|` as an inline comment marker. The `stripInlineComment()` helper is **quote-aware**: it tracks whether the scan position is inside a single- or double-quoted string and only treats `|` as a comment marker when outside quotes. Pipe characters inside string literals are preserved.
-
-Free-format `*>` inline comment stripping uses the same quote-aware approach: the scanner walks character by character, toggling quote state, and only recognizes `*>` as a comment marker when not inside a quoted string.
+Enterprise COBOL (particularly Italian dialect) uses the pipe character `|` as an inline comment marker. Everything from `|` to end of line is stripped before processing.

 ### Patch Marker Handling

@@ -113,7 +111,7 @@ All patterns are compiled once as module-level constants and reused across calls

 | Constant | Pattern | Purpose | Example Match |
 |----------|---------|---------|---------------|
-| `RE_SELECT_START` | `\bSELECT\s+(?:OPTIONAL\s+)?([A-Z][A-Z0-9-]+)` | File SELECT start (with optional `SELECT OPTIONAL` support) | `SELECT MASTER-FILE`, `SELECT OPTIONAL TRANS-FILE` |
+| `RE_SELECT_START` | `\bSELECT\s+([A-Z][A-Z0-9-]+)` | File SELECT start | `SELECT MASTER-FILE` |

 SELECT statements are accumulated across multiple lines until a period terminator is found, then parsed for ASSIGN, ORGANIZATION, ACCESS, RECORD KEY, and FILE STATUS clauses.

@@ -137,9 +135,7 @@ The trailing clauses of `RE_DATA_ITEM` are parsed by `parseDataItemClauses()` fo
 | `RE_PERFORM` | `\bPERFORM\s+([A-Z][A-Z0-9-]+)(?:\s+THRU\s+([A-Z][A-Z0-9-]+))?` | PERFORM call | `PERFORM CALC-TAX THRU CALC-TAX-EXIT` |
 | `RE_PROC_USING` | `\bPROCEDURE\s+DIVISION\s+USING\s+([\s\S]*?)(?:\.\|$)` | USING parameters | `PROCEDURE DIVISION USING WK-PARAM` |
 | `RE_ENTRY` | `\bENTRY\s+"([^"]+)"(?:\s+USING\s+([\s\S]*?))?(?:\.\|$)` | ENTRY point | `ENTRY "SUBPROG" USING WK-DATA` |
-| `RE_MOVE` | `\bMOVE\s+((?:CORRESPONDING\|CORR)\s+)?([A-Z][A-Z0-9-]+)\s+TO\s+(.+)` | MOVE statement (supports CORR abbreviation and multi-target) | `MOVE WK-NAME TO OUT-NAME`, `MOVE CORR WK-IN TO WK-OUT` |
-
-The USING parameter list (`RE_PROC_USING`) is split on `\bRETURNING\b` before tokenization -- any RETURNING clause and everything after it is excluded from the parameter list (`.split(/\bRETURNING\b/i)[0]`).
+| `RE_MOVE` | `\bMOVE\s+(CORRESPONDING\s+)?([A-Z][A-Z0-9-]+)\s+TO\s+([A-Z][A-Z0-9-]+)` | MOVE statement | `MOVE WK-NAME TO OUT-NAME` |

 Note: `RE_PROC_SECTION` and `RE_PROC_PARAGRAPH` require exactly 7 spaces of leading indentation (COBOL area A starting at column 8). This is the standard COBOL paragraph indentation.

@@ -153,22 +149,6 @@ These patterns are checked regardless of current division:
 | `RE_COPY_UNQUOTED` | `\bCOPY\s+([A-Z][A-Z0-9-]+)(?:\s\|\.)` | COPY (unquoted) | `COPY CPSESP.` |
 | `RE_COPY_QUOTED` | `\bCOPY\s+"([^"]+)"(?:\s\|\.)` | COPY (quoted) | `COPY "WORKGRID.CPY".` |

-### SORT/MERGE Support
-
-| Constant | Purpose |
-|----------|---------|
-| `SORT_CLAUSE_NOISE` | Set of SORT/MERGE clause keywords filtered from USING/GIVING file lists: `ON`, `ASCENDING`, `DESCENDING`, `KEY`, `WITH`, `DUPLICATES`, `IN`, `ORDER`, `COLLATING`, `SEQUENCE`, `IS`, `THROUGH`, `THRU`, `INPUT`, `OUTPUT`, `PROCEDURE` |
-
-SORT and MERGE statements are accumulated across multiple lines (like SELECT) until a period terminator is found, then parsed for USING/GIVING file lists and INPUT/OUTPUT PROCEDURE targets. The `flushSort()` helper encapsulates the flush-and-parse logic, mirroring the existing `flushSelect()` pattern. Both helpers are called at EOF to handle truncated files.
-
-### GO TO Multi-Target
-
-`RE_GOTO` captures all paragraph names in a `GO TO` statement, including the multi-target form `GO TO p1 p2 p3 DEPENDING ON x`. The captured group contains all target names (space-separated), which are split into individual targets. Each target produces a separate `gotos` entry.
-
-### PROGRAM-ID Detection
-
-PROGRAM-ID is detected regardless of the current division state. This handles sibling programs that appear after `END PROGRAM` and omit the `IDENTIFICATION DIVISION` header -- the extractor will still capture the PROGRAM-ID and push a new program boundary.
-
 ### EXEC Block Patterns

 | Constant | Pattern | Purpose | Example Match |
@@ -1,326 +0,0 @@
---
-title: "feat: Complete COBOL language feature coverage for maximum knowledge graph value"
-type: feat
-status: active
-date: 2026-03-26
-origin: Feature audit from v3-integration-architect agent (session 8642401e)
---
-
-## Enhancement Summary
-
-**Deepened on:** 2026-03-26
-**Research agents used:** COBOL expert (Phase 1+2), graph value analyst, codebase explorer
-**Sections enhanced:** Phase 1 (5 features), Phase 2 (4 features), graph value ranking
-
-### Key Improvements from Research
-1. **CALL USING** is the #1 highest-value edge type (9.2/10) — fixes ~40% of missing caller references
-2. **EXEC DLI** requires dual-interface support (EXEC DLI + CBLTDLI CALL) for full IMS coverage
-3. **DECLARATIVES** is lowest-risk Phase 2 item — existing section/paragraph detection already captures structure
-4. **SET TO TRUE** accounts for 80-90% of all SET statements — prioritize this form
-5. **INSPECT** needs multi-line accumulator (like SORT) — can span 5+ continuation lines
-6. **Graph value ranking**: cobol-call-using (9.2) > cobol-error-handler (9.0) > dli-gu (8.2) > cobol-string (6.2)
-
-### New Edge Cases Discovered
- CALL USING supports mixed modes: `USING BY REFERENCE WS-A BY CONTENT WS-B BY VALUE WS-C`
- CALL USING `ADDRESS OF` and `OMITTED` must be filtered from parameter lists
- EXEC DLI can have multiple SEGMENT levels in hierarchical retrieval (use matchAll)
- DECLARATIVES can have multiple USE sections (one per file + catch-all for INPUT/OUTPUT/I-O/EXTEND)
- INSPECT TALLYING can have multiple counters in a single statement
- STRING/UNSTRING can span multiple lines (need accumulator pattern)
-
---
-
-# Complete COBOL Language Feature Coverage
-
-## Overview
-
-Implement the remaining 25 unhandled COBOL language features and fix 10 partial features to achieve ~95% coverage (up from 71.9%). The goal is to build the richest possible knowledge graph from COBOL codebases, enabling a future `modernize` MCP command (out of scope for this plan) that would use the graph to assist with COBOL-to-modern-language migration.
-
-## Problem Statement
-
-The COBOL processor currently handles 54 of 89 applicable language features (71.9%). The 25 unhandled features represent real data loss in the knowledge graph:
- **Cross-program data flow** is invisible (CALL ... USING parameters not extracted)
- **IMS/DB programs** produce empty graphs (EXEC DLI not recognized)
- **String transformation logic** is invisible (STRING/UNSTRING/INSPECT not tracked)
- **SQL copybook dependencies** are missing (EXEC SQL INCLUDE not mapped)
- **Error handling flows** are lost (DECLARATIVES/USE AFTER not captured)
-
-## Proposed Solution
-
-Implement features in 4 phases, ordered by graph value density (edges created per LOC of implementation). Each phase is independently shippable and testable.
-
-## Technical Approach
-
-### Phase 1: High-Value Data Flow Edges (~150 LOC, ~8 new edge types)
-
-The highest-ROI features: they create new ACCESSES and IMPORTS edges that directly improve impact analysis.
-
-**Critical research finding**: Multi-line statement accumulation is the dominant challenge. CALL USING, STRING/UNSTRING, and multi-line data item clauses all span multiple lines in production COBOL. The free-format path processes each line independently — these features need statement accumulators (like SORT/SELECT) or the free-format path needs multi-line awareness. Estimated LOC increased from 110 to 150 to account for accumulator infrastructure.
-
-#### 1.1 EXEC SQL INCLUDE -> IMPORTS edges
- **File:** `cobol-preprocessor.ts` (parseExecSqlBlock)
- **What:** Detect `INCLUDE` as the operation, extract member name, emit as a `copies[]` entry
- **Graph:** IMPORTS edge from File to included copybook/SQLCA with reason `sql-include`
- **Tests:** Unit test for `EXEC SQL INCLUDE SQLCA END-EXEC` and `EXEC SQL INCLUDE CUSTCOPY END-EXEC`
-
-**Research insights (EXEC SQL INCLUDE):**
- DB2 member names can contain underscores: `EXEC SQL INCLUDE CUST_TBL_DCL END-EXEC` — regex must use `[A-Z][A-Z0-9_-]+`
- Quoted literal form: `EXEC SQL INCLUDE 'DBRMLIB.MEMBER' END-EXEC` (z/OS PDS qualified name)
- SQLCA/SQLDA are DB2 builtins — won't resolve to repo files. Emit unresolved IMPORTS edge (still valuable)
- No REPLACING support on EXEC SQL INCLUDE (unlike COPY)
- Add `INCLUDE` to `OP_MAP` in `parseExecSqlBlock`; extract member via `RE_SQL_INCLUDE = /^INCLUDE\s+(?:'([^']+)'|"([^"]+)"|([A-Z][A-Z0-9_-]+))/i`
-
-#### 1.2 CALL ... USING parameter extraction -> ACCESSES edges (Graph value: 9.2/10)
- **File:** `cobol-preprocessor.ts` (processLogicalLine CALL section)
- **What:** After capturing CALL target, scan for USING clause. Extract parameter names (reuse USING_KEYWORDS filter). Store as `calls[].parameters: string[]`
- **Interface:** Add `parameters?: string[]` to calls array type in CobolRegexResults
- **File:** `cobol-processor.ts` (CALL edge block)
- **Graph:** For each USING parameter, create ACCESSES edge from caller to data item Property node with reason `cobol-call-using`
- **Tests:** `CALL 'AUDITLOG' USING CUST-ID WS-AMOUNT` -> 2 ACCESSES edges
-
-**Research insights (CALL USING forms):**
- Mixed modes: `CALL 'PGM' USING BY REFERENCE WS-A BY CONTENT WS-B BY VALUE WS-C`
- Pointer passing: `CALL 'PGM' USING ADDRESS OF WS-A`
- Placeholder: `CALL 'PGM' USING OMITTED WS-B`
- Filter keywords: add `ADDRESS`, `OMITTED`, `LENGTH` to USING_KEYWORDS (already has BY/VALUE/REFERENCE/CONTENT)
- **Impact tool enhancement:** CALL-USING edges enable BFS traversal through parameter data flow — single most impactful edge type for COBOL impact analysis
-
-#### 1.3 STRING/UNSTRING data flow -> ACCESSES edges
- **File:** `cobol-preprocessor.ts` (new section in extractProcedure)
- **What:** Accumulate multi-line STRING/UNSTRING until period or END-STRING/END-UNSTRING. Extract sources and INTO targets.
- **Interface:** Add `strings: Array<{ sources: string[]; target: string; type: 'string' | 'unstring'; line: number; caller: string | null }>` to CobolRegexResults
- **Graph:** read-ACCESSES on sources, write-ACCESSES on INTO target with reason `cobol-string-read` / `cobol-string-write`
- **Tests:** 2 unit tests + integration test assertions
-
-**Research insights (STRING/UNSTRING):**
- **Needs statement accumulator** — STRING/UNSTRING always span multiple lines in production
- Terminate accumulation at: period, END-STRING/END-UNSTRING, or start of next COBOL verb
- STRING sources: identifiers before each `DELIMITED BY`. Filter: STRING, DELIMITED, BY, SIZE, ALL, INTO, WITH, POINTER, ON, OVERFLOW, NOT, END-STRING
- UNSTRING: source is first identifier after UNSTRING; INTO targets are identifiers after INTO. Filter: DELIMITER, IN, COUNT, TALLYING, OR
- WITH POINTER field is both read AND written (starting position updated)
- TALLYING IN / COUNT IN fields are write targets
- Literal sources (`'text'`) must be filtered — quote-aware tokenization needed
- **Edge case**: STRING terminated by next verb, not period — existing fixture has `STRING ... DISPLAY` without period between them
-
-#### 1.4 OCCURS DEPENDING ON -> ACCESSES edge
- **File:** `cobol-preprocessor.ts` (parseDataItemClauses)
- **What:** Extend OCCURS regex to capture DEPENDING ON field, KEY fields, and INDEXED BY names
- **Interface:** Add `dependingOn?: string`, `occursMax?: number`, `occursKeys?: Array<{direction: string; fields: string[]}>`, `indexedBy?: string[]` to data items
- **Graph:** ACCESSES edge from table item to controlling field with reason `cobol-depends-on`
- **Tests:** `05 WS-TABLE OCCURS 100 DEPENDING ON WS-COUNT` -> edge
-
-**Research insights (OCCURS):**
- IBM allows `OCCURS 0 TO n DEPENDING ON` (zero minimum) and `OCCURS UNBOUNDED DEPENDING ON` (V6.4)
- Subscripted controlling fields: `DEPENDING ON WS-COUNT(WS-IDX)` — strip subscripts before storing
- **Pre-existing gap**: Multi-line data item clauses without continuation indicator are NOT captured. `05 WS-TABLE\n    OCCURS 100\n    DEPENDING ON WS-COUNT.` — the current RE_DATA_ITEM only gets the first line, `rest` is empty. Fixing properly requires a data item accumulator (like SELECT). **Defer full fix to Phase 3; implement same-line capture now.**
- KEY IS fields: `ASCENDING KEY IS WS-KEY-1 WS-KEY-2` — capture for SEARCH ALL resolution
- INDEXED BY: `INDEXED BY IDX-1 IDX-2` — capture for SET/SEARCH context
-
-#### 1.5 VALUE clause for standard data items
- **File:** `cobol-preprocessor.ts` (parseDataItemClauses)
- **What:** Extract VALUE using a pragmatic function that handles quoted strings, numerics, figurative constants, hex/national literals
- **Interface:** Already exists as `values?: string[]` on data items (currently only populated for 88-level)
- **Graph:** Stored in Property node description (no new edges)
- **Tests:** `01 WS-STATUS PIC X VALUE 'A'` -> values: ['A']
-
-**Research insights (VALUE forms):**
- Hex literals: `VALUE X'F1F2F3F4'`, National: `VALUE N'text'`, DBCS: `VALUE G'text'`
- Figurative constants: SPACES, ZEROS, ZEROES, LOW-VALUES, HIGH-VALUES, QUOTES, NULL, NULLS
- ALL literal: `VALUE ALL '*'`
- Numeric with sign/decimal: `VALUE -123.45`, `VALUE +1`
- `VALUE IS` optional — both `VALUE 'A'` and `VALUE IS 'A'` valid
- **Decimal vs period ambiguity**: `VALUE 100.` — is `.` decimal or terminator? `parseDataItemClauses` already strips trailing period, so this is handled
- IBM V6.4: floating-point `VALUE 1.0E5` — extend numeric regex if needed
- Implementation: use a pragmatic `extractValue(rest)` function, not a single complex regex
-
-### Phase 2: EXEC DLI + DECLARATIVES (~90 LOC, ~4 new edge types)
-
-IMS/DB support and error handling flows.
-
-#### 2.1 EXEC DLI (IMS/DB) -> ACCESSES edges (Graph value: 8.2/10)
- **File:** `cobol-preprocessor.ts` (processLogicalLine — add RE_EXEC_DLI_START check alongside SQL/CICS)
- **What:** Accumulate EXEC DLI blocks like EXEC SQL. Parse DLI verbs (GU, GN, GNP, GHU, GHN, GHNP, ISRT, DLET, REPL, CHKP, SCHD, TERM). Extract segment name, PCB number, INTO/FROM areas, WHERE fields, PSB name.
- **Interface:** Add `execDliBlocks: Array<{ line: number; verb: string; pcbNumber?: number; segmentName?: string; intoField?: string; fromField?: string; whereField?: string; psbName?: string }>` to CobolRegexResults
- **Graph:** CodeElement node + ACCESSES edge to `<ims>:<segmentName>` Record node with reason `dli-{verb}`; ACCESSES edges to INTO/FROM data areas; PSB ACCESSES for SCHD
- **Tests:** `EXEC DLI GU USING PCB(1) SEGMENT(CUSTOMER) INTO(WS-CUST) END-EXEC`
-
-**Research insights (dual IMS interface):**
- **EXEC DLI**: Embedded command interface for CICS-DL/I programs only
- **CBLTDLI CALL**: Batch interface via `CALL 'CBLTDLI' USING function-code PCB io-area SSA1..SSA15`
- CBLTDLI is already captured as a CALL to 'CBLTDLI' — enrich with USING parameter semantics later
- Multiple SEGMENT levels in hierarchical retrieval — use `matchAll` on segment regex
- DLI verbs: GU (most common), GN, GNP, GHU, GHN, GHNP, ISRT, REPL, DLET, CHKP, SCHD, TERM, ROLL, ROLB
- **Edge case**: DLET/REPL have no SEGMENT clause (operate on current position)
- **Recommended order**: Implement AFTER DECLARATIVES and SET (lower risk, higher frequency)
-
-#### 2.2 DECLARATIVES / USE AFTER STANDARD EXCEPTION (Graph value: 9.0/10)
- **File:** `cobol-preprocessor.ts` (processLogicalLine — detect DECLARATIVES keyword, track USE AFTER blocks)
- **What:** When `DECLARATIVES.` is encountered, switch to declaratives mode. Extract USE statements binding sections to files/modes.
- **Interface:** Add `declaratives: Array<{ sectionName: string; useType: 'error' | 'debug' | 'label' | 'reporting'; target: string; line: number }>` to CobolRegexResults
- **Graph:** ACCESSES edge from declarative Namespace to file Record with reason `cobol-declarative-error-handler`
- **Tests:** Unit test with DECLARATIVES section, integration test for error flow
-
-**Research insights (DECLARATIVES syntax):**
- `USE AFTER STANDARD {EXCEPTION|ERROR} ON {file-name|INPUT|OUTPUT|I-O|EXTEND}`
- EXCEPTION and ERROR are synonymous; STANDARD is optional in IBM dialects
- Multiple USE sections allowed (one per file + catch-all for I/O modes)
- `END DECLARATIVES.` must NOT reset PROCEDURE DIVISION state
- `DECLARATIVES` is already in EXCLUDED_PARA_NAMES — no false paragraph risk
- Existing section/paragraph detection already captures structural elements — just need USE binding
- **Lowest risk Phase 2 item** — implement first
-
-#### 2.3 SET statement -> ACCESSES edges
- **File:** `cobol-preprocessor.ts` (extractProcedure — new RE_SET regex)
- **Interface:** Add `sets: Array<{ targets: string[]; form: 'to-true'|'to-value'|'up-by'|'down-by'|'address-of'|'to-null'|'to-entry'; value?: string; entryTarget?: string; entryIsLiteral?: boolean; line: number; caller: string | null }>` to CobolRegexResults
- **Graph:** ACCESSES write edge with reason `cobol-set-condition` (TO TRUE), `cobol-set-index` (TO/UP/DOWN), `cobol-set-address` (ADDRESS OF). SET ENTRY with literal -> CALLS edge.
- **Tests:** `SET WS-EOF TO TRUE`, `SET IDX-1 TO 5`, `SET IDX-1 UP BY 1`
-
-**Research insights (SET forms by frequency):**
- `SET condition TO TRUE` — 80-90% of all SET usage. Multiple targets: `SET COND-A COND-B TO TRUE`
- `SET index TO/UP BY/DOWN BY` — ~8%. Multiple indices: `SET IDX-1 IDX-2 UP BY 1`
- `SET pointer TO ADDRESS OF data-item` / `SET ADDRESS OF data-item TO pointer` — ~2%
- `SET proc-ptr TO ENTRY "PROGNAME"` — rare but creates CALLS edge (like dynamic CALL)
- Filter OF/IN qualifiers: `SET COND-A OF WS-RECORD TO TRUE` (strip OF WS-RECORD)
- **Prioritize**: SET TO TRUE alone covers 80-90% — implement this form first
-
-#### 2.4 INSPECT -> ACCESSES edges
- **File:** `cobol-preprocessor.ts` (extractProcedure — new `inspectAccum` accumulator like SORT)
- **What:** Accumulate multi-line INSPECT until period. Extract inspected field + tally counters.
- **Interface:** Add `inspects: Array<{ inspectedField: string; counters: string[]; form: 'tallying'|'replacing'|'converting'|'tallying-replacing'; line: number; caller: string | null }>` to CobolRegexResults
- **Graph:** ACCESSES read on inspected field always; write if REPLACING/CONVERTING. Write edges for tally counters. Reason: `cobol-inspect-read`/`cobol-inspect-write`/`cobol-inspect-tally`
- **Tests:** `INSPECT WS-FIELD TALLYING WS-COUNT FOR ALL 'A'` -> read on WS-FIELD, write on WS-COUNT
-
-**Research insights (INSPECT forms by frequency):**
- REPLACING (~60%): `INSPECT WS-STR REPLACING ALL 'A' BY 'B'`
- TALLYING (~25%): `INSPECT WS-STR TALLYING WS-CNT FOR ALL 'A'` — multiple counters possible
- CONVERTING (~10%): `INSPECT WS-STR CONVERTING 'abc' TO 'ABC'`
- Combined (~5%): TALLYING + REPLACING in single statement
- **Needs multi-line accumulator** — INSPECT frequently spans 3-5 lines in production
- Extract tally counters with `([A-Z][A-Z0-9-]+)\s+FOR\b` matchAll pattern
- Filter figurative constants (SPACES, ZEROS) using existing MOVE_SKIP set
-
-### Phase 3: Completeness Fixes (~60 LOC)
-
-Fix the 10 partial features and small gaps.
-
-#### 3.1 CALL ... RETURNING extraction
- Extend RE_CALL processing to capture RETURNING target after the USING clause
- Store as `calls[].returning?: string`
- Graph: ACCESSES write edge with reason `cobol-call-returning`
-
-#### 3.2 SELECT OPTIONAL flag preservation
- Store `isOptional: boolean` in FileDeclaration interface
- Include in Record node description
-
-#### 3.3 ALTERNATE RECORD KEY extraction
- Add regex in parseSelectStatement: `/\bALTERNATE\s+RECORD\s+KEY\s+(?:IS\s+)?([A-Z][A-Z0-9-]+)/i`
- Store as `alternateKeys?: string[]`
-
-#### 3.4 COMMON attribute on nested programs
- Extend RE_PROGRAM_ID: `/\bPROGRAM-ID\.\s*([A-Z][A-Z0-9-]+)(?:\s+IS\s+COMMON)?/i`
- Store `isCommon: boolean` on Module node
- Affects cross-program CALL resolution scope
-
-#### 3.5 IS EXTERNAL / IS GLOBAL as first-class properties
- Change from usage string hack to proper boolean fields on data items
- Add `isExternal?: boolean`, `isGlobal?: boolean` to data item interface
-
-#### 3.6 AUTHOR / DATE-WRITTEN mapped to Module node
- Already extracted as programMetadata — map to Module node properties
- `graph.addNode({ ..., properties: { ..., author, dateWritten } })`
-
-#### 3.7 REPLACE statement
- Track REPLACE / REPLACE OFF state in preprocessor
- Apply text substitutions during preprocessing (before regex extraction)
- Complex: requires careful scoping rules
-
-### Phase 4: Niche Features (~30 LOC)
-
-Low-priority but nice for completeness.
-
-#### 4.1 INITIALIZE statement -> write ACCESSES
- `/\bINITIALIZE\s+([A-Z][A-Z0-9-]+)/i`
- ACCESSES write edge with reason `cobol-initialize`
-
-#### 4.2 Remaining IDENTIFICATION DIVISION paragraphs
- DATE-COMPILED, INSTALLATION, SECURITY, REMARKS
- Map to Module node description properties
-
-#### 4.3 EXEC SQL INCLUDE -> IMPORTS edge (expansion)
- For EXEC SQL INCLUDE inside EXEC blocks that reference copybooks containing SQL
- Create IMPORTS edge similar to COPY
-
-## Acceptance Criteria
-
-### Functional Requirements
-
- [ ] Phase 1: All 5 features implemented with unit + integration tests
- [ ] Phase 2: All 4 features implemented with unit + integration tests
- [ ] Phase 3: All 7 partial features fixed
- [ ] Phase 4: At least 2 of 3 niche features implemented
- [ ] All existing 145 tests continue to pass
- [ ] TypeScript compiles cleanly
-
-### Non-Functional Requirements
-
- [ ] No performance regression: CardDemo benchmark stays under 8s
- [ ] No file exceeds 1500 LOC (preprocessor currently 1326)
- [ ] ACAS benchmark shows increased node/edge counts (more data extracted)
- [ ] CardDemo benchmark shows increased edge counts (CALL USING, STRING, etc.)
-
-### Quality Gates
-
- [ ] Each phase has its own commit
- [ ] Integration test assertions updated with exact counts per phase
- [ ] Benchmark run after each phase to track graph growth
-
-## Dependencies & Risks
-
-### Dependencies
- None. All changes are additive to existing COBOL processor code.
- No LanguageProvider changes needed.
- No graph schema changes needed (all new constructs map to existing node labels + edge types).
-
-### Risks
- **preprocessor.ts size**: Currently 1326 LOC. Phase 1+2 adds ~200 LOC -> 1526 LOC. May need to extract helpers into a separate `cobol-data-flow.ts` module if it exceeds 1500.
- **REPLACE statement** (Phase 3.7) is the most complex feature — requires tracking text substitution state across logical lines. Consider deferring to a separate PR if it takes >100 LOC.
- **EXEC DLI** (Phase 2.1) is only testable against IMS codebases. Need fixture data or synthetic test cases.
-
-## Graph Value Ranking by MCP Tool Impact
-
-Research agent analyzed all 5 MCP tools (query, context, impact, detect_changes, rename) against planned edge types:
-
-| Edge Type | QUERY | CONTEXT | IMPACT | DETECT | RENAME | **Overall** |
-|-----------|-------|---------|--------|--------|--------|-------------|
-| `cobol-call-using` | 4/5 | 5/5 | 5/5 | 4/5 | 4/5 | **9.2/10** |
-| `cobol-error-handler` | 5/5 | 4/5 | 5/5 | 5/5 | 2/5 | **9.0/10** |
-| `dli-*` (IMS verbs) | 4/5 | 4/5 | 5/5 | 4/5 | 2/5 | **8.2/10** |
-| `cobol-string-*` | 4/5 | 3/5 | 3/5 | 3/5 | 2/5 | **6.2/10** |
-
-**Key finding**: `cobol-call-using` alone would fix ~40% of missing caller references in COBOL graphs.
-
-## Future Considerations
-
-This plan provides the graph data foundation for a future `modernize` MCP command (out of scope) that would:
- Use CALL USING edges to map data contracts between programs
- Use STRING/UNSTRING edges to identify data transformation logic
- Use EXEC SQL/DLI edges to map database access patterns
- Use DECLARATIVES to understand error handling architecture
- Use the complete knowledge graph to generate migration plans
-
-**MCP tool enhancements needed** (after this plan ships):
- Add `cobol-call-using`, `cobol-error-handler`, `dli-*` to IMPACT tool's default `relationTypes` for COBOL repos
- Add confidence floors for new edge types in `IMPACT_RELATION_CONFIDENCE`
- Register new edge types in `VALID_RELATION_TYPES` set (`local-backend.ts:52`)
-
-## Sources & References
-
-### Internal References
- Feature audit: session 8642401e (COBOL expert agent, 123 features audited)
- Prior plans: `docs/plans/2026-03-25-feat-cobol-100-percent-feature-coverage-plan.md`
- Architecture: `docs/code-indexing/cobol/` (7 documentation files)
-
-### External References
- COBOL features reference: mainframestechhelp.com/tutorials/cobol/features.htm
- COBOL-85 standard: ISO/IEC 1989:1985
- IBM Enterprise COBOL reference
@@ -1,725 +0,0 @@
-# PR #626 HIGH-Priority Fixes Implementation Plan
-
-> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
-
-**Goal:** Fix 4 HIGH-priority issues from PR #626 code review before merge.
-
-**Architecture:** Minimal targeted fixes — each task is independent. TDD: tests first, then implementation. No refactoring beyond what's needed.
-
-**Tech Stack:** TypeScript, Vitest, Node.js fs/path APIs
-
-**Spec:** `docs/superpowers/specs/2026-04-02-pr626-high-fixes-design.md`
-
-**Paths:** All file paths are relative to the monorepo root (`GitNexus/`). Git commands run from the root. The `gitnexus/` prefix is a package subdirectory, not a separate repo.
-
---
-
-### Task 1: Path Traversal — Validate Group Name
-
-**Files:**
- Modify: `gitnexus/src/core/group/storage.ts:17-19` (getGroupDir) and `:63-68` (createGroupDir)
- Test: `gitnexus/test/unit/group/storage.test.ts`
-
- [ ] **Step 1: Write failing tests for validateGroupName**
-
-In `gitnexus/test/unit/group/storage.test.ts`, add `createGroupDir` and `validateGroupName` to the existing import from `'../../../src/core/group/storage.js'` (line 6-11). Then add these describe blocks at the end of the outer `describe('Group storage', ...)`:
-
-```typescript
-  describe('validateGroupName', () => {
-    it('test_validateGroupName_traversal_path_throws', () => {
-      expect(() => validateGroupName('../../evil')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_slash_in_name_throws', () => {
-      expect(() => validateGroupName('foo/bar')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_empty_string_throws', () => {
-      expect(() => validateGroupName('')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_starts_with_dash_throws', () => {
-      expect(() => validateGroupName('-leading-dash')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_starts_with_underscore_throws', () => {
-      expect(() => validateGroupName('_leading')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_dots_throws', () => {
-      expect(() => validateGroupName('com.example')).toThrow(/Invalid group name/);
-    });
-
-    it('test_validateGroupName_valid_alphanumeric_passes', () => {
-      expect(() => validateGroupName('my-group_01')).not.toThrow();
-    });
-
-    it('test_validateGroupName_single_char_passes', () => {
-      expect(() => validateGroupName('A')).not.toThrow();
-    });
-
-    it('test_validateGroupName_all_digits_passes', () => {
-      expect(() => validateGroupName('123')).not.toThrow();
-    });
-  });
-
-  describe('getGroupDir rejects invalid names', () => {
-    it('test_getGroupDir_traversal_throws', () => {
-      expect(() => getGroupDir(tmpDir, '../../etc')).toThrow(/Invalid group name/);
-    });
-
-    it('test_getGroupDir_valid_name_returns_path', () => {
-      const dir = getGroupDir(tmpDir, 'company');
-      expect(dir).toBe(path.join(tmpDir, 'groups', 'company'));
-    });
-  });
-
-  describe('createGroupDir rejects invalid names', () => {
-    it('test_createGroupDir_traversal_throws', async () => {
-      await expect(createGroupDir(tmpDir, '../evil')).rejects.toThrow(/Invalid group name/);
-    });
-  });
-```
-
- [ ] **Step 2: Run tests to verify they fail**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/storage.test.ts`
-Expected: FAIL — `validateGroupName` is not exported, `getGroupDir` does not throw.
-
- [ ] **Step 3: Implement validateGroupName and wire into getGroupDir and createGroupDir**
-
-In `gitnexus/src/core/group/storage.ts`, add the validation function before `getGroupDir` and call it:
-
-```typescript
-const GROUP_NAME_RE = /^[a-zA-Z0-9][a-zA-Z0-9_-]*$/;
-
-export function validateGroupName(name: string): void {
-  if (!GROUP_NAME_RE.test(name)) {
-    throw new Error(
-      `Invalid group name "${name}". Names must start with a letter or digit and contain only [a-zA-Z0-9_-].`,
-    );
-  }
-}
-
-export function getGroupDir(gitnexusDir: string, groupName: string): string {
-  validateGroupName(groupName);
-  return path.join(gitnexusDir, 'groups', groupName);
-}
-```
-
-`createGroupDir` already calls `getGroupDir` at line 68, so it inherits validation automatically. No change needed in `createGroupDir`.
-
- [ ] **Step 4: Run tests to verify they pass**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/storage.test.ts`
-Expected: ALL PASS
-
- [ ] **Step 5: Commit**
-
-```bash
-cd gitnexus && git add src/core/group/storage.ts test/unit/group/storage.test.ts
-git commit -m "fix(group): validate group name to prevent path traversal
-
-Add validateGroupName() with regex [a-zA-Z0-9][a-zA-Z0-9_-]*.
-Called in getGroupDir (defense in depth) which covers all CLI entry
-points: create, add, remove, status, sync.
-
-Addresses PR #626 review item 1 (HIGH).
-
-Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>"
-```
-
---
-
-### Task 2: Directory Exclusions in Service Boundary Detector
-
-**Files:**
- Modify: `gitnexus/src/core/group/service-boundary-detector.ts:24-51` (add constant), `:78` (walkForBoundaries), `:130` (hasSourceFilesInSubdirs)
- Test: `gitnexus/test/unit/group/service-boundary-detector.test.ts`
-
- [ ] **Step 1: Write failing tests for excluded directories**
-
-Add this describe block inside the existing `detectServiceBoundaries` describe in `gitnexus/test/unit/group/service-boundary-detector.test.ts`:
-
-```typescript
-    it('test_detect_skips_vendor_directory', async () => {
-      writeFile('services/auth/package.json', '{}');
-      writeFile('services/auth/src/index.ts', '');
-      // vendor should be skipped — its contents should not create a boundary
-      writeFile('vendor/some-dep/package.json', '{}');
-      writeFile('vendor/some-dep/src/lib.go', '');
-
-      const boundaries = await detectServiceBoundaries(tmpDir);
-
-      const paths = boundaries.map((b) => b.servicePath);
-      expect(paths).toContain('services/auth');
-      expect(paths).not.toContain('vendor/some-dep');
-    });
-
-    it('test_detect_skips_target_directory', async () => {
-      writeFile('services/api/go.mod', 'module api');
-      writeFile('services/api/main.go', '');
-      writeFile('target/classes/Main.java', '');
-      writeFile('target/pom.xml', '<project/>');
-
-      const boundaries = await detectServiceBoundaries(tmpDir);
-
-      const paths = boundaries.map((b) => b.servicePath);
-      expect(paths).toContain('services/api');
-      expect(paths).not.toContain('target');
-    });
-
-    it('test_detect_skips_pycache_directory', async () => {
-      writeFile('services/ml/pyproject.toml', '[project]');
-      writeFile('services/ml/model.py', '');
-      // __pycache__ with a marker + source files — would be detected as
-      // a boundary if not excluded, since it has package.json + .py file
-      writeFile('__pycache__/package.json', '{}');
-      writeFile('__pycache__/cached.py', '');
-
-      const boundaries = await detectServiceBoundaries(tmpDir);
-
-      const paths = boundaries.map((b) => b.servicePath);
-      expect(paths).toContain('services/ml');
-      expect(paths.every((p) => !p.includes('__pycache__'))).toBe(true);
-    });
-
-    it('test_detect_skips_dotfile_directories_regression', async () => {
-      writeFile('services/api/package.json', '{}');
-      writeFile('services/api/src/index.ts', '');
-      writeFile('.hidden/package.json', '{}');
-      writeFile('.hidden/src/index.ts', '');
-
-      const boundaries = await detectServiceBoundaries(tmpDir);
-
-      const paths = boundaries.map((b) => b.servicePath);
-      expect(paths).toContain('services/api');
-      expect(paths).not.toContain('.hidden');
-    });
-
-    it('test_detect_does_not_skip_regular_source_directories', async () => {
-      writeFile('services/api/package.json', '{}');
-      writeFile('services/api/src/index.ts', '');
-
-      const boundaries = await detectServiceBoundaries(tmpDir);
-
-      expect(boundaries).toHaveLength(1);
-      expect(boundaries[0].serviceName).toBe('api');
-    });
-```
-
- [ ] **Step 2: Run tests to verify `vendor` and `target` tests fail**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/service-boundary-detector.test.ts`
-Expected: `test_detect_skips_vendor_directory` and `test_detect_skips_target_directory` FAIL (vendor/target not excluded). Other new tests may pass since dotfile exclusion already exists.
-
- [ ] **Step 3: Add EXCLUDED_DIRS constant and update both walking functions**
-
-In `gitnexus/src/core/group/service-boundary-detector.ts`:
-
-After `SOURCE_EXTENSIONS` (after line 51), add:
-
-```typescript
-const EXCLUDED_DIRS = new Set([
-  'node_modules',
-  'vendor',
-  'target',
-  'build',
-  'dist',
-  '__pycache__',
-  '.venv',
-  'venv',
-  '.tox',
-  '.mypy_cache',
-  '.gradle',
-  '.mvn',
-  'out',
-  'bin',
-]);
-```
-
-In `walkForBoundaries`, replace line 78:
-```typescript
-    if (entry.name.startsWith('.') || entry.name === 'node_modules') continue;
-```
-with:
-```typescript
-    if (entry.name.startsWith('.') || EXCLUDED_DIRS.has(entry.name)) continue;
-```
-
-In `hasSourceFilesInSubdirs`, replace line 130:
-```typescript
-      if (entry.isDirectory() && !entry.name.startsWith('.') && entry.name !== 'node_modules') {
-```
-with:
-```typescript
-      if (entry.isDirectory() && !entry.name.startsWith('.') && !EXCLUDED_DIRS.has(entry.name)) {
-```
-
- [ ] **Step 4: Run tests to verify they pass**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/service-boundary-detector.test.ts`
-Expected: ALL PASS
-
- [ ] **Step 5: Commit**
-
-```bash
-cd gitnexus && git add src/core/group/service-boundary-detector.ts test/unit/group/service-boundary-detector.test.ts
-git commit -m "fix(group): add directory exclusions to service boundary detector
-
-Add EXCLUDED_DIRS set: vendor, target, build, dist, __pycache__,
-.venv, venv, .tox, .mypy_cache, .gradle, .mvn, out, bin.
-Applied in walkForBoundaries and hasSourceFilesInSubdirs.
-Replaces inline node_modules check.
-
-Addresses PR #626 review item 3 (HIGH).
-
-Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>"
-```
-
---
-
-### Task 3: Remove Double-Close of LadybugDB Pools
-
-**Files:**
- Modify: `gitnexus/src/cli/group.ts:160` (remove import), `:187-189` (remove finally block body)
- Test: `gitnexus/test/unit/group/sync.test.ts` (add pool cleanup test)
- Test: `gitnexus/test/integration/group/group-cli.test.ts` (verify no blanket close in source)
-
- [ ] **Step 1: Write unit tests for per-id pool cleanup in sync.ts**
-
-Add to `gitnexus/test/unit/group/sync.test.ts`, inside the existing `describe('syncGroup', ...)`:
-
-```typescript
-  it('test_syncGroup_closes_only_opened_pools', async () => {
-    const config = makeConfig({
-      'app/backend': 'backend-repo',
-      'app/frontend': 'frontend-repo',
-    });
-
-    const closedIds: string[] = [];
-
-    // Mock initLbug/closeLbug via per-repo override that tracks pool lifecycle
-    const { vi } = await import('vitest');
-    const poolAdapter = await import('../../../src/core/lbug/pool-adapter.js');
-    const initSpy = vi.spyOn(poolAdapter, 'initLbug').mockResolvedValue(undefined);
-    const closeSpy = vi.spyOn(poolAdapter, 'closeLbug').mockImplementation(async (id?: string) => {
-      if (id) closedIds.push(id);
-    });
-
-    try {
-      await syncGroup(config, {
-        resolveRepoHandle: async (_name, groupPath) => ({
-          id: groupPath.replace(/\//g, '-'),
-          path: groupPath,
-          repoPath: '/tmp/' + groupPath,
-          storagePath: '/tmp/' + groupPath + '/.gitnexus',
-        }),
-        skipWrite: true,
-      }).catch(() => {});
-      // Regardless of extraction errors, closeLbug should be called per id
-      // closeLbug should only receive specific pool ids, never undefined/empty
-      for (const id of closedIds) {
-        expect(id).toBeTruthy();
-        expect(typeof id).toBe('string');
-      }
-      // No blanket close (no-arg call)
-      const blanketCalls = closeSpy.mock.calls.filter((args) => args.length === 0 || !args[0]);
-      expect(blanketCalls).toHaveLength(0);
-    } finally {
-      initSpy.mockRestore();
-      closeSpy.mockRestore();
-    }
-  });
-```
-
- [ ] **Step 2: Run sync unit test to verify it passes (sync.ts already does per-id cleanup)**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/sync.test.ts`
-Expected: PASS — sync.ts already cleans up correctly. This test locks the behavior.
-
- [ ] **Step 3: Write test verifying CLI source has no blanket closeLbug()**
-
-Add to `gitnexus/test/integration/group/group-cli.test.ts`:
-
-```typescript
-  it('test_sync_command_source_does_not_call_blanket_closeLbug', () => {
-    const cliGroupPath = path.join(repoRoot, 'src', 'cli', 'group.ts');
-    const source = fs.readFileSync(cliGroupPath, 'utf-8');
-
-    // closeLbug() without arguments (blanket close) must not appear.
-    // closeLbug(id) with argument is fine (that's in sync.ts, not here).
-    // Match closeLbug() but not closeLbug(someArg)
-    const blanketClosePattern = /closeLbug\s*\(\s*\)/;
-    expect(source).not.toMatch(blanketClosePattern);
-  });
-```
-
- [ ] **Step 4: Run test to verify it fails**
-
-Run: `cd gitnexus && npx vitest run test/integration/group/group-cli.test.ts`
-Expected: FAIL — `closeLbug()` (no args) exists at line 188.
-
- [ ] **Step 5: Remove blanket closeLbug() from cli/group.ts**
-
-In `gitnexus/src/cli/group.ts`:
-
-Remove the `closeLbug` import at line 160:
-```typescript
-      const { closeLbug } = await import('../core/lbug/pool-adapter.js');
-```
-
-Replace the try/finally wrapper (lines 162-189):
-```typescript
-      try {
-        const groupDir = getGroupDir(getDefaultGitnexusDir(), name);
-        const config = await loadGroupConfig(groupDir);
-
-        console.log(`Syncing group "${name}" (${Object.keys(config.repos).length} repos)...\n`);
-
-        const result = await syncGroup(config, {
-          groupDir,
-          allowStale: Boolean(opts.allowStale),
-          verbose: Boolean(opts.verbose),
-          skipEmbeddings: Boolean(opts.skipEmbeddings),
-          exactOnly: Boolean(opts.exactOnly),
-        });
-
-        if (opts.json) {
-          console.log(JSON.stringify(result, null, 2));
-        } else {
-          console.log(`\nMatching cascade:`);
-          const exactLinks = result.crossLinks.filter((l) => l.matchType === 'exact');
-          console.log(`  exact:     ${exactLinks.length} cross-links (confidence 1.0)`);
-          console.log(`  unmatched: ${result.unmatched.length} contracts`);
-          console.log(
-            `\nWrote contracts.json (${result.contracts.length} contracts, ${result.crossLinks.length} cross-links)`,
-          );
-        }
-      } finally {
-        await closeLbug().catch(() => {});
-      }
-```
-
-Becomes (remove try/finally entirely, since sync.ts handles its own cleanup):
-```typescript
-        const groupDir = getGroupDir(getDefaultGitnexusDir(), name);
-        const config = await loadGroupConfig(groupDir);
-
-        console.log(`Syncing group "${name}" (${Object.keys(config.repos).length} repos)...\n`);
-
-        const result = await syncGroup(config, {
-          groupDir,
-          allowStale: Boolean(opts.allowStale),
-          verbose: Boolean(opts.verbose),
-          skipEmbeddings: Boolean(opts.skipEmbeddings),
-          exactOnly: Boolean(opts.exactOnly),
-        });
-
-        if (opts.json) {
-          console.log(JSON.stringify(result, null, 2));
-        } else {
-          console.log(`\nMatching cascade:`);
-          const exactLinks = result.crossLinks.filter((l) => l.matchType === 'exact');
-          console.log(`  exact:     ${exactLinks.length} cross-links (confidence 1.0)`);
-          console.log(`  unmatched: ${result.unmatched.length} contracts`);
-          console.log(
-            `\nWrote contracts.json (${result.contracts.length} contracts, ${result.crossLinks.length} cross-links)`,
-          );
-        }
-```
-
- [ ] **Step 6: Run tests to verify they pass**
-
-Run: `cd gitnexus && npx vitest run test/integration/group/group-cli.test.ts test/unit/group/sync.test.ts`
-Expected: ALL PASS
-
- [ ] **Step 7: Commit**
-
-```bash
-cd gitnexus && git add src/cli/group.ts test/integration/group/group-cli.test.ts test/unit/group/sync.test.ts
-git commit -m "fix(group): remove blanket closeLbug() from CLI sync command
-
-sync.ts already closes pools per-id in its finally block.
-The blanket closeLbug() in cli/group.ts tears down ALL active pools
-including unrelated ones in MCP server context.
-
-Addresses PR #626 review item 4 (HIGH).
-
-Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>"
-```
-
---
-
-### Task 4: gRPC Proto Regex — Brace-Depth Counter
-
-**Files:**
- Modify: `gitnexus/src/core/group/extractors/grpc-extractor.ts:101-130` (parseProtoFile)
- Test: `gitnexus/test/unit/group/grpc-extractor.test.ts`
-
- [ ] **Step 1: Write failing tests for nested braces in proto services**
-
-Add this describe block inside the existing `proto file parsing` describe in `gitnexus/test/unit/group/grpc-extractor.test.ts`:
-
-```typescript
-    it('test_extract_proto_with_google_api_http_nested_braces', async () => {
-      writeFile(
-        'api/gateway.proto',
-        `syntax = "proto3";
-package gateway.v1;
-
-import "google/api/annotations.proto";
-
-service GatewayService {
-  rpc GetUser (GetUserRequest) returns (UserResponse) {
-    option (google.api.http) = {
-      get: "/v1/users/{user_id}"
-    };
-  }
-  rpc CreateUser (CreateUserRequest) returns (UserResponse) {
-    option (google.api.http) = {
-      post: "/v1/users"
-      body: "*"
-    };
-  }
-}`,
-      );
-
-      const contracts = await extractor.extract(null, tmpDir, makeRepo(tmpDir));
-      const providers = contracts.filter(
-        (c) => c.role === 'provider' && c.symbolRef.filePath === 'api/gateway.proto',
-      );
-
-      expect(providers).toHaveLength(2);
-      const ids = providers.map((c) => c.contractId).sort();
-      expect(ids).toEqual([
-        'grpc::gateway.v1.GatewayService/CreateUser',
-        'grpc::gateway.v1.GatewayService/GetUser',
-      ]);
-    });
-
-    it('test_extract_proto_with_multiple_services', async () => {
-      writeFile(
-        'api/multi.proto',
-        `syntax = "proto3";
-package multi;
-
-service ServiceA {
-  rpc MethodA (Req) returns (Res);
-}
-
-service ServiceB {
-  rpc MethodB1 (Req) returns (Res);
-  rpc MethodB2 (Req) returns (Res);
-}`,
-      );
-
-      const contracts = await extractor.extract(null, tmpDir, makeRepo(tmpDir));
-      const providers = contracts.filter(
-        (c) => c.role === 'provider' && c.symbolRef.filePath === 'api/multi.proto',
-      );
-
-      expect(providers).toHaveLength(3);
-      const ids = providers.map((c) => c.contractId).sort();
-      expect(ids).toEqual([
-        'grpc::multi.ServiceA/MethodA',
-        'grpc::multi.ServiceB/MethodB1',
-        'grpc::multi.ServiceB/MethodB2',
-      ]);
-    });
-
-    it('test_extract_proto_with_nested_option_blocks_in_rpc', async () => {
-      writeFile(
-        'api/nested.proto',
-        `syntax = "proto3";
-package nested;
-
-service DeepService {
-  rpc DeepMethod (Req) returns (Res) {
-    option (google.api.http) = {
-      post: "/v1/deep"
-      body: "*"
-      additional_bindings {
-        get: "/v1/deep/{id}"
-      }
-    };
-  }
-}`,
-      );
-
-      const contracts = await extractor.extract(null, tmpDir, makeRepo(tmpDir));
-      const providers = contracts.filter(
-        (c) => c.role === 'provider' && c.symbolRef.filePath === 'api/nested.proto',
-      );
-
-      expect(providers).toHaveLength(1);
-      expect(providers[0].contractId).toBe('grpc::nested.DeepService/DeepMethod');
-    });
-
-    it('test_extract_proto_malformed_unclosed_brace_skips_service', async () => {
-      writeFile(
-        'api/broken.proto',
-        `syntax = "proto3";
-package broken;
-
-service IncompleteService {
-  rpc SomeMethod (Req) returns (Res);
-  // Missing closing brace — EOF before depth returns to 0
-`,
-      );
-
-      // Should not throw; incomplete service is silently skipped
-      const contracts = await extractor.extract(null, tmpDir, makeRepo(tmpDir));
-      const providers = contracts.filter(
-        (c) => c.role === 'provider' && c.symbolRef.filePath === 'api/broken.proto',
-      );
-
-      // The old regex would find partial match; the new parser should skip it
-      expect(providers).toHaveLength(0);
-    });
-```
-
- [ ] **Step 2: Run tests to verify the nested brace test fails**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/grpc-extractor.test.ts`
-Expected: `test_extract_proto_with_google_api_http_nested_braces` FAIL — regex stops at first `}` inside the `option` block.
-
- [ ] **Step 3: Replace serviceRe regex with extractServiceBlocks function**
-
-In `gitnexus/src/core/group/extractors/grpc-extractor.ts`, replace the `parseProtoFile` method (lines 101-130):
-
-```typescript
-  private parseProtoFile(content: string, filePath: string): ExtractedContract[] {
-    const out: ExtractedContract[] = [];
-
-    const pkgMatch = content.match(/^package\s+([\w.]+)\s*;/m);
-    const pkg = pkgMatch ? pkgMatch[1] : '';
-
-    for (const { name: serviceName, body } of extractServiceBlocks(content)) {
-      const rpcRe = /rpc\s+(\w+)\s*\(/g;
-      let rpcMatch: RegExpExecArray | null;
-      while ((rpcMatch = rpcRe.exec(body)) !== null) {
-        const methodName = rpcMatch[1];
-        const cid = contractId(pkg, serviceName, methodName);
-        out.push(
-          makeContract(cid, 'provider', filePath, `${serviceName}.${methodName}`, 0.85, {
-            package: pkg,
-            service: serviceName,
-            method: methodName,
-            source: 'proto',
-          }),
-        );
-      }
-    }
-
-    return out;
-  }
-```
-
-Add this function before the class (e.g. after `serviceOnlyContractId`, around line 26):
-
-```typescript
-function extractServiceBlocks(content: string): Array<{ name: string; body: string }> {
-  const results: Array<{ name: string; body: string }> = [];
-  const headerRe = /service\s+(\w+)\s*\{/g;
-  let headerMatch: RegExpExecArray | null;
-
-  while ((headerMatch = headerRe.exec(content)) !== null) {
-    const serviceName = headerMatch[1];
-    const bodyStart = headerMatch.index + headerMatch[0].length;
-    let depth = 1;
-    let pos = bodyStart;
-
-    while (pos < content.length && depth > 0) {
-      const ch = content[pos];
-      if (ch === '{') depth++;
-      else if (ch === '}') depth--;
-      pos++;
-    }
-
-    // If EOF before depth returns to 0, skip incomplete service
-    if (depth !== 0) continue;
-
-    // body is between opening { (consumed by regex) and closing } (pos is one past it)
-    const body = content.slice(bodyStart, pos - 1);
-    results.push({ name: serviceName, body });
-  }
-
-  return results;
-}
-```
-
- [ ] **Step 4: Run tests to verify they pass**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/grpc-extractor.test.ts`
-Expected: ALL PASS (including existing regression tests)
-
- [ ] **Step 5: Commit**
-
-```bash
-cd gitnexus && git add src/core/group/extractors/grpc-extractor.ts test/unit/group/grpc-extractor.test.ts
-git commit -m "fix(group): replace gRPC proto regex with brace-depth counter
-
-The serviceRe regex used [^}]* which stopped at the first '}'.
-Proto services with google.api.http annotations contain nested {}
-blocks, causing methods to be missed.
-
-New extractServiceBlocks() uses a brace-depth counter (init depth=1
-after opening {, scan char-by-char). Malformed protos with unclosed
-braces are silently skipped.
-
-Addresses PR #626 review item 2 (HIGH).
-
-Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>"
-```
-
---
-
-### Task 5: Run Full Test Suite
-
- [ ] **Step 1: Run all group-related tests**
-
-Run: `cd gitnexus && npx vitest run test/unit/group/ test/integration/group/`
-Expected: ALL PASS
-
- [ ] **Step 2: Run full test suite to catch regressions**
-
-Run: `cd gitnexus && npx vitest run`
-Expected: ALL PASS, 0 failures
-
- [ ] **Step 3: Run typecheck**
-
-Run: `cd gitnexus && npx tsc --noEmit`
-Expected: No errors
-
---
-
-### Task 6: CLI Integration Smoke Test
-
- [ ] **Step 1: Add CLI smoke test for path traversal**
-
-Add to `gitnexus/test/integration/group/group-cli.test.ts` inside the existing `group CLI` describe:
-
-```typescript
-  it('test_create_with_invalid_name_fails', () => {
-    const result = runGroup(['create', '../../evil']);
-    expect(result.status).not.toBe(0);
-    expect(result.stderr).toContain('Invalid group name');
-  });
-```
-
- [ ] **Step 2: Run test**
-
-Run: `cd gitnexus && npx vitest run test/integration/group/group-cli.test.ts`
-Expected: ALL PASS
-
- [ ] **Step 3: Commit**
-
-```bash
-cd gitnexus && git add test/integration/group/group-cli.test.ts
-git commit -m "test(group): add CLI smoke test for path traversal rejection
-
-Verifies that 'group create ../../evil' fails with Invalid group name.
-
-Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>"
-```
@@ -1,175 +0,0 @@
-# PR #626 HIGH-Priority Fixes Design
-
-**Date:** 2026-04-02
-**PR:** abhigyanpatwari/GitNexus#626 — Intra-repo service communication tracking
-**Scope:** 4 HIGH-priority issues identified by abhigyanpatwari and xkonjin
-**Approach:** Minimal targeted fixes (option A) — no refactoring, no scope creep
-
---
-
-## Fix 1: Path Traversal via Group Name
-
-**File:** `gitnexus/src/core/group/storage.ts`
-**Risk:** A group name like `../../etc` creates directories outside the intended path.
-
-### Solution
-
-Add `validateGroupName(name: string): void` that enforces `/^[a-zA-Z0-9][a-zA-Z0-9_-]*$/`.
-
- Call in `createGroupDir` (primary entry point)
- Call in `getGroupDir` (defense in depth)
- Throw descriptive error on invalid names
-
-**Legacy:** Groups already on disk with names outside this pattern are not auto-renamed; only new `create` / resolved paths are validated.
-
-### Why regex over path.resolve + startsWith
-
- abhigyanpatwari explicitly requested `[a-zA-Z0-9_-]`
- Stricter: disallows spaces, dots, Unicode edge cases
- Simpler to reason about
-
-### Tests
-
- `../../evil` throws
- `foo/bar` throws
- Empty string throws
- `my-group_01` passes
- `A` (single char) passes
- CLI smoke: one integration test that hits `getGroupDir` / `createGroupDir` (e.g. `group create` or `group add`) with an invalid name proves wiring for every subcommand that resolves a group through storage
-
-### CLI/API entry points accepting groupName
-
-All paths flow through `getGroupDir` (which validates), so coverage is implicit. For reference:
-
-| Command | Entry | Calls |
-|---------|-------|-------|
-| `group create` | `cli/group.ts` action | `createGroupDir` -> `getGroupDir` |
-| `group add` | `cli/group.ts` action | `getGroupDir` |
-| `group remove` | `cli/group.ts` action | `getGroupDir` |
-| `group list` | `cli/group.ts` action | reads `groups/` dir directly — no traversal risk (reads, not writes) |
-| `group status` | `cli/group.ts` action | `getGroupDir` |
-| `group sync` | `cli/group.ts` action | `getGroupDir` |
-
-**`listGroups`:** Reads directory names from disk without validation. Not a write path, so no traversal risk. May surface manually-created directories with non-conforming names — accepted as-is, not in scope.
-
---
-
-## Fix 2: gRPC Proto Regex -> Brace-Depth Counter
-
-**File:** `gitnexus/src/core/group/extractors/grpc-extractor.ts`
-**Risk:** `serviceRe = /service\s+(\w+)\s*\{([^}]*)}/gs` stops at first `}`. Proto services with `google.api.http` annotations inside RPCs contain nested `{ }` blocks.
-
-### Solution
-
-Replace `serviceRe` regex with `extractServiceBlocks(content: string): Array<{ name: string; body: string }>`:
-
-1. Use regex only to find `service <Name> {` start positions (regex consumes the opening `{`)
-2. Initialise depth to 1 immediately after the opening `{`
-3. Scan forward char by char: `{` -> depth++, `}` -> depth--; collect into body
-4. Stop when depth reaches 0 (the matching closing `}`)
-5. Return name + body pairs
-
-Inner `rpcRe` regex remains unchanged — it operates on the already-extracted body.
-
-**Malformed input:** If EOF is reached before `depth` returns to 0, skip the incomplete service (do not add to results). Lock this in the test.
-
-**Scope limitation (v1):** Brace-depth only — no lexer for string literals or comments containing `{`/`}`. Sufficient for `google.api.http` annotations. Known false positive: braces inside `//` comments or quoted strings within proto options. Accepted for v1; a proper proto lexer is out of scope.
-
-### Tests
-
- Proto with single service, no nesting (regression)
- Proto with `google.api.http` nested braces inside RPC options
- Proto with multiple services
- Proto with nested `option` blocks inside RPC (e.g. `google.api.http`)
- Malformed proto with unclosed brace (graceful handling)
-
---
-
-## Fix 3: Directory Exclusions in Service Boundary Detector
-
-**File:** `gitnexus/src/core/group/service-boundary-detector.ts`
-**Risk:** Walks entire repo tree, only skipping dotfiles and `node_modules`. Extremely slow on repos with `vendor/`, `target/`, `__pycache__/`, `.venv/`.
-
-### Solution
-
-Create `EXCLUDED_DIRS` as a `Set<string>` (alongside existing `SERVICE_MARKERS`, `SOURCE_EXTENSIONS`), for example:
-
-```text
-node_modules, vendor, target, build, dist,
-__pycache__, .venv, venv, .tox, .mypy_cache,
-.gradle, .mvn, out, bin
-```
-
-(Implement as `new Set([...])` — the list above is the membership, not a string literal.)
-
-Apply in both:
- `walkForBoundaries` (line 77-78) — replace current inline `=== 'node_modules'` check with `EXCLUDED_DIRS.has(entry.name)`
- `hasSourceFilesInSubdirs` (line 130) — replace `entry.name !== 'node_modules'` with `!EXCLUDED_DIRS.has(entry.name)`
-
-Note: remove the old `=== 'node_modules'` literal from both locations — it is covered by `EXCLUDED_DIRS`.
-Dotfile exclusion (`.` prefix) remains as a separate check since it's a pattern, not a name.
-Exclusions apply only to `isDirectory()` entries — file names are never checked against `EXCLUDED_DIRS`.
-
-**Tradeoff:** Rare layouts that keep source under names like `out/` or `bin/` will be skipped; accepted for performance on typical monorepos.
-
-**Case sensitivity:** `Set.has` is case-sensitive (matches current `=== 'node_modules'` behavior). Windows case-insensitive FS not handled — accepted as-is, consistent with existing code.
-
-### Tests
-
- Directory named `vendor/` is skipped
- Directory named `target/` is skipped
- Directory named `__pycache__/` is skipped
- Regular source directories are NOT skipped
- Dotfile directories still skipped (regression)
-
---
-
-## Fix 4: Double-Close of LadybugDB Pools
-
-**Files:**
- `gitnexus/src/core/group/sync.ts` (lines 155-157) — per-id cleanup (KEEP)
- `gitnexus/src/cli/group.ts` (line 188) — blanket `closeLbug()` (REMOVE)
-
-**Risk:** In MCP server context, `closeLbug()` without arguments tears down ALL active pools, including ones from unrelated operations.
-
-### Solution
-
-Remove the `closeLbug()` call (no arguments) from `cli/group.ts` finally block. The per-id cleanup in `sync.ts` is sufficient:
-
-```typescript
-// sync.ts — KEEP: cleans up only pools opened by this sync
-finally {
-  for (const id of [...new Set(openPoolIds)]) {
-    await closeLbug(id).catch(() => {});
-  }
-}
-```
-
-```typescript
-// cli/group.ts — REMOVE: blanket close that kills all pools
-finally {
-  await closeLbug().catch(() => {});  // DELETE THIS
-}
-```
-
-Remove the `closeLbug` import from `cli/group.ts` — after removing the `finally` call it has no remaining usages.
-
-### Tests (unit level — mock pool adapter)
-
- `syncGroup` closes only the pools it opened (mock `closeLbug`, assert called with specific ids)
- Two-pool scenario: sync opens pools A and B, both closed in finally; pool C (opened elsewhere) not touched
- CLI `sync` command does not call blanket `closeLbug()` (verify no zero-arg call in source — static check or grep-based test)
-
---
-
-## Out of Scope
-
- JSON -> LadybugDB migration (tracked in #606)
- MEDIUM/LOW issues (items 5-10 from review summary)
- Test gap coverage beyond what's needed for these 4 fixes
- Any refactoring or architectural changes
-
-## Execution Order
-
-Fixes are independent — can be implemented in parallel or any order.
-Recommended order for review clarity: 1 -> 3 -> 4 -> 2 (simplest to most complex).
@@ -1,83 +0,0 @@
-import tsPlugin from '@typescript-eslint/eslint-plugin';
-import tsParser from '@typescript-eslint/parser';
-import unusedImports from 'eslint-plugin-unused-imports';
-import reactHooks from 'eslint-plugin-react-hooks';
-import prettierConfig from 'eslint-config-prettier';
-
-export default [
-  // Global ignores
-  {
-    ignores: [
-      '**/dist/**',
-      '**/node_modules/**',
-      '**/coverage/**',
-      'gitnexus/vendor/**',
-      'gitnexus-web/src/vendor/**',
-      'gitnexus/test/fixtures/**',
-      'gitnexus-web/playwright-report/**',
-      'gitnexus-web/test-results/**',
-      '**/*.d.ts',
-      '.claude/**',
-      '.history/**',
-    ],
-  },
-
-  // Base TypeScript config for all packages
-  {
-    files: ['**/*.{ts,tsx}'],
-    languageOptions: {
-      parser: tsParser,
-      parserOptions: {
-        ecmaVersion: 2022,
-        sourceType: 'module',
-      },
-    },
-    plugins: {
-      '@typescript-eslint': tsPlugin,
-      'unused-imports': unusedImports,
-    },
-    rules: {
-      // Unused imports — auto-fixable
-      'unused-imports/no-unused-imports': 'error',
-      'unused-imports/no-unused-vars': [
-        'warn',
-        { vars: 'all', varsIgnorePattern: '^_', args: 'after-used', argsIgnorePattern: '^_' },
-      ],
-
-      // TypeScript quality
-      '@typescript-eslint/no-unused-vars': 'off', // handled by unused-imports plugin
-      'no-unused-vars': 'off', // handled by unused-imports plugin
-      '@typescript-eslint/no-explicit-any': 'warn',
-      '@typescript-eslint/no-non-null-assertion': 'warn',
-
-      // General quality
-      'no-debugger': 'error',
-      'prefer-const': 'error',
-      'no-var': 'error',
-      eqeqeq: ['error', 'always', { null: 'ignore' }],
-    },
-  },
-
-  // CLI package — allow console.log (it's a CLI tool)
-  {
-    files: ['gitnexus/src/cli/**/*.ts', 'gitnexus/src/server/**/*.ts'],
-    rules: {
-      'no-console': 'off',
-    },
-  },
-
-  // React-specific rules for gitnexus-web
-  {
-    files: ['gitnexus-web/src/**/*.{ts,tsx}'],
-    plugins: {
-      'react-hooks': reactHooks,
-    },
-    rules: {
-      'react-hooks/rules-of-hooks': 'error',
-      'react-hooks/exhaustive-deps': 'warn',
-    },
-  },
-
-  // Disable formatting rules (prettier handles those)
-  prettierConfig,
-];
@@ -50,10 +50,6 @@ All models are routed through **OpenRouter** by default, so a single `OPENROUTER
 docker pull swebench/sweb.eval.x86_64.django_1776_django-16527:latest
 ```

-### Debug logging
-
-Set `GITNEXUS_EVAL_DEBUG=1` to include full Python tracebacks in run summaries and logs. By default, errors are sanitized to avoid leaking host paths or stack traces.
-
 ## Quick Start

 ### Debug a single instance
@@ -22,10 +22,8 @@ import time
 from enum import Enum
 from pathlib import Path

-from constants import AUGMENT_TIMEOUT_SECONDS
 from minisweagent import Environment, Model
 from minisweagent.agents.default import AgentConfig, DefaultAgent
-from tool_registry import BINARIES_BY_KEY, TOOL_METRIC_KEYS

 logger = logging.getLogger("gitnexus_agent")

@@ -42,7 +40,7 @@ class GitNexusMode(str, Enum):
 class GitNexusAgentConfig(AgentConfig):
    """Extended config for GitNexus evaluation agent."""
    gitnexus_mode: GitNexusMode = GitNexusMode.BASELINE
-    augment_timeout: float = AUGMENT_TIMEOUT_SECONDS
+    augment_timeout: float = 5.0
    augment_min_pattern_length: int = 3
    track_gitnexus_usage: bool = True

@@ -154,10 +152,16 @@ class GitNexusAgent(DefaultAgent):
        """Track which GitNexus tools the agent uses."""
        for action in message.get("extra", {}).get("actions", []):
            command = action.get("command", "")
-            for key, binary in BINARIES_BY_KEY.items():
-                if binary in command and key in self.gitnexus_metrics.tool_calls:
-                    self.gitnexus_metrics.tool_calls[key] += 1
-                    break
+            if "gitnexus-query" in command:
+                self.gitnexus_metrics.tool_calls["query"] += 1
+            elif "gitnexus-context" in command:
+                self.gitnexus_metrics.tool_calls["context"] += 1
+            elif "gitnexus-impact" in command:
+                self.gitnexus_metrics.tool_calls["impact"] += 1
+            elif "gitnexus-cypher" in command:
+                self.gitnexus_metrics.tool_calls["cypher"] += 1
+            elif "gitnexus-overview" in command:
+                self.gitnexus_metrics.tool_calls["overview"] += 1

    def serialize(self, *extra_dicts) -> dict:
        """Serialize with GitNexus-specific metrics."""
@@ -176,7 +180,13 @@ class GitNexusMetrics:
    """Tracks GitNexus-specific metrics during evaluation."""

    def __init__(self):
-        self.tool_calls: dict[str, int] = {key: 0 for key in TOOL_METRIC_KEYS}
+        self.tool_calls: dict[str, int] = {
+            "query": 0,
+            "context": 0,
+            "impact": 0,
+            "cypher": 0,
+            "overview": 0,
+        }
        self.augmentation_calls: int = 0
        self.augmentation_hits: int = 0
        self.augmentation_errors: int = 0
@@ -27,8 +27,6 @@ import typer
 from rich.console import Console
 from rich.table import Table

-from tool_registry import TOOL_METRIC_KEYS
-
 logger = logging.getLogger("analyze_results")
 console = Console()
 app = typer.Typer(rich_markup_mode="rich", add_completion=False)
@@ -79,20 +77,13 @@ def load_run_results(results_dir: Path) -> dict[str, dict]:


 def parse_run_id(run_id: str) -> tuple[str, str]:
-    """Parse 'model_mode' into (model, mode) using known suffixes."""
-    # Match the longest known suffix first to avoid hyphen collisions in model names.
-    known_modes = [
-        "native_augment",
-        "native",
-        "baseline",
-        "mcp",
-        "augment",
-        "full",
-    ]
-    for mode in known_modes:
-        suffix = f"_{mode}"
-        if run_id.endswith(suffix):
-            return run_id[: -len(suffix)], mode
+    """Parse 'model_mode' into (model, mode)."""
+    # Handle multi-word model names like 'minimax-2.5'
+    # Modes are: baseline, mcp, augment, full
+    known_modes = {"baseline", "mcp", "augment", "full"}
+    parts = run_id.rsplit("_", 1)
+    if len(parts) == 2 and parts[1] in known_modes:
+        return parts[0], parts[1]
    return run_id, "unknown"


@@ -275,17 +266,12 @@ def compare_modes(
        _, mode = parse_run_id(run_id)
        metrics[mode] = compute_metrics(run_data)

-    mode_order = [
-        mode
-        for mode in ["baseline", "native", "native_augment", "mcp", "augment", "full"]
-        if mode in metrics
-    ] or sorted(metrics.keys())
-
    # Print comparison table
    table = Table(title=f"Mode Comparison: {model}")
    table.add_column("Metric", style="bold")
-    for mode in mode_order:
-        table.add_column(mode, justify="right")
+    for mode in ["baseline", "mcp", "augment", "full"]:
+        if mode in metrics:
+            table.add_column(mode, justify="right")

    rows = [
        ("Instances", "n_instances", "d"),
@@ -302,7 +288,7 @@ def compare_modes(

    for label, key, fmt in rows:
        values = []
-        for mode in mode_order:
+        for mode in ["baseline", "mcp", "augment", "full"]:
            if mode in metrics:
                v = metrics[mode].get(key, 0)
                if fmt == ".1%":
@@ -321,8 +307,8 @@ def compare_modes(
        baseline_calls = metrics["baseline"]["avg_api_calls"]

        table.add_section()
-        for mode in mode_order:
-            if mode == "baseline":
+        for mode in ["mcp", "augment", "full"]:
+            if mode not in metrics:
                continue
            mode_cost = metrics[mode]["avg_cost"]
            mode_calls = metrics[mode]["avg_api_calls"]
@@ -354,8 +340,10 @@ def gitnexus_usage(

    table = Table(title="Tool Usage by Run")
    table.add_column("Run", style="bold")
-    for key in TOOL_METRIC_KEYS:
-        table.add_column(key, justify="right")
+    table.add_column("query", justify="right")
+    table.add_column("context", justify="right")
+    table.add_column("impact", justify="right")
+    table.add_column("cypher", justify="right")
    table.add_column("Total", justify="right")
    table.add_column("Augment Hits", justify="right")

@@ -365,7 +353,7 @@ def gitnexus_usage(
            continue

        # Aggregate tool calls across trajectories
-        tool_totals: dict[str, int] = {key: 0 for key in TOOL_METRIC_KEYS}
+        tool_totals: dict[str, int] = {"query": 0, "context": 0, "impact": 0, "cypher": 0, "overview": 0}
        augment_hits = 0

        for traj in run_data.get("trajectories", {}).values():
@@ -385,7 +373,10 @@ def gitnexus_usage(
        if total > 0 or augment_hits > 0:
            table.add_row(
                run_id,
-                *[str(tool_totals.get(key, 0)) for key in TOOL_METRIC_KEYS],
+                str(tool_totals.get("query", 0)),
+                str(tool_totals.get("context", 0)),
+                str(tool_totals.get("impact", 0)),
+                str(tool_totals.get("cypher", 0)),
                str(total),
                str(augment_hits),
            )
@@ -17,14 +17,6 @@ import time
 from pathlib import Path
 from typing import Any

-from constants import (
-    MCP_FIND_GITNEXUS_FALLBACK_TIMEOUT_SECONDS,
-    MCP_FIND_GITNEXUS_TIMEOUT_SECONDS,
-    MCP_READ_TIMEOUT_SECONDS,
-    MCP_STOP_WAIT_SECONDS,
-)
-from utils.errors import is_debug_enabled, log_safe_exception
-
 logger = logging.getLogger("mcp_bridge")


@@ -86,7 +78,7 @@ class MCPBridge:
            return True

        except Exception as e:
-            log_safe_exception(logger, "Failed to start MCP bridge", e, include_debug=is_debug_enabled())
+            logger.error(f"Failed to start MCP bridge: {e}")
            self.stop()
            return False

@@ -94,14 +86,9 @@ class MCPBridge:
        """Stop the MCP server subprocess."""
        if self.process:
            try:
-                if self.process.stdin:
-                    self.process.stdin.close()
-                if self.process.stdout:
-                    self.process.stdout.close()
-                if self.process.stderr:
-                    self.process.stderr.close()
+                self.process.stdin.close()
                self.process.terminate()
-                self.process.wait(timeout=MCP_STOP_WAIT_SECONDS)
+                self.process.wait(timeout=5)
            except Exception:
                try:
                    self.process.kill()
@@ -159,9 +146,7 @@ class MCPBridge:
            try:
                result = subprocess.run(
                    [cmd, "gitnexus", "--version"],
-                    capture_output=True,
-                    text=True,
-                    timeout=MCP_FIND_GITNEXUS_TIMEOUT_SECONDS,
+                    capture_output=True, text=True, timeout=15,
                    cwd=self.repo_path,
                )
                if result.returncode == 0:
@@ -173,9 +158,7 @@ class MCPBridge:
        try:
            result = subprocess.run(
                ["gitnexus", "--version"],
-                capture_output=True,
-                text=True,
-                timeout=MCP_FIND_GITNEXUS_FALLBACK_TIMEOUT_SECONDS,
+                capture_output=True, text=True, timeout=10,
            )
            if result.returncode == 0:
                return "gitnexus"
@@ -211,7 +194,7 @@ class MCPBridge:
            self.process.stdin.flush()

            # Read response
-            response = self._read_response(timeout=MCP_READ_TIMEOUT_SECONDS)
+            response = self._read_response(timeout=30)
            if response and response.get("id") == request_id:
                if "error" in response:
                    logger.error(f"MCP error: {response['error']}")
@@ -220,7 +203,7 @@ class MCPBridge:
            return None

        except Exception as e:
-            log_safe_exception(logger, "MCP request failed", e, include_debug=is_debug_enabled())
+            logger.error(f"MCP request failed: {e}")
            return None

    def _send_notification(self, method: str, params: dict):
@@ -241,67 +224,42 @@ class MCPBridge:
            self.process.stdin.write(message.encode("utf-8"))
            self.process.stdin.flush()
        except Exception as e:
-            log_safe_exception(logger, "MCP notification failed", e, include_debug=is_debug_enabled())
+            logger.error(f"MCP notification failed: {e}")

-    def _read_content_length(self, deadline: float) -> int | None:
-        """Read Content-Length header, returning the byte length or None."""
-        if not self.process or not self.process.stdout:
-            return None
-
-        header_line = b""
-        while time.time() < deadline:
-            byte = self.process.stdout.read(1)
-            if not byte:
-                return None
-            header_line += byte
-            if header_line.endswith(b"\r\n\r\n") or header_line.endswith(b"\n\n"):
-                break
-
-        if not header_line:
-            return None
-
-        header_str = header_line.decode("utf-8").strip()
-        for line in header_str.split("\r\n"):
-            if line.lower().startswith("content-length:"):
-                try:
-                    return int(line.split(":", 1)[1].strip())
-                except (ValueError, IndexError):
-                    return None
-        return None
-
-    def _read_body(self, content_length: int, deadline: float) -> bytes | None:
-        """Read a response body of the expected length before deadline."""
-        if not self.process or not self.process.stdout:
-            return None
-
-        remaining = content_length
-        chunks: list[bytes] = []
-
-        while remaining > 0 and time.time() < deadline:
-            chunk = self.process.stdout.read(remaining)
-            if not chunk:
-                return None
-            chunks.append(chunk)
-            remaining -= len(chunk)
-
-        if remaining > 0:
-            return None
-
-        return b"".join(chunks)
-
-    def _read_response(self, timeout: float = MCP_READ_TIMEOUT_SECONDS) -> dict | None:
+    def _read_response(self, timeout: float = 30) -> dict | None:
        """Read a JSON-RPC response from the MCP server."""
        if not self.process or not self.process.stdout:
            return None

+        start = time.time()
+
        try:
-            deadline = time.time() + timeout
-            while time.time() < deadline:
-                content_length = self._read_content_length(deadline)
+            while time.time() - start < timeout:
+                # Read Content-Length header
+                header_line = b""
+                while True:
+                    byte = self.process.stdout.read(1)
+                    if not byte:
+                        return None
+                    header_line += byte
+                    if header_line.endswith(b"\r\n\r\n"):
+                        break
+                    if header_line.endswith(b"\n\n"):
+                        break
+
+                # Parse content length
+                header_str = header_line.decode("utf-8").strip()
+                content_length = None
+                for line in header_str.split("\r\n"):
+                    if line.lower().startswith("content-length:"):
+                        content_length = int(line.split(":")[1].strip())
+                        break
+
                if content_length is None:
                    continue

-                body = self._read_body(content_length, deadline)
+                # Read body
+                body = self.process.stdout.read(content_length)
                if not body:
                    return None

@@ -314,7 +272,7 @@ class MCPBridge:
            return None

        except Exception as e:
-            log_safe_exception(logger, "Error reading MCP response", e, include_debug=is_debug_enabled())
+            logger.error(f"Error reading MCP response: {e}")
            return None


@@ -1,8 +1,8 @@
 # Claude Haiku 4.5 — fast, cheap, good baseline
 # Via OpenRouter (set OPENROUTER_API_KEY in .env)
 model:
-  model_name: 'openrouter/anthropic/claude-haiku-4.5'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/anthropic/claude-haiku-4.5"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 8192
    temperature: 0
@@ -2,8 +2,8 @@
 # Via OpenRouter (set OPENROUTER_API_KEY in .env)
 # To use Anthropic directly, change to: anthropic/claude-opus-4-20250514
 model:
-  model_name: 'openrouter/anthropic/claude-opus-4'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/anthropic/claude-opus-4"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 16384
    temperature: 0
@@ -2,8 +2,8 @@
 # Via OpenRouter (set OPENROUTER_API_KEY in .env)
 # To use Anthropic directly, change to: anthropic/claude-sonnet-4-20250514
 model:
-  model_name: 'openrouter/anthropic/claude-sonnet-4'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/anthropic/claude-sonnet-4"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 16384
    temperature: 0
@@ -1,9 +1,9 @@
 model: deepseek-ai/deepseek-chat
 provider: openrouter
 cost:
-  input: 0.14 # per 1M tokens
-  output: 0.28 # per 1M tokens
-
+  input: 0.14  # per 1M tokens
+  output: 0.28  # per 1M tokens
+  
 # Native DeepSeek API (direct)
 api_key: null
 base_url: null
@@ -1,9 +1,9 @@
 model: deepseek-ai/DeepSeek-V3
 provider: openrouter
 cost:
-  input: 0.27 # per 1M tokens
-  output: 1.10 # per 1M tokens
-
+  input: 0.27  # per 1M tokens
+  output: 1.10  # per 1M tokens
+  
 # Native DeepSeek API (direct)
 # Get your API key at: https://platform.deepseek.com/
 # Or use OpenRouter with: OPENROUTER_API_KEY
@@ -1,7 +1,7 @@
 # GLM 4.7 — via OpenRouter (set OPENROUTER_API_KEY in .env)
 model:
-  model_name: 'openrouter/zhipuai/glm-4.7'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/zhipuai/glm-4.7"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 8192
    temperature: 0
@@ -1,7 +1,7 @@
 # GLM 5 — via OpenRouter (set OPENROUTER_API_KEY in .env)
 model:
-  model_name: 'openrouter/zhipuai/glm-5'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/zhipuai/glm-5"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 8192
    temperature: 0
@@ -1,7 +1,7 @@
 # MiniMax M1 2.5 — via OpenRouter (set OPENROUTER_API_KEY in .env)
 model:
-  model_name: 'openrouter/minimax/minimax-m1-2.5'
-  cost_tracking: 'ignore_errors'
+  model_name: "openrouter/minimax/minimax-m1-2.5"
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 8192
    temperature: 0
@@ -3,9 +3,9 @@
 # The action_regex tells mini-swe-agent to parse ```bash blocks from responses.
 model:
  model_class: litellm_textbased
-  model_name: 'openrouter/minimax/minimax-m2.5'
+  model_name: "openrouter/minimax/minimax-m2.5"
  action_regex: "```(?:bash|mswea_bash_command)\\s*\\n(.*?)\\n```"
-  cost_tracking: 'ignore_errors'
+  cost_tracking: "ignore_errors"
  model_kwargs:
    max_tokens: 8192
    temperature: 0
@@ -1,9 +1,9 @@
 # Baseline mode — no GitNexus, pure mini-swe-agent (control group)
 agent:
-  agent_class: 'eval.agents.gitnexus_agent.GitNexusAgent'
-  gitnexus_mode: 'baseline'
+  agent_class: "eval.agents.gitnexus_agent.GitNexusAgent"
+  gitnexus_mode: "baseline"
  step_limit: 30
  cost_limit: 3.0

 environment:
-  environment_class: 'docker'
+  environment_class: "docker"
@@ -5,14 +5,14 @@
 #
 # Use this mode to isolate the value of explicit tools without grep augmentation.
 agent:
-  agent_class: 'eval.agents.gitnexus_agent.GitNexusAgent'
-  gitnexus_mode: 'native'
+  agent_class: "eval.agents.gitnexus_agent.GitNexusAgent"
+  gitnexus_mode: "native"
  step_limit: 30
  cost_limit: 3.0
  track_gitnexus_usage: true

 environment:
-  environment_class: 'eval.environments.gitnexus_docker.GitNexusDockerEnvironment'
+  environment_class: "eval.environments.gitnexus_docker.GitNexusDockerEnvironment"
  enable_gitnexus: true
  skip_embeddings: true
  gitnexus_timeout: 120
@@ -8,8 +8,8 @@
 #
 # The agent decides when to use explicit tools vs rely on enriched grep results.
 agent:
-  agent_class: 'eval.agents.gitnexus_agent.GitNexusAgent'
-  gitnexus_mode: 'native_augment'
+  agent_class: "eval.agents.gitnexus_agent.GitNexusAgent"
+  gitnexus_mode: "native_augment"
  step_limit: 30
  cost_limit: 3.0
  augment_timeout: 5.0
@@ -17,7 +17,7 @@ agent:
  track_gitnexus_usage: true

 environment:
-  environment_class: 'eval.environments.gitnexus_docker.GitNexusDockerEnvironment'
+  environment_class: "eval.environments.gitnexus_docker.GitNexusDockerEnvironment"
  enable_gitnexus: true
  skip_embeddings: true
  gitnexus_timeout: 120
@@ -1,15 +0,0 @@
-DEBUG_ENV_VAR = "GITNEXUS_EVAL_DEBUG"
-
-# GitNexus eval-server health checks
-EVAL_SERVER_HEALTH_RETRIES = 30
-EVAL_SERVER_HEALTH_INTERVAL_SECONDS = 0.5
-EVAL_SERVER_HEALTH_TIMEOUT_SECONDS = 3
-
-# MCP bridge timeouts
-MCP_FIND_GITNEXUS_TIMEOUT_SECONDS = 15
-MCP_FIND_GITNEXUS_FALLBACK_TIMEOUT_SECONDS = 10
-MCP_READ_TIMEOUT_SECONDS = 30
-MCP_STOP_WAIT_SECONDS = 5
-
-# Agent defaults
-AUGMENT_TIMEOUT_SECONDS = 5.0
@@ -26,20 +26,72 @@ import shutil
 import time
 from pathlib import Path

-from constants import (
-    EVAL_SERVER_HEALTH_INTERVAL_SECONDS,
-    EVAL_SERVER_HEALTH_RETRIES,
-    EVAL_SERVER_HEALTH_TIMEOUT_SECONDS,
-)
 from minisweagent.environments.docker import DockerEnvironment
-from tool_registry import TOOL_SPECS, ToolScriptSpec
-from utils.errors import is_debug_enabled, log_safe_exception

 logger = logging.getLogger("gitnexus_docker")

 DEFAULT_CACHE_DIR = Path.home() / ".gitnexus-eval-cache"
 EVAL_SERVER_PORT = 4848

+# Standalone tool scripts installed into /usr/local/bin/ inside the container.
+# Each script calls the eval-server via curl, with a CLI fallback.
+# These are standalone — no sourcing, no env inheritance needed.
+
+TOOL_SCRIPT_QUERY = r'''#!/bin/bash
+PORT="${GITNEXUS_EVAL_PORT:-__PORT__}"
+query="$1"; task_ctx="${2:-}"; goal="${3:-}"
+[ -z "$query" ] && echo "Usage: gitnexus-query <query> [task_context] [goal]" && exit 1
+args="{\"query\": \"$query\""
+[ -n "$task_ctx" ] && args="$args, \"task_context\": \"$task_ctx\""
+[ -n "$goal" ] && args="$args, \"goal\": \"$goal\""
+args="$args}"
+result=$(curl -sf -X POST "http://127.0.0.1:${PORT}/tool/query" -H "Content-Type: application/json" -d "$args" 2>/dev/null)
+if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi
+cd /testbed && npx gitnexus query "$query" 2>&1
+'''
+
+TOOL_SCRIPT_CONTEXT = r'''#!/bin/bash
+PORT="${GITNEXUS_EVAL_PORT:-__PORT__}"
+name="$1"; file_path="${2:-}"
+[ -z "$name" ] && echo "Usage: gitnexus-context <symbol_name> [file_path]" && exit 1
+args="{\"name\": \"$name\""
+[ -n "$file_path" ] && args="$args, \"file_path\": \"$file_path\""
+args="$args}"
+result=$(curl -sf -X POST "http://127.0.0.1:${PORT}/tool/context" -H "Content-Type: application/json" -d "$args" 2>/dev/null)
+if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi
+cd /testbed && npx gitnexus context "$name" 2>&1
+'''
+
+TOOL_SCRIPT_IMPACT = r'''#!/bin/bash
+PORT="${GITNEXUS_EVAL_PORT:-__PORT__}"
+target="$1"; direction="${2:-upstream}"
+[ -z "$target" ] && echo "Usage: gitnexus-impact <symbol_name> [upstream|downstream]" && exit 1
+result=$(curl -sf -X POST "http://127.0.0.1:${PORT}/tool/impact" -H "Content-Type: application/json" -d "{\"target\": \"$target\", \"direction\": \"$direction\"}" 2>/dev/null)
+if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi
+cd /testbed && npx gitnexus impact "$target" --direction "$direction" 2>&1
+'''
+
+TOOL_SCRIPT_CYPHER = r'''#!/bin/bash
+PORT="${GITNEXUS_EVAL_PORT:-__PORT__}"
+query="$1"
+[ -z "$query" ] && echo "Usage: gitnexus-cypher <cypher_query>" && exit 1
+result=$(curl -sf -X POST "http://127.0.0.1:${PORT}/tool/cypher" -H "Content-Type: application/json" -d "{\"query\": \"$query\"}" 2>/dev/null)
+if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi
+cd /testbed && npx gitnexus cypher "$query" 2>&1
+'''
+
+TOOL_SCRIPT_AUGMENT = r'''#!/bin/bash
+cd /testbed && npx gitnexus augment "$1" 2>&1 || true
+'''
+
+TOOL_SCRIPT_OVERVIEW = r'''#!/bin/bash
+PORT="${GITNEXUS_EVAL_PORT:-__PORT__}"
+echo "=== Code Knowledge Graph Overview ==="
+result=$(curl -sf -X POST "http://127.0.0.1:${PORT}/tool/list_repos" -H "Content-Type: application/json" -d "{}" 2>/dev/null)
+if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi
+cd /testbed && npx gitnexus list 2>&1
+'''
+

 class GitNexusDockerEnvironment(DockerEnvironment):
    """
@@ -81,13 +133,7 @@ class GitNexusDockerEnvironment(DockerEnvironment):
            try:
                self._setup_gitnexus()
            except Exception as e:
-                log_safe_exception(
-                    logger,
-                    "GitNexus setup failed, continuing without it",
-                    e,
-                    include_debug=is_debug_enabled(),
-                    level="warning",
-                )
+                logger.warning(f"GitNexus setup failed, continuing without it: {e}")
                self._gitnexus_ready = False

        return result
@@ -176,59 +222,27 @@ class GitNexusDockerEnvironment(DockerEnvironment):
            "timeout": 5,
        })

-        # Wait for the server to be ready (up to ~15s for KuzuDB init)
-        for i in range(EVAL_SERVER_HEALTH_RETRIES):
-            time.sleep(EVAL_SERVER_HEALTH_INTERVAL_SECONDS)
+        # Wait for the server to be ready (up to 15s for KuzuDB init)
+        for i in range(30):
+            time.sleep(0.5)
            health = self.execute({
                "command": f"curl -sf http://127.0.0.1:{self.eval_server_port}/health 2>/dev/null || echo 'NOT_READY'",
-                "timeout": EVAL_SERVER_HEALTH_TIMEOUT_SECONDS,
+                "timeout": 3,
            })
            output = health.get("output", "").strip()
            if "NOT_READY" not in output and "ok" in output:
-                logger.info(
-                    f"Eval-server ready after {(i + 1) * EVAL_SERVER_HEALTH_INTERVAL_SECONDS:.1f}s"
-                )
+                logger.info(f"Eval-server ready after {(i + 1) * 0.5:.1f}s")
                return

        log_output = self.execute({
            "command": "cat /tmp/gitnexus-eval-server.log 2>/dev/null | tail -20",
        })
        logger.warning(
-            f"Eval-server didn't become ready in "
-            f"{EVAL_SERVER_HEALTH_RETRIES * EVAL_SERVER_HEALTH_INTERVAL_SECONDS:.1f}s. "
+            f"Eval-server didn't become ready in 15s. "
            f"Tools will fall back to direct CLI.\n"
            f"Server log: {log_output.get('output', 'N/A')}"
        )

-    @staticmethod
-    def _render_tool_script(spec: ToolScriptSpec, port: str) -> str:
-        """
-        Render a standalone bash script for a GitNexus tool.
-
-        Scripts call the eval-server fast path when an endpoint is present,
-        and fall back to the CLI otherwise.
-        """
-        lines = ["#!/bin/bash"]
-
-        if spec.endpoint:
-            lines.append(f'PORT="${{GITNEXUS_EVAL_PORT:-{port}}}"')
-
-        if spec.header:
-            lines.append(spec.header.strip())
-
-        if spec.payload_builder:
-            lines.append(spec.payload_builder.strip())
-
-        if spec.endpoint:
-            lines.append(
-                f'result=$(curl -sf -X POST "http://127.0.0.1:${{PORT}}{spec.endpoint}" '
-                '-H "Content-Type: application/json" -d "$payload" 2>/dev/null)'
-            )
-            lines.append('if [ $? -eq 0 ] && [ -n "$result" ]; then echo "$result"; exit 0; fi')
-
-        lines.append(spec.fallback.strip())
-        return "\n".join(lines)
-
    def _install_tools(self):
        """
        Install standalone GitNexus tool scripts in /usr/local/bin/.
@@ -245,20 +259,24 @@ class GitNexusDockerEnvironment(DockerEnvironment):
        """
        port = str(self.eval_server_port)

-        for spec in TOOL_SPECS.values():
-            script_content = self._render_tool_script(spec, port).strip()
+        tools = {
+            "gitnexus-query": TOOL_SCRIPT_QUERY,
+            "gitnexus-context": TOOL_SCRIPT_CONTEXT,
+            "gitnexus-impact": TOOL_SCRIPT_IMPACT,
+            "gitnexus-cypher": TOOL_SCRIPT_CYPHER,
+            "gitnexus-augment": TOOL_SCRIPT_AUGMENT,
+            "gitnexus-overview": TOOL_SCRIPT_OVERVIEW,
+        }
+
+        for name, script in tools.items():
+            script_content = script.replace("__PORT__", port).strip()
            # Use heredoc with quoted delimiter — prevents all variable expansion and quoting issues
            self.execute({
-                "command": (
-                    f"cat << 'GITNEXUS_SCRIPT_EOF' > /usr/local/bin/{spec.bin_name}\n"
-                    f"{script_content}\n"
-                    "GITNEXUS_SCRIPT_EOF\n"
-                    f"chmod +x /usr/local/bin/{spec.bin_name}"
-                ),
+                "command": f"cat << 'GITNEXUS_SCRIPT_EOF' > /usr/local/bin/{name}\n{script_content}\nGITNEXUS_SCRIPT_EOF\nchmod +x /usr/local/bin/{name}",
                "timeout": 5,
            })

-        logger.info(f"Installed {len(TOOL_SPECS)} GitNexus tool scripts in /usr/local/bin/")
+        logger.info(f"Installed {len(tools)} GitNexus tool scripts in /usr/local/bin/")

    def _get_repo_info(self) -> dict:
        """Get repository identity info from the container."""
@@ -307,13 +325,7 @@ class GitNexusDockerEnvironment(DockerEnvironment):
                    logger.info(f"Cached GitNexus index: {cache_path}")

        except Exception as e:
-            log_safe_exception(
-                logger,
-                "Failed to cache GitNexus index",
-                e,
-                include_debug=is_debug_enabled(),
-                level="warning",
-            )
+            logger.warning(f"Failed to cache GitNexus index: {e}")
            if cache_path.exists():
                shutil.rmtree(cache_path, ignore_errors=True)

@@ -349,13 +361,7 @@ class GitNexusDockerEnvironment(DockerEnvironment):
                logger.info("GitNexus index restored from cache")

        except Exception as e:
-            log_safe_exception(
-                logger,
-                "Failed to restore cache, re-indexing",
-                e,
-                include_debug=is_debug_enabled(),
-                level="warning",
-            )
+            logger.warning(f"Failed to restore cache, re-indexing: {e}")
            self._index_repository()

    def stop(self) -> dict:
@@ -6,7 +6,7 @@ readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
    "mini-swe-agent>=2.0.0",
-    "litellm>=1.50.0,!=1.82.7,!=1.82.8",
+    "litellm>=1.50.0",
    "datasets>=3.0.0",
    "typer>=0.12.0",
    "rich>=13.0.0",
@@ -20,8 +20,6 @@ dependencies = [
 dev = [
    "pytest>=8.0.0",
    "ruff>=0.5.0",
-    "hypothesis>=6.88.0",
-    "coverage>=7.6.0",
 ]

 [project.scripts]
@@ -33,8 +31,8 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"

 [tool.hatch.build.targets.wheel]
-packages = ["agents", "environments", "analysis", "bridge", "utils"]
-extra-files = ["run_eval.py", "tool_registry.py", "constants.py"]
+packages = ["agents", "environments", "analysis", "bridge"]
+extra-files = ["run_eval.py"]

 [tool.ruff]
 line-length = 120
@@ -25,6 +25,7 @@ import logging
 import os
 import threading
 import time
+import traceback
 from itertools import product
 from pathlib import Path
 from typing import Any
@@ -35,8 +36,6 @@ from rich.console import Console
 from rich.live import Live
 from rich.table import Table

-from utils.errors import is_debug_enabled, log_safe_exception
-
 # Load .env file from eval/ directory
 _env_file = Path(__file__).parent / ".env"
 if _env_file.exists():
@@ -139,65 +138,6 @@ def get_swebench_docker_image(instance: dict) -> str:
    return image_name


-def _build_model(config: dict):
-    """Construct the model from config."""
-    from minisweagent.models import get_model
-
-    return get_model(config=config.get("model", {}))
-
-
-def _build_environment(config: dict, instance: dict):
-    """Construct the environment for the instance."""
-    env_config = dict(config.get("environment", {}))
-    env_class_name = env_config.pop("environment_class", "docker")
-
-    if env_class_name == "eval.environments.gitnexus_docker.GitNexusDockerEnvironment":
-        from environments.gitnexus_docker import GitNexusDockerEnvironment
-
-        env_config["image"] = get_swebench_docker_image(instance)
-        return GitNexusDockerEnvironment(**env_config)
-
-    from minisweagent.environments.docker import DockerEnvironment
-
-    return DockerEnvironment(image=get_swebench_docker_image(instance), **env_config)
-
-
-def _build_agent(config: dict, model, env, instance_dir: Path, instance_id: str):
-    """Construct the GitNexus agent with trajectory output configured."""
-    from agents.gitnexus_agent import GitNexusAgent
-
-    agent_config = dict(config.get("agent", {}))
-    agent_config.pop("agent_class", "eval.agents.gitnexus_agent.GitNexusAgent")
-    traj_path = instance_dir / f"{instance_id}.traj.json"
-    agent_config["output_path"] = traj_path
-    return GitNexusAgent(model, env, **agent_config)
-
-
-def _extract_submission(env, info: dict, run_id: str) -> str:
-    """Pull the git diff patch from the container, falling back to the agent submission."""
-    try:
-        patch_output = env.execute({"command": "cd /testbed && git diff"})
-        return patch_output.get("output", "").strip()
-    except Exception as patch_err:
-        logger.warning(f"[{run_id}] Failed to extract patch: {patch_err}")
-        return info.get("submission", "")
-
-
-def _record_failure(run_id: str, instance_id: str, result: dict, error: Exception):
-    sanitized = log_safe_exception(
-        logger,
-        f"[{run_id}] Error on {instance_id}",
-        error,
-        include_debug=is_debug_enabled(),
-    )
-    result["exit_status"] = sanitized["error_type"]
-    result["error_type"] = sanitized["error_type"]
-    result["error_message"] = sanitized["error_message"]
-    result["error"] = sanitized["error_message"]
-    if "error_detail_debug" in sanitized:
-        result["error_detail_debug"] = sanitized["error_detail_debug"]
-
-
 def process_instance(
    instance: dict,
    config: dict,
@@ -209,6 +149,8 @@ def process_instance(
    Process a single SWE-bench instance with the given config.
    Returns result dict with instance_id, exit_status, submission, metrics.
    """
+    from minisweagent.models import get_model
+
    instance_id = instance["instance_id"]
    run_id = f"{model_name}_{mode_name}"
    instance_dir = output_dir / run_id / instance_id
@@ -226,12 +168,31 @@ def process_instance(
    }

    agent = None
-    env = None

    try:
-        model = _build_model(config)
-        env = _build_environment(config, instance)
-        agent = _build_agent(config, model, env, instance_dir, instance_id)
+        # Build model
+        model = get_model(config=config.get("model", {}))
+
+        # Build environment
+        env_config = dict(config.get("environment", {}))
+        env_class_name = env_config.pop("environment_class", "docker")
+
+        if env_class_name == "eval.environments.gitnexus_docker.GitNexusDockerEnvironment":
+            from environments.gitnexus_docker import GitNexusDockerEnvironment
+            env_config["image"] = get_swebench_docker_image(instance)
+            env = GitNexusDockerEnvironment(**env_config)
+        else:
+            from minisweagent.environments.docker import DockerEnvironment
+            env = DockerEnvironment(image=get_swebench_docker_image(instance), **env_config)
+
+        # Build agent
+        agent_config = dict(config.get("agent", {}))
+        agent_class_name = agent_config.pop("agent_class", "eval.agents.gitnexus_agent.GitNexusAgent")
+
+        from agents.gitnexus_agent import GitNexusAgent
+        traj_path = instance_dir / f"{instance_id}.traj.json"
+        agent_config["output_path"] = traj_path
+        agent = GitNexusAgent(model, env, **agent_config)

        # Run
        logger.info(f"[{run_id}] Starting {instance_id}")
@@ -243,10 +204,18 @@ def process_instance(
        result["gitnexus_metrics"] = agent.gitnexus_metrics.to_dict()

        # Extract git diff patch from the container (SWE-bench needs the model_patch)
-        result["submission"] = _extract_submission(env, info, run_id)
+        try:
+            patch_output = env.execute({"command": "cd /testbed && git diff"})
+            result["submission"] = patch_output.get("output", "").strip()
+        except Exception as patch_err:
+            logger.warning(f"[{run_id}] Failed to extract patch: {patch_err}")
+            result["submission"] = info.get("submission", "")

    except Exception as e:
-        _record_failure(run_id, instance_id, result, e)
+        logger.error(f"[{run_id}] Error on {instance_id}: {e}")
+        result["exit_status"] = type(e).__name__
+        result["error"] = str(e)
+        result["traceback"] = traceback.format_exc()

    finally:
        if agent:
@@ -318,12 +287,7 @@ def run_configuration(
                    results.append(future.result())
                except Exception as e:
                    iid = futures[future]
-                    log_safe_exception(
-                        logger,
-                        f"[{run_id}] Uncaught error for {iid}",
-                        e,
-                        include_debug=is_debug_enabled(),
-                    )
+                    logger.error(f"[{run_id}] Uncaught error for {iid}: {e}")

    # Save run summary
    summary = {
@@ -1 +0,0 @@
-"""Tests for the GitNexus eval harness."""
@@ -1,6 +0,0 @@
-import sys
-from pathlib import Path
-
-ROOT = Path(__file__).resolve().parents[1]
-if str(ROOT) not in sys.path:
-    sys.path.insert(0, str(ROOT))
@@ -1,29 +0,0 @@
-from utils.errors import sanitize_exception
-
-
-def _raise_value_error():
-    raise ValueError("boom")
-
-
-def test_sanitize_exception_without_debug(monkeypatch):
-    monkeypatch.delenv("GITNEXUS_EVAL_DEBUG", raising=False)
-    try:
-        _raise_value_error()
-    except Exception as exc:  # noqa: BLE001
-        data = sanitize_exception(exc, include_debug=False)
-
-    assert data["error_type"] == "ValueError"
-    assert data["error_message"] == "boom"
-    assert "error_detail_debug" not in data
-
-
-def test_sanitize_exception_with_debug(monkeypatch):
-    monkeypatch.setenv("GITNEXUS_EVAL_DEBUG", "1")
-    try:
-        _raise_value_error()
-    except Exception as exc:  # noqa: BLE001
-        data = sanitize_exception(exc)
-
-    assert data["error_type"] == "ValueError"
-    assert "error_detail_debug" in data
-    assert "ValueError" in data["error_detail_debug"]
@@ -1,20 +0,0 @@
-import pytest
-
-analysis_module = pytest.importorskip("analysis.analyze_results")
-parse_run_id = analysis_module.parse_run_id
-
-
-def test_parse_run_id_native_augment():
-    model, mode = parse_run_id("claude-sonnet_native_augment")
-    assert model == "claude-sonnet"
-    assert mode == "native_augment"
-
-
-def test_parse_run_id_hyphenated_model():
-    model, mode = parse_run_id("glm-4.7_native")
-    assert model == "glm-4.7"
-    assert mode == "native"
-
-
-def test_parse_run_id_unknown():
-    assert parse_run_id("custom_model") == ("custom_model", "unknown")
@@ -1,63 +0,0 @@
-from __future__ import annotations
-
-from hypothesis import given
-from hypothesis import strategies as st
-
-from analysis.analyze_results import parse_run_id
-from environments.gitnexus_docker import GitNexusDockerEnvironment
-from tool_registry import TOOL_SPECS
-from utils.errors import sanitize_exception
-
-
-KNOWN_MODES = [
-    "native_augment",
-    "native",
-    "baseline",
-    "mcp",
-    "augment",
-    "full",
-]
-
-
-def _model_strategy():
-    base_chars = st.characters(
-        blacklist_categories=("Cs",),
-        blacklist_characters={" ", "\n", "\t"},
-    )
-    text = st.text(alphabet=base_chars, min_size=1)
-    return text.filter(lambda s: not any(s.endswith(f"_{m}") for m in KNOWN_MODES))
-
-
-@given(_model_strategy(), st.sampled_from(KNOWN_MODES))
-def test_parse_run_id_round_trip(model: str, mode: str) -> None:
-    run_id = f"{model}_{mode}"
-    parsed_model, parsed_mode = parse_run_id(run_id)
-    assert parsed_model == model
-    assert parsed_mode == mode
-
-
-@given(st.text())
-def test_sanitize_exception_respects_debug_flag(message: str) -> None:
-    exc = ValueError(message)
-    data = sanitize_exception(exc, include_debug=False)
-    assert data["error_type"] == "ValueError"
-    assert data["error_message"] == (message or "ValueError")
-    assert "error_detail_debug" not in data
-
-    data_debug = sanitize_exception(exc, include_debug=True)
-    assert data_debug["error_type"] == "ValueError"
-    assert "error_detail_debug" in data_debug
-    assert data_debug["error_detail_debug"]
-
-
-@given(st.sampled_from(list(TOOL_SPECS.values())), st.integers(min_value=1, max_value=99999))
-def test_render_tool_script_contains_expected_paths(spec, port: int) -> None:
-    script = GitNexusDockerEnvironment._render_tool_script(spec, str(port))
-
-    assert spec.fallback.strip() in script
-    if spec.endpoint:
-        assert spec.endpoint in script
-        assert f"${{GITNEXUS_EVAL_PORT:-{port}}}" in script
-        assert "curl" in script
-    else:
-        assert "curl" not in script
@@ -1,21 +0,0 @@
-import pytest
-
-GitNexusDockerEnvironment = pytest.importorskip(
-    "environments.gitnexus_docker"
-).GitNexusDockerEnvironment
-tool_registry = pytest.importorskip("tool_registry")
-TOOL_SPECS = tool_registry.TOOL_SPECS
-
-
-def test_render_query_script_uses_endpoint_and_fallback():
-    script = GitNexusDockerEnvironment._render_tool_script(TOOL_SPECS["query"], "4848")
-    assert "/tool/query" in script
-    assert "gitnexus query" in script
-    assert "GITNEXUS_EVAL_PORT" in script
-
-
-def test_render_augment_script_skips_curl():
-    script = GitNexusDockerEnvironment._render_tool_script(TOOL_SPECS["augment"], "4848")
-    assert "/tool/" not in script
-    assert "curl" not in script
-    assert "gitnexus augment" in script
@@ -1,79 +0,0 @@
-from __future__ import annotations
-
-from dataclasses import dataclass
-from typing import Dict, Tuple
-
-
-@dataclass(frozen=True)
-class ToolScriptSpec:
-    key: str
-    bin_name: str
-    endpoint: str | None
-    payload_builder: str
-    fallback: str
-    header: str | None = None
-
-
-TOOL_METRIC_KEYS: Tuple[str, ...] = ("query", "context", "impact", "cypher", "overview")
-
-TOOL_SPECS: Dict[str, ToolScriptSpec] = {
-    "query": ToolScriptSpec(
-        key="query",
-        bin_name="gitnexus-query",
-        endpoint="/tool/query",
-        payload_builder=r'''query="$1"; task_ctx="${2:-}"; goal="${3:-}"
-[ -z "$query" ] && echo "Usage: gitnexus-query <query> [task_context] [goal]" && exit 1
-payload="{\"query\": \"$query\""
-[ -n "$task_ctx" ] && payload="$payload, \"task_context\": \"$task_ctx\""
-[ -n "$goal" ] && payload="$payload, \"goal\": \"$goal\""
-payload="$payload}"''',
-        fallback='cd /testbed && npx gitnexus query "$query" 2>&1',
-    ),
-    "context": ToolScriptSpec(
-        key="context",
-        bin_name="gitnexus-context",
-        endpoint="/tool/context",
-        payload_builder=r'''name="$1"; file_path="${2:-}"
-[ -z "$name" ] && echo "Usage: gitnexus-context <symbol_name> [file_path]" && exit 1
-payload="{\"name\": \"$name\""
-[ -n "$file_path" ] && payload="$payload, \"file_path\": \"$file_path\""
-payload="$payload}"''',
-        fallback='cd /testbed && npx gitnexus context "$name" 2>&1',
-    ),
-    "impact": ToolScriptSpec(
-        key="impact",
-        bin_name="gitnexus-impact",
-        endpoint="/tool/impact",
-        payload_builder=r'''target="$1"; direction="${2:-upstream}"
-[ -z "$target" ] && echo "Usage: gitnexus-impact <symbol_name> [upstream|downstream]" && exit 1
-payload="{\"target\": \"$target\", \"direction\": \"$direction\"}"''',
-        fallback='cd /testbed && npx gitnexus impact "$target" --direction "$direction" 2>&1',
-    ),
-    "cypher": ToolScriptSpec(
-        key="cypher",
-        bin_name="gitnexus-cypher",
-        endpoint="/tool/cypher",
-        payload_builder=r'''query="$1"
-[ -z "$query" ] && echo "Usage: gitnexus-cypher <cypher_query>" && exit 1
-payload="{\"query\": \"$query\"}"''',
-        fallback='cd /testbed && npx gitnexus cypher "$query" 2>&1',
-    ),
-    "overview": ToolScriptSpec(
-        key="overview",
-        bin_name="gitnexus-overview",
-        endpoint="/tool/list_repos",
-        header='echo "=== Code Knowledge Graph Overview ==="',
-        payload_builder='payload="{}"',
-        fallback='cd /testbed && npx gitnexus list 2>&1',
-    ),
-    "augment": ToolScriptSpec(
-        key="augment",
-        bin_name="gitnexus-augment",
-        endpoint=None,
-        payload_builder="",
-        fallback='cd /testbed && npx gitnexus augment "$1" 2>&1 || true',
-    ),
-}
-
-BINARIES_BY_KEY: Dict[str, str] = {spec.key: spec.bin_name for spec in TOOL_SPECS.values()}
-ENDPOINTS_BY_KEY: Dict[str, str | None] = {spec.key: spec.endpoint for spec in TOOL_SPECS.values()}
@@ -1 +0,0 @@
-"""Utility package for the eval harness."""
@@ -1,60 +0,0 @@
-from __future__ import annotations
-
-import os
-import traceback
-from typing import Any, Callable
-
-from constants import DEBUG_ENV_VAR
-
-
-def is_debug_enabled() -> bool:
-    """Return True when debug output (full tracebacks) should be emitted."""
-    return os.getenv(DEBUG_ENV_VAR, "").strip().lower() in {"1", "true", "yes", "on"}
-
-
-def sanitize_exception(exc: BaseException, *, include_debug: bool | None = None) -> dict[str, str]:
-    """
-    Produce a log-safe, JSON-friendly view of an exception.
-
-    - Always returns error_type and error_message.
-    - Only includes error_detail_debug (full traceback) when debug is enabled.
-    """
-    debug = is_debug_enabled() if include_debug is None else include_debug
-
-    error_type = type(exc).__name__
-    message = str(exc) or error_type
-
-    data: dict[str, str] = {
-        "error_type": error_type,
-        "error_message": message,
-    }
-
-    if debug:
-        tb = "".join(traceback.format_exception(type(exc), exc, exc.__traceback__))
-        if tb:
-            data["error_detail_debug"] = tb
-
-    return data
-
-
-def log_safe_exception(
-    logger: Any,
-    prefix: str,
-    exc: BaseException,
-    *,
-    include_debug: bool | None = None,
-    level: str = "error",
-) -> dict[str, str]:
-    """
-    Log an exception without leaking stack traces unless debug is enabled.
-
-    Returns the sanitized dict so callers can persist it.
-    """
-    data = sanitize_exception(exc, include_debug=include_debug)
-    debug = "error_detail_debug" in data
-
-    log_fn: Callable[..., None] = getattr(logger, level, logger.error)
-    message = f"{prefix}: {data['error_type']}: {data['error_message']}"
-    log_kwargs = {"exc_info": True} if debug else {}
-    log_fn(message, **log_kwargs)
-    return data
@@ -64,26 +64,10 @@ function extractPattern(toolName, toolInput) {
    const tokens = cmd.split(/\s+/);
    let foundCmd = false;
    let skipNext = false;
-    const flagsWithValues = new Set([
-      '-e',
-      '-f',
-      '-m',
-      '-A',
-      '-B',
-      '-C',
-      '-g',
-      '--glob',
-      '-t',
-      '--type',
-      '--include',
-      '--exclude',
-    ]);
+    const flagsWithValues = new Set(['-e', '-f', '-m', '-A', '-B', '-C', '-g', '--glob', '-t', '--type', '--include', '--exclude']);

    for (const token of tokens) {
-      if (skipNext) {
-        skipNext = false;
-        continue;
-      }
+      if (skipNext) { skipNext = false; continue; }
      if (!foundCmd) {
        if (/\brg$|\bgrep$/.test(token)) foundCmd = true;
        continue;
@@ -114,42 +98,33 @@ function runGitNexusCli(args, cwd, timeout) {
  // Detect whether 'gitnexus' is on PATH (cheap check, no execution)
  let useDirectBinary = false;
  try {
-    const which = spawnSync(isWin ? 'where' : 'which', ['gitnexus'], {
-      encoding: 'utf-8',
-      timeout: 3000,
-      stdio: ['pipe', 'pipe', 'pipe'],
-    });
+    const which = spawnSync(
+      isWin ? 'where' : 'which', ['gitnexus'],
+      { encoding: 'utf-8', timeout: 3000, stdio: ['pipe', 'pipe', 'pipe'] }
+    );
    useDirectBinary = which.status === 0;
-  } catch {
-    /* not on PATH */
-  }
+  } catch { /* not on PATH */ }

  if (useDirectBinary) {
-    return spawnSync(isWin ? 'gitnexus.cmd' : 'gitnexus', args, {
-      encoding: 'utf-8',
-      timeout,
-      cwd,
-      stdio: ['pipe', 'pipe', 'pipe'],
-    });
+    return spawnSync(
+      isWin ? 'gitnexus.cmd' : 'gitnexus', args,
+      { encoding: 'utf-8', timeout, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+    );
  }
  // npx fallback needs shell on Windows since npx is a .cmd script
-  return spawnSync(isWin ? 'npx.cmd' : 'npx', ['-y', 'gitnexus', ...args], {
-    encoding: 'utf-8',
-    timeout: timeout + 5000,
-    cwd,
-    stdio: ['pipe', 'pipe', 'pipe'],
-  });
+  return spawnSync(
+    isWin ? 'npx.cmd' : 'npx', ['-y', 'gitnexus', ...args],
+    { encoding: 'utf-8', timeout: timeout + 5000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+  );
 }

 /**
 * Emit a hook response with additional context for the agent.
 */
 function sendHookResponse(hookEventName, message) {
-  console.log(
-    JSON.stringify({
-      hookSpecificOutput: { hookEventName, additionalContext: message },
-    }),
-  );
+  console.log(JSON.stringify({
+    hookSpecificOutput: { hookEventName, additionalContext: message }
+  }));
 }

 /**
@@ -174,9 +149,7 @@ function handlePreToolUse(input) {
    if (!child.error && child.status === 0) {
      result = child.stderr || '';
    }
-  } catch {
-    /* graceful failure */
-  }
+  } catch { /* graceful failure */ }

  if (result && result.trim()) {
    sendHookResponse('PreToolUse', result.trim());
@@ -212,15 +185,10 @@ function handlePostToolUse(input) {
  let currentHead = '';
  try {
    const headResult = spawnSync('git', ['rev-parse', 'HEAD'], {
-      encoding: 'utf-8',
-      timeout: 3000,
-      cwd,
-      stdio: ['pipe', 'pipe', 'pipe'],
+      encoding: 'utf-8', timeout: 3000, cwd, stdio: ['pipe', 'pipe', 'pipe'],
    });
    currentHead = (headResult.stdout || '').trim();
-  } catch {
-    return;
-  }
+  } catch { return; }

  if (!currentHead) return;

@@ -229,19 +197,16 @@ function handlePostToolUse(input) {
  try {
    const meta = JSON.parse(fs.readFileSync(path.join(gitNexusDir, 'meta.json'), 'utf-8'));
    lastCommit = meta.lastCommit || '';
-    hadEmbeddings = meta.stats && meta.stats.embeddings > 0;
-  } catch {
-    /* no meta — treat as stale */
-  }
+    hadEmbeddings = (meta.stats && meta.stats.embeddings > 0);
+  } catch { /* no meta — treat as stale */ }

  // If HEAD matches last indexed commit, no reindex needed
  if (currentHead && currentHead === lastCommit) return;

  const analyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
-  sendHookResponse(
-    'PostToolUse',
+  sendHookResponse('PostToolUse',
    `GitNexus index is stale (last indexed: ${lastCommit ? lastCommit.slice(0, 7) : 'never'}). ` +
-      `Run \`${analyzeCmd}\` to update the knowledge graph.`,
+    `Run \`${analyzeCmd}\` to update the knowledge graph.`
  );
 }

@@ -1,29 +0,0 @@
-{
-  "name": "gitnexus-shared",
-  "version": "1.0.0",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "gitnexus-shared",
-      "version": "1.0.0",
-      "devDependencies": {
-        "typescript": "^6.0.2"
-      }
-    },
-    "node_modules/typescript": {
-      "version": "6.0.2",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-6.0.2.tgz",
-      "integrity": "sha512-bGdAIrZ0wiGDo5l8c++HWtbaNCWTS4UTv7RaTH/ThVIgjkveJt83m74bBHMJkuCbslY8ixgLBVZJIOiQlQTjfQ==",
-      "dev": true,
-      "license": "Apache-2.0",
-      "bin": {
-        "tsc": "bin/tsc",
-        "tsserver": "bin/tsserver"
-      },
-      "engines": {
-        "node": ">=14.17"
-      }
-    }
-  }
-}
@@ -1,25 +0,0 @@
-{
-  "name": "gitnexus-shared",
-  "version": "1.0.0",
-  "private": true,
-  "description": "Shared type definitions for GitNexus CLI and web",
-  "type": "module",
-  "main": "dist/index.js",
-  "types": "dist/index.d.ts",
-  "exports": {
-    ".": {
-      "types": "./dist/index.d.ts",
-      "default": "./dist/index.js"
-    }
-  },
-  "scripts": {
-    "build": "tsc"
-  },
-  "files": [
-    "dist",
-    "src"
-  ],
-  "devDependencies": {
-    "typescript": "^6.0.2"
-  }
-}
@@ -1,134 +0,0 @@
-/**
- * Graph type definitions — single source of truth.
- *
- * Both gitnexus (CLI) and gitnexus-web import from this package.
- * Do NOT add Node.js-specific or browser-specific imports here.
- */
-
-import { SupportedLanguages } from '../languages.js';
-
-export type NodeLabel =
-  | 'Project'
-  | 'Package'
-  | 'Module'
-  | 'Folder'
-  | 'File'
-  | 'Class'
-  | 'Function'
-  | 'Method'
-  | 'Variable'
-  | 'Interface'
-  | 'Enum'
-  | 'Decorator'
-  | 'Import'
-  | 'Type'
-  | 'CodeElement'
-  | 'Community'
-  | 'Process'
-  // Multi-language node types
-  | 'Struct'
-  | 'Macro'
-  | 'Typedef'
-  | 'Union'
-  | 'Namespace'
-  | 'Trait'
-  | 'Impl'
-  | 'TypeAlias'
-  | 'Const'
-  | 'Static'
-  | 'Property'
-  | 'Record'
-  | 'Delegate'
-  | 'Annotation'
-  | 'Constructor'
-  | 'Template'
-  | 'Section'
-  | 'Route'
-  | 'Tool';
-
-export type NodeProperties = {
-  name: string;
-  filePath: string;
-  startLine?: number;
-  endLine?: number;
-  language?: SupportedLanguages | string;
-  isExported?: boolean;
-  astFrameworkMultiplier?: number;
-  astFrameworkReason?: string;
-  // Community
-  heuristicLabel?: string;
-  cohesion?: number;
-  symbolCount?: number;
-  keywords?: string[];
-  description?: string;
-  enrichedBy?: 'heuristic' | 'llm';
-  // Process
-  processType?: 'intra_community' | 'cross_community';
-  stepCount?: number;
-  communities?: string[];
-  entryPointId?: string;
-  terminalId?: string;
-  entryPointScore?: number;
-  entryPointReason?: string;
-  // Method/property
-  parameterCount?: number;
-  level?: number;
-  returnType?: string;
-  declaredType?: string;
-  visibility?: string;
-  isStatic?: boolean;
-  isReadonly?: boolean;
-  isAbstract?: boolean;
-  isFinal?: boolean;
-  isVirtual?: boolean;
-  isOverride?: boolean;
-  isAsync?: boolean;
-  isPartial?: boolean;
-  annotations?: string[];
-  // Route/response
-  responseKeys?: string[];
-  errorKeys?: string[];
-  middleware?: string[];
-  // Extensible
-  [key: string]: unknown;
-};
-
-export type RelationshipType =
-  | 'CONTAINS'
-  | 'CALLS'
-  | 'INHERITS'
-  | 'METHOD_OVERRIDES'
-  | 'METHOD_IMPLEMENTS'
-  | 'IMPORTS'
-  | 'USES'
-  | 'DEFINES'
-  | 'DECORATES'
-  | 'IMPLEMENTS'
-  | 'EXTENDS'
-  | 'HAS_METHOD'
-  | 'HAS_PROPERTY'
-  | 'ACCESSES'
-  | 'MEMBER_OF'
-  | 'STEP_IN_PROCESS'
-  | 'HANDLES_ROUTE'
-  | 'FETCHES'
-  | 'HANDLES_TOOL'
-  | 'ENTRY_POINT_OF'
-  | 'WRAPS'
-  | 'QUERIES';
-
-export interface GraphNode {
-  id: string;
-  label: NodeLabel;
-  properties: NodeProperties;
-}
-
-export interface GraphRelationship {
-  id: string;
-  sourceId: string;
-  targetId: string;
-  type: RelationshipType;
-  confidence: number;
-  reason: string;
-  step?: number;
-}
@@ -1,24 +0,0 @@
-// Graph types
-export type {
-  NodeLabel,
-  NodeProperties,
-  RelationshipType,
-  GraphNode,
-  GraphRelationship,
-} from './graph/types.js';
-
-// Schema constants
-export {
-  NODE_TABLES,
-  REL_TABLE_NAME,
-  REL_TYPES,
-  EMBEDDING_TABLE_NAME,
-} from './lbug/schema-constants.js';
-export type { NodeTableName, RelType } from './lbug/schema-constants.js';
-
-// Language support
-export { SupportedLanguages } from './languages.js';
-export { getLanguageFromFilename, getSyntaxLanguageFromFilename } from './language-detection.js';
-
-// Pipeline progress
-export type { PipelinePhase, PipelineProgress } from './pipeline.js';
@@ -1,148 +0,0 @@
-/**
- * Language Detection — maps file paths to SupportedLanguages enum values.
- *
- * Shared between CLI (ingestion pipeline) and web (syntax highlighting).
- *
- * ADDING A NEW LANGUAGE:
- * 1. Add enum member to SupportedLanguages in languages.ts
- * 2. Add file extensions to EXTENSION_MAP below
- * 3. TypeScript will error if you miss either step (exhaustive Record)
- */
-
-import { SupportedLanguages } from './languages.js';
-
-/** Ruby extensionless filenames recognised as Ruby source */
-const RUBY_EXTENSIONLESS_FILES = new Set([
-  'Rakefile',
-  'Gemfile',
-  'Guardfile',
-  'Vagrantfile',
-  'Brewfile',
-]);
-
-/**
- * Exhaustive map: every SupportedLanguages member → its file extensions.
- *
- * If a new language is added to the enum without adding an entry here,
- * TypeScript emits a compile error: "Property 'NewLang' is missing in type..."
- */
-const EXTENSION_MAP: Record<SupportedLanguages, readonly string[]> = {
-  [SupportedLanguages.JavaScript]: ['.js', '.jsx', '.mjs', '.cjs'],
-  [SupportedLanguages.TypeScript]: ['.ts', '.tsx', '.mts', '.cts'],
-  [SupportedLanguages.Python]: ['.py'],
-  [SupportedLanguages.Java]: ['.java'],
-  [SupportedLanguages.C]: ['.c'],
-  [SupportedLanguages.CPlusPlus]: ['.cpp', '.cc', '.cxx', '.h', '.hpp', '.hxx', '.hh'],
-  [SupportedLanguages.CSharp]: ['.cs'],
-  [SupportedLanguages.Go]: ['.go'],
-  [SupportedLanguages.Ruby]: ['.rb', '.rake', '.gemspec'],
-  [SupportedLanguages.Rust]: ['.rs'],
-  [SupportedLanguages.PHP]: ['.php', '.phtml', '.php3', '.php4', '.php5', '.php8'],
-  [SupportedLanguages.Kotlin]: ['.kt', '.kts'],
-  [SupportedLanguages.Swift]: ['.swift'],
-  [SupportedLanguages.Dart]: ['.dart'],
-  [SupportedLanguages.Vue]: ['.vue'],
-  [SupportedLanguages.Cobol]: ['.cbl', '.cob', '.cpy', '.cobol'],
-} satisfies Record<SupportedLanguages, readonly string[]>; // Ensure exhaustiveness
-
-/** Pre-built reverse lookup: extension → language (built once at module load). */
-const extToLang = new Map<string, SupportedLanguages>();
-for (const [lang, exts] of Object.entries(EXTENSION_MAP) as [
-  SupportedLanguages,
-  readonly string[],
-][]) {
-  for (const ext of exts) {
-    extToLang.set(ext, lang);
-  }
-}
-
-/**
- * Map file extension to SupportedLanguage enum.
- * Returns null if the file extension is not recognized.
- */
-export const getLanguageFromFilename = (filename: string): SupportedLanguages | null => {
-  // Fast path: check the extension map
-  const lastDot = filename.lastIndexOf('.');
-  if (lastDot >= 0) {
-    const ext = filename.slice(lastDot).toLowerCase();
-    const lang = extToLang.get(ext);
-    if (lang !== undefined) return lang;
-  }
-
-  // Ruby extensionless files (Rakefile, Gemfile, etc.)
-  const basename = filename.split('/').pop() || filename;
-  if (RUBY_EXTENSIONLESS_FILES.has(basename)) {
-    return SupportedLanguages.Ruby;
-  }
-
-  return null;
-};
-
-/**
- * Exhaustive map: every SupportedLanguages member → Prism syntax identifier.
- *
- * If a new language is added to the enum without adding an entry here,
- * TypeScript emits a compile error.
- */
-const SYNTAX_MAP: Record<SupportedLanguages, string> = {
-  [SupportedLanguages.JavaScript]: 'javascript',
-  [SupportedLanguages.TypeScript]: 'typescript',
-  [SupportedLanguages.Python]: 'python',
-  [SupportedLanguages.Java]: 'java',
-  [SupportedLanguages.C]: 'c',
-  [SupportedLanguages.CPlusPlus]: 'cpp',
-  [SupportedLanguages.CSharp]: 'csharp',
-  [SupportedLanguages.Go]: 'go',
-  [SupportedLanguages.Ruby]: 'ruby',
-  [SupportedLanguages.Rust]: 'rust',
-  [SupportedLanguages.PHP]: 'php',
-  [SupportedLanguages.Kotlin]: 'kotlin',
-  [SupportedLanguages.Swift]: 'swift',
-  [SupportedLanguages.Dart]: 'dart',
-  [SupportedLanguages.Vue]: 'typescript',
-  [SupportedLanguages.Cobol]: 'cobol',
-} satisfies Record<SupportedLanguages, string>; // Ensure exhaustiveness
-
-/** Non-code file extensions → Prism-compatible syntax identifiers */
-const AUXILIARY_SYNTAX_MAP: Record<string, string> = {
-  json: 'json',
-  yaml: 'yaml',
-  yml: 'yaml',
-  md: 'markdown',
-  mdx: 'markdown',
-  html: 'markup',
-  htm: 'markup',
-  erb: 'markup',
-  xml: 'markup',
-  css: 'css',
-  scss: 'css',
-  sass: 'css',
-  sh: 'bash',
-  bash: 'bash',
-  zsh: 'bash',
-  sql: 'sql',
-  toml: 'toml',
-  ini: 'ini',
-  dockerfile: 'docker',
-};
-
-/** Extensionless filenames → Prism-compatible syntax identifiers */
-const AUXILIARY_BASENAME_MAP: Record<string, string> = {
-  Makefile: 'makefile',
-  Dockerfile: 'docker',
-};
-
-/**
- * Map file path to a Prism-compatible syntax highlight language string.
- * Covers all SupportedLanguages (code files) plus common non-code formats.
- * Returns 'text' for unrecognised files.
- */
-export const getSyntaxLanguageFromFilename = (filePath: string): string => {
-  const lang = getLanguageFromFilename(filePath);
-  if (lang) return SYNTAX_MAP[lang];
-  const ext = filePath.split('.').pop()?.toLowerCase();
-  if (ext && ext in AUXILIARY_SYNTAX_MAP) return AUXILIARY_SYNTAX_MAP[ext];
-  const basename = filePath.split('/').pop() || '';
-  if (basename in AUXILIARY_BASENAME_MAP) return AUXILIARY_BASENAME_MAP[basename];
-  return 'text';
-};
@@ -1,25 +0,0 @@
-/**
- * Supported language enum — single source of truth.
- *
- * Both CLI and web use this to identify which language a file/node belongs to.
- * The CLI uses it throughout the ingestion pipeline; the web uses it for display.
- */
-export enum SupportedLanguages {
-  JavaScript = 'javascript',
-  TypeScript = 'typescript',
-  Python = 'python',
-  Java = 'java',
-  C = 'c',
-  CPlusPlus = 'cpp',
-  CSharp = 'csharp',
-  Go = 'go',
-  Ruby = 'ruby',
-  Rust = 'rust',
-  PHP = 'php',
-  Kotlin = 'kotlin',
-  Swift = 'swift',
-  Dart = 'dart',
-  Vue = 'vue',
-  /** Standalone regex processor — no tree-sitter, no LanguageProvider. */
-  Cobol = 'cobol',
-}
@@ -1,73 +0,0 @@
-/**
- * LadybugDB schema constants — single source of truth.
- *
- * NODE_TABLES and REL_TYPES define what the knowledge graph can contain.
- * Both CLI and web must agree on these for data compatibility.
- *
- * Full DDL schemas remain in each package's own schema.ts because
- * the CLI uses native LadybugDB and the web uses WASM.
- */
-
-export const NODE_TABLES = [
-  'File',
-  'Folder',
-  'Function',
-  'Class',
-  'Interface',
-  'Method',
-  'CodeElement',
-  'Community',
-  'Process',
-  'Section',
-  'Struct',
-  'Enum',
-  'Macro',
-  'Typedef',
-  'Union',
-  'Namespace',
-  'Trait',
-  'Impl',
-  'TypeAlias',
-  'Const',
-  'Static',
-  'Property',
-  'Record',
-  'Delegate',
-  'Annotation',
-  'Constructor',
-  'Template',
-  'Module',
-  'Route',
-  'Tool',
-] as const;
-
-export type NodeTableName = (typeof NODE_TABLES)[number];
-
-export const REL_TABLE_NAME = 'CodeRelation';
-
-export const REL_TYPES = [
-  'CONTAINS',
-  'DEFINES',
-  'IMPORTS',
-  'CALLS',
-  'EXTENDS',
-  'IMPLEMENTS',
-  'HAS_METHOD',
-  'HAS_PROPERTY',
-  'ACCESSES',
-  'METHOD_OVERRIDES',
-  'OVERRIDES', // Legacy compat alias — kept until all stored indexes are migrated
-  'METHOD_IMPLEMENTS',
-  'MEMBER_OF',
-  'STEP_IN_PROCESS',
-  'HANDLES_ROUTE',
-  'FETCHES',
-  'HANDLES_TOOL',
-  'ENTRY_POINT_OF',
-  'WRAPS',
-  'QUERIES',
-] as const;
-
-export type RelType = (typeof REL_TYPES)[number];
-
-export const EMBEDDING_TABLE_NAME = 'CodeEmbedding';
@@ -1,29 +0,0 @@
-/**
- * Pipeline progress types — shared between CLI and web.
- */
-
-export type PipelinePhase =
-  | 'idle'
-  | 'extracting'
-  | 'structure'
-  | 'parsing'
-  | 'imports'
-  | 'calls'
-  | 'heritage'
-  | 'communities'
-  | 'processes'
-  | 'enriching'
-  | 'complete'
-  | 'error';
-
-export interface PipelineProgress {
-  phase: PipelinePhase;
-  percent: number;
-  message: string;
-  detail?: string;
-  stats?: {
-    filesProcessed: number;
-    totalFiles: number;
-    nodesCreated: number;
-  };
-}
@@ -1,18 +0,0 @@
-{
-  "compilerOptions": {
-    "target": "ES2022",
-    "module": "NodeNext",
-    "moduleResolution": "NodeNext",
-    "strict": true,
-    "declaration": true,
-    "declarationMap": true,
-    "sourceMap": true,
-    "esModuleInterop": true,
-    "skipLibCheck": true,
-    "forceConsistentCasingInFileNames": true,
-    "composite": true,
-    "rootDir": "src",
-    "outDir": "dist"
-  },
-  "include": ["src"]
-}
@@ -0,0 +1,104 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+
+/**
+ * CORS Proxy for isomorphic-git
+ * 
+ * isomorphic-git calls: /api/proxy?url=https://github.com/...
+ */
+export default async function handler(req: VercelRequest, res: VercelResponse) {
+  // Handle CORS preflight
+  if (req.method === 'OPTIONS') {
+    res.setHeader('Access-Control-Allow-Origin', '*');
+    res.setHeader('Access-Control-Allow-Methods', 'GET, POST, OPTIONS');
+    res.setHeader('Access-Control-Allow-Headers', 'Content-Type, Authorization, Git-Protocol, Accept');
+    res.status(200).end();
+    return;
+  }
+
+  // Get URL from query parameter
+  const { url } = req.query;
+  
+  if (!url || typeof url !== 'string') {
+    res.status(400).json({ error: 'Missing url query parameter' });
+    return;
+  }
+
+  // Only allow GitHub URLs for security
+  const allowedHosts = ['github.com', 'raw.githubusercontent.com'];
+  let parsedUrl: URL;
+  
+  try {
+    parsedUrl = new URL(url);
+  } catch {
+    res.status(400).json({ error: 'Invalid URL' });
+    return;
+  }
+  
+  if (!allowedHosts.some(host => parsedUrl.hostname.endsWith(host))) {
+    res.status(403).json({ error: 'Only GitHub URLs are allowed' });
+    return;
+  }
+
+  try {
+    const headers: Record<string, string> = {
+      'User-Agent': 'git/isomorphic-git',
+    };
+    
+    // Forward relevant headers
+    if (req.headers.authorization) {
+      headers['Authorization'] = req.headers.authorization as string;
+    }
+    if (req.headers['content-type']) {
+      headers['Content-Type'] = req.headers['content-type'] as string;
+    }
+    if (req.headers['git-protocol']) {
+      headers['Git-Protocol'] = req.headers['git-protocol'] as string;
+    }
+    if (req.headers.accept) {
+      headers['Accept'] = req.headers.accept as string;
+    }
+
+    // Get request body for POST requests
+    let body: Buffer | undefined;
+    if (req.method === 'POST') {
+      const chunks: Buffer[] = [];
+      for await (const chunk of req) {
+        chunks.push(typeof chunk === 'string' ? Buffer.from(chunk) : chunk);
+      }
+      body = Buffer.concat(chunks);
+    }
+
+    const response = await fetch(url, {
+      method: req.method || 'GET',
+      headers,
+      body: body ? new Uint8Array(body) : undefined,
+    });
+
+    // Set CORS headers
+    res.setHeader('Access-Control-Allow-Origin', '*');
+    res.setHeader('Access-Control-Expose-Headers', '*');
+
+    // Forward response headers (except ones that cause issues)
+    const skipHeaders = [
+      'content-encoding', 
+      'transfer-encoding', 
+      'connection',
+      'www-authenticate', // IMPORTANT: Strip this to prevent browser's native auth popup!
+    ];
+    
+    response.headers.forEach((value, key) => {
+      if (!skipHeaders.includes(key.toLowerCase())) {
+        res.setHeader(key, value);
+      }
+    });
+
+    res.status(response.status);
+    const buffer = await response.arrayBuffer();
+    res.send(Buffer.from(buffer));
+    
+  } catch (error) {
+    console.error('Proxy error:', error);
+    res.status(500).json({ error: 'Proxy request failed', details: String(error) });
+  }
+}
+
@@ -1,4 +1,4 @@
-import { test, expect } from '@playwright/test';
+import { test, expect, type TestInfo } from '@playwright/test';

 /**
 * Debug harnesses for investigating specific UI issues.
@@ -9,7 +9,7 @@ const BACKEND_URL = process.env.BACKEND_URL ?? 'http://localhost:4747';
 const debugTest = process.env.DEBUG_E2E ? test : test.skip;

 async function connectToServer(page: import('@playwright/test').Page) {
-  page.on('console', (msg) => {
+  page.on('console', msg => {
    if (msg.type() === 'error') console.log(`[error] ${msg.text()}`);
  });

@@ -86,10 +86,7 @@ debugTest('debug: process view Reset View button', async ({ page }, testInfo) =>

  const transformAfterReset = await diagramDiv.getAttribute('style');
  console.log('Transform AFTER reset:', transformAfterReset);
-  await page.screenshot({
-    path: testInfo.outputPath('debug-modal-after-reset.png'),
-    fullPage: true,
-  });
+  await page.screenshot({ path: testInfo.outputPath('debug-modal-after-reset.png'), fullPage: true });

  // Verify transform actually changed back
  expect(transformAfterZoom).not.toBe(transformBefore);
@@ -126,8 +123,5 @@ debugTest('debug: lightbulb clears node selection dimming', async ({ page }, tes
  // Click it again to toggle back on
  await lightbulbBtn.click();
  await page.waitForTimeout(500);
-  await page.screenshot({
-    path: testInfo.outputPath('debug-after-lightbulb-toggle-back.png'),
-    fullPage: true,
-  });
+  await page.screenshot({ path: testInfo.outputPath('debug-after-lightbulb-toggle-back.png'), fullPage: true });
 });
@@ -1,109 +0,0 @@
-import { test, expect } from '@playwright/test';
-
-/**
- * E2E tests for heartbeat disconnect/reconnect behavior.
- *
- * Verifies the key regression: when the heartbeat fails, the UI shows a
- * "reconnecting" banner instead of resetting to the onboarding screen.
- *
- * Strategy: block /api/heartbeat via route interception BEFORE loading the
- * graph. The heartbeat EventSource can never connect, so onReconnecting
- * fires on the first retry attempt. This reliably tests the banner behavior
- * without depending on setOffline timing (which varies across CI environments).
- */
-
-const BACKEND_URL = process.env.BACKEND_URL ?? 'http://localhost:4747';
-const FRONTEND_URL = process.env.FRONTEND_URL ?? 'http://localhost:5173';
-
-test.beforeAll(async () => {
-  if (process.env.E2E) return;
-  try {
-    const [backendRes, frontendRes] = await Promise.allSettled([
-      fetch(`${BACKEND_URL}/api/repos`),
-      fetch(FRONTEND_URL),
-    ]);
-    if (
-      backendRes.status === 'rejected' ||
-      (backendRes.status === 'fulfilled' && !backendRes.value.ok)
-    ) {
-      test.skip(true, 'gitnexus serve not available');
-      return;
-    }
-    if (
-      frontendRes.status === 'rejected' ||
-      (frontendRes.status === 'fulfilled' && !frontendRes.value.ok)
-    ) {
-      test.skip(true, 'Vite dev server not available');
-      return;
-    }
-    if (backendRes.status === 'fulfilled') {
-      const repos = await backendRes.value.json();
-      if (!repos.length) {
-        test.skip(true, 'No indexed repos');
-        return;
-      }
-    }
-  } catch {
-    test.skip(true, 'servers not available');
-  }
-});
-
-test.describe('Heartbeat Reconnect', () => {
-  test('shows reconnecting banner instead of onboarding reset when heartbeat is unavailable', async ({
-    page,
-  }) => {
-    // Block the heartbeat BEFORE navigating — the EventSource will fail
-    // immediately on every connection attempt, triggering onReconnecting.
-    await page.route('**/api/heartbeat', (route) => route.abort('connectionrefused'));
-
-    // Load the app and connect to a repo (all other endpoints work normally)
-    await page.goto('/');
-
-    const landingCard = page.locator('[data-testid="landing-repo-card"]').first();
-    try {
-      await landingCard.waitFor({ state: 'visible', timeout: 15_000 });
-      await landingCard.click();
-    } catch {
-      // auto-connect may skip the landing screen
-    }
-
-    // Wait for graph to load (heartbeat is blocked, but graph loads fine)
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-
-    // The reconnecting banner should appear (heartbeat is failing)
-    const banner = page.getByText('Server connection lost');
-    await expect(banner).toBeVisible({ timeout: 15_000 });
-
-    // The graph canvas should STILL be visible — NOT reset to onboarding
-    await expect(page.locator('canvas').first()).toBeVisible();
-  });
-
-  test('banner clears when heartbeat becomes available', async ({ page }) => {
-    // Start with heartbeat blocked
-    await page.route('**/api/heartbeat', (route) => route.abort('connectionrefused'));
-
-    await page.goto('/');
-    const landingCard = page.locator('[data-testid="landing-repo-card"]').first();
-    try {
-      await landingCard.waitFor({ state: 'visible', timeout: 15_000 });
-      await landingCard.click();
-    } catch {
-      // auto-connect may skip the landing screen
-    }
-
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-
-    // Verify banner appears
-    const banner = page.getByText('Server connection lost');
-    await expect(banner).toBeVisible({ timeout: 15_000 });
-
-    // Unblock heartbeat — the real server is running, so reconnect will succeed
-    await page.unroute('**/api/heartbeat');
-
-    // Banner should disappear as heartbeat reconnects
-    await expect(banner).not.toBeVisible({ timeout: 30_000 });
-
-    // Graph should still be there
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible();
-  });
-});
@@ -12,16 +12,16 @@ import { test } from '@playwright/test';
 */
 test.skip(
  !!process.env.CI || process.env.PWDEBUG !== '1',
-  'Manual recording requires --headed and PWDEBUG=1. Run: PWDEBUG=1 npx playwright test e2e/manual-record.spec.ts --headed --timeout=0',
+  'Manual recording requires --headed and PWDEBUG=1. Run: PWDEBUG=1 npx playwright test e2e/manual-record.spec.ts --headed --timeout=0'
 );

 test('manual recording session', async ({ page }) => {
-  page.on('console', (msg) => {
+  page.on('console', msg => {
    if (msg.type() === 'error' || msg.type() === 'warning') {
      console.log(`[${msg.type()}] ${msg.text()}`);
    }
  });
-  page.on('pageerror', (err) => console.log(`[crash] ${err.message}`));
+  page.on('pageerror', err => console.log(`[crash] ${err.message}`));

  await page.goto('http://localhost:5173');
  await page.pause();
@@ -1,112 +0,0 @@
-import { test, expect } from '@playwright/test';
-
-/**
- * E2E tests for multi-repo scoping and URL persistence.
- *
- * Verifies that:
- * - Connecting via ?server= loads data and sets ?project= in the URL
- * - The repo name appears in the UI after connecting
- * - F5 with ?server=&project= reconnects to the correct repo
- *
- * Runs against the single indexed repo in CI — validates the plumbing
- * works end-to-end even with one repo.
- */
-
-const BACKEND_URL = process.env.BACKEND_URL ?? 'http://localhost:4747';
-const FRONTEND_URL = process.env.FRONTEND_URL ?? 'http://localhost:5173';
-
-let firstRepoName: string;
-
-test.beforeAll(async () => {
-  if (process.env.E2E) {
-    // Still need to fetch the repo name for assertions
-    try {
-      const res = await fetch(`${BACKEND_URL}/api/repos`);
-      const repos = await res.json();
-      firstRepoName = repos[0]?.name ?? '';
-    } catch {
-      firstRepoName = '';
-    }
-    return;
-  }
-  try {
-    const [backendRes, frontendRes] = await Promise.allSettled([
-      fetch(`${BACKEND_URL}/api/repos`),
-      fetch(FRONTEND_URL),
-    ]);
-    if (
-      backendRes.status === 'rejected' ||
-      (backendRes.status === 'fulfilled' && !backendRes.value.ok)
-    ) {
-      test.skip(true, 'gitnexus serve not available');
-      return;
-    }
-    if (
-      frontendRes.status === 'rejected' ||
-      (frontendRes.status === 'fulfilled' && !frontendRes.value.ok)
-    ) {
-      test.skip(true, 'Vite dev server not available');
-      return;
-    }
-    if (backendRes.status === 'fulfilled') {
-      const repos = await backendRes.value.json();
-      if (!repos.length) {
-        test.skip(true, 'No indexed repos');
-        return;
-      }
-      firstRepoName = repos[0].name;
-    }
-  } catch {
-    test.skip(true, 'servers not available');
-  }
-});
-
-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=${encodeURIComponent(BACKEND_URL)}`);
-
-    // Wait for graph to load
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-
-    // URL should now contain ?project= with the repo name
-    const url = new URL(page.url());
-    const project = url.searchParams.get('project');
-    expect(project).toBeTruthy();
-    expect(project).toBe(firstRepoName);
-  });
-
-  test('?server= is preserved in URL for F5 recovery', async ({ page }) => {
-    await page.goto(`/?server=${encodeURIComponent(BACKEND_URL)}`);
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-
-    // URL should still have ?server=
-    const url = new URL(page.url());
-    expect(url.searchParams.get('server')).toBeTruthy();
-
-    // F5 should reconnect (not show onboarding)
-    await page.reload();
-    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=${encodeURIComponent(BACKEND_URL)}`);
-    await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-
-    // Fetch expected node count from backend
-    const res = await fetch(`${BACKEND_URL}/api/repo?repo=${encodeURIComponent(firstRepoName)}`);
-    const repoInfo = await res.json();
-    const expectedNodes = repoInfo.stats?.nodes;
-
-    if (expectedNodes) {
-      // Status bar shows node count — use the status-ready area to avoid
-      // matching multiple elements (file tree, header may also show counts)
-      const statusBar = page.locator('footer');
-      const nodeText = statusBar.getByText(/\d+ nodes/).first();
-      await expect(nodeText).toBeVisible({ timeout: 10_000 });
-      const text = await nodeText.textContent();
-      const displayedNodes = parseInt(text?.match(/(\d+)\s*nodes/)?.[1] ?? '0', 10);
-      expect(displayedNodes).toBeGreaterThan(0);
-    }
-  });
-});
@@ -1,300 +0,0 @@
-import { test, expect } from '@playwright/test';
-
-/**
- * E2E tests for the onboarding and analysis user flows.
- *
- * These tests cover:
- *   - Flow 1: OnboardingGuide shown when no server is running
- *   - Flow 2: Analyze form when server has zero repos
- *   - Flow 3: Auto-connect when server has repos
- *   - Flow 4: Repo dropdown in exploring view
- *
- * Most tests mock the backend at the network level so they don't
- * require a live gitnexus server.
- */
-
-const BACKEND_URL = 'http://localhost:4747';
-
-async function enterExploringView(page: import('@playwright/test').Page) {
-  await page.goto('/');
-
-  const landingCard = page.locator('[data-testid="landing-repo-card"]').first();
-  try {
-    await landingCard.waitFor({ state: 'visible', timeout: 15_000 });
-    await landingCard.click();
-  } catch {
-    // Landing screen may not appear (e.g. ?server auto-connect)
-  }
-
-  await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
-}
-
-// ── Flow 1: Onboarding (no server running) ─────────────────────────────────
-
-test.describe('Flow 1: Onboarding — no server', () => {
-  test('shows OnboardingGuide when backend is unreachable', async ({ page }, testInfo) => {
-    // Block all requests to the backend so the probe fails
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-
-    await page.goto('/');
-
-    // Wait for initial probe to complete and onboarding to appear
-    await expect(page.getByText('Start your local server')).toBeVisible({ timeout: 10_000 });
-    await page.screenshot({ path: testInfo.outputPath('onboarding-visible.png') });
-  });
-
-  test('shows step-by-step instructions', async ({ page }) => {
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-    await page.goto('/');
-
-    // Step 1 is active (done once polling starts)
-    await expect(page.getByText('Copy the command')).toBeAttached({ timeout: 10_000 });
-    // Step 2 title changes to "Waiting for server to start" once polling begins
-    await expect(page.getByText('Waiting for server to start')).toBeAttached({ timeout: 10_000 });
-    // Step 3 is always rendered
-    await expect(page.getByText('Auto-connects and opens the graph')).toBeAttached({
-      timeout: 5_000,
-    });
-  });
-
-  test('shows terminal window with command', async ({ page }) => {
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-    await page.goto('/');
-
-    // Should show either dev or prod command in a terminal block
-    const terminal = page.locator('code');
-    await expect(terminal.first()).toBeVisible({ timeout: 10_000 });
-
-    // The $ prompt should be present
-    await expect(page.getByText('$')).toBeVisible();
-  });
-
-  test('shows polling indicator', async ({ page }) => {
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-    await page.goto('/');
-
-    // Polling starts after initial probe fails
-    await expect(page.getByText('Listening for server')).toBeVisible({ timeout: 10_000 });
-  });
-
-  test('shows Node.js version requirement', async ({ page }) => {
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-    await page.goto('/');
-
-    await expect(page.getByText(/Node\.js.*\d+/)).toBeVisible({ timeout: 10_000 });
-    await expect(page.getByText('Port 4747')).toBeVisible();
-  });
-
-  test('copy button has accessible label', async ({ page }) => {
-    await page.route(`${BACKEND_URL}/**`, (route) => route.abort('connectionrefused'));
-    await page.goto('/');
-
-    await expect(page.getByText('Copy the command')).toBeVisible({ timeout: 10_000 });
-    const copyBtn = page.getByLabel('Copy to clipboard').first();
-    await expect(copyBtn).toBeVisible();
-  });
-});
-
-// ── Flow 2: Server detected → success → auto-connect ──────────────────────
-
-test.describe('Flow 2: Server detected — auto-connect', () => {
-  test('shows success card when server becomes reachable', async ({ page }, testInfo) => {
-    // Start with server unreachable
-    let blockBackend = true;
-    await page.route(`${BACKEND_URL}/**`, (route) => {
-      if (blockBackend) return route.abort('connectionrefused');
-      // Let it through to the real handler below
-      return route.fallback();
-    });
-
-    // Mock the backend responses for when we "start" the server
-    await page.route(`${BACKEND_URL}/api/repos`, async (route) => {
-      if (blockBackend) return route.abort('connectionrefused');
-      await route.fulfill({ json: [{ name: 'test-repo', path: '/tmp/test' }] });
-    });
-    await page.route(`${BACKEND_URL}/api/repo`, async (route) => {
-      if (blockBackend) return route.abort('connectionrefused');
-      await route.fulfill({
-        json: { name: 'test-repo', path: '/tmp/test', repoPath: '/tmp/test' },
-      });
-    });
-    await page.route(`${BACKEND_URL}/api/graph**`, async (route) => {
-      if (blockBackend) return route.abort('connectionrefused');
-      await route.fulfill({ json: { nodes: [], relationships: [] } });
-    });
-    await page.route(`${BACKEND_URL}/api/heartbeat`, async (route) => {
-      if (blockBackend) return route.abort('connectionrefused');
-      // SSE response
-      await route.fulfill({
-        status: 200,
-        headers: { 'Content-Type': 'text/event-stream', 'Cache-Control': 'no-cache' },
-        body: ':ok\n\n',
-      });
-    });
-
-    await page.goto('/');
-
-    // Verify onboarding is shown first
-    await expect(page.getByText('Start your local server')).toBeVisible({ timeout: 10_000 });
-    await page.screenshot({ path: testInfo.outputPath('before-server-start.png') });
-
-    // "Start" the server by unblocking requests
-    blockBackend = false;
-
-    // Wait for success card
-    await expect(page.getByText('Server Connected')).toBeVisible({ timeout: 15_000 });
-    await page.screenshot({ path: testInfo.outputPath('success-card.png') });
-  });
-
-  test('transitions to analyze phase when server has zero repos', async ({ page }, testInfo) => {
-    // Mock server with zero repos — repos endpoint returns empty array
-    await page.route(`${BACKEND_URL}/api/repos`, (route) => route.fulfill({ json: [] }));
-    await page.route(`${BACKEND_URL}/api/info`, (route) =>
-      route.fulfill({ json: { version: '1.0.0', launchContext: 'npx', nodeVersion: 'v22.0.0' } }),
-    );
-    await page.route(`${BACKEND_URL}/api/heartbeat`, (route) =>
-      route.fulfill({
-        status: 200,
-        headers: { 'Content-Type': 'text/event-stream' },
-        body: ':ok\n\n',
-      }),
-    );
-
-    await page.goto('/');
-
-    // Should transition: onboarding → success → analyze (zero repos)
-    // The analyze form tabs should be visible
-    await expect(page.getByRole('tab', { name: 'GitHub URL' })).toBeVisible({ timeout: 20_000 });
-    await expect(page.getByRole('tab', { name: 'Local Folder' })).toBeVisible();
-    await page.screenshot({ path: testInfo.outputPath('analyze-empty-state.png') });
-  });
-});
-
-// ── Flow 3: Analyze form ───────────────────────────────────────────────────
-
-test.describe('Flow 3: Analyze form', () => {
-  test.beforeEach(async ({ page }) => {
-    // Mock server with zero repos to show the analyze form
-    await page.route(`${BACKEND_URL}/api/repos`, (route) => route.fulfill({ json: [] }));
-    await page.route(`${BACKEND_URL}/api/info`, (route) =>
-      route.fulfill({ json: { version: '1.0.0', launchContext: 'npx', nodeVersion: 'v22.0.0' } }),
-    );
-    await page.route(`${BACKEND_URL}/api/heartbeat`, (route) =>
-      route.fulfill({
-        status: 200,
-        headers: { 'Content-Type': 'text/event-stream' },
-        body: ':ok\n\n',
-      }),
-    );
-  });
-
-  test('GitHub URL tab validates input', async ({ page }, testInfo) => {
-    await page.goto('/');
-
-    // Wait for analyze form (transition: onboarding → success → analyze)
-    await expect(page.getByRole('tab', { name: 'GitHub URL' })).toBeVisible({ timeout: 20_000 });
-
-    // Type an invalid URL
-    const input = page.locator('input[type="url"]');
-    await input.fill('not-a-url');
-
-    // Analyze button should be visible but disabled
-    const analyzeBtn = page.getByRole('button', { name: /Analyze Repository/ });
-    await expect(analyzeBtn).toBeVisible();
-
-    // Type a valid GitHub URL
-    await input.fill('https://github.com/anthropics/courses');
-    await page.screenshot({ path: testInfo.outputPath('valid-github-url.png') });
-  });
-
-  test('Local Folder tab shows browse button', async ({ page }, testInfo) => {
-    await page.goto('/');
-
-    await expect(page.getByRole('tab', { name: 'Local Folder' })).toBeVisible({ timeout: 20_000 });
-
-    // Switch to Local Folder tab
-    await page.getByRole('tab', { name: 'Local Folder' }).click();
-
-    // Browse button should be visible
-    await expect(page.getByText('Browse for folder')).toBeVisible();
-    await page.screenshot({ path: testInfo.outputPath('local-folder-tab.png') });
-  });
-
-  test('switching tabs clears input', async ({ page }) => {
-    await page.goto('/');
-
-    await expect(page.getByRole('tab', { name: 'GitHub URL' })).toBeVisible({ timeout: 20_000 });
-
-    // Type in GitHub URL
-    const urlInput = page.locator('input[type="url"]');
-    await urlInput.fill('https://github.com/test/repo');
-
-    // Switch to Local Folder
-    await page.getByRole('tab', { name: 'Local Folder' }).click();
-
-    // Switch back to GitHub URL — input should be empty
-    await page.getByRole('tab', { name: 'GitHub URL' }).click();
-    const newUrlInput = page.locator('input[type="url"]');
-    await expect(newUrlInput).toHaveValue('');
-  });
-});
-
-// ── Flow 4: Repo dropdown (requires running server) ────────────────────────
-
-test.describe('Flow 4: Repo dropdown in exploring view', () => {
-  const SKIP_MSG = 'Requires running gitnexus server with indexed repos';
-
-  test.beforeAll(async () => {
-    if (process.env.E2E) return;
-    try {
-      const res = await fetch(`${BACKEND_URL}/api/repos`);
-      if (!res.ok) {
-        test.skip(true, SKIP_MSG);
-        return;
-      }
-      const repos = await res.json();
-      if (!repos.length) {
-        test.skip(true, 'Server has no indexed repos');
-        return;
-      }
-    } catch {
-      test.skip(true, SKIP_MSG);
-    }
-  });
-
-  test('project badge opens repo dropdown', async ({ page }, testInfo) => {
-    await enterExploringView(page);
-    await page.screenshot({ path: testInfo.outputPath('exploring-loaded.png') });
-
-    // Click the project badge (has a chevron)
-    const badge = page
-      .locator('header button')
-      .filter({ has: page.locator('svg') })
-      .first();
-    await badge.click();
-
-    // Repo dropdown should be visible
-    await expect(page.getByText('Repositories')).toBeVisible({ timeout: 5_000 });
-    await expect(page.getByText('Analyze a new repository')).toBeVisible();
-    await page.screenshot({ path: testInfo.outputPath('repo-dropdown-open.png') });
-  });
-
-  test('analyze option opens inline form', async ({ page }, testInfo) => {
-    await enterExploringView(page);
-
-    // Open repo dropdown
-    const badge = page
-      .locator('header button')
-      .filter({ has: page.locator('svg') })
-      .first();
-    await badge.click();
-
-    // Click "Analyze a new repository..."
-    await page.getByText('Analyze a new repository').click();
-
-    // Should show the analyze form inline
-    await expect(page.getByText('GitHub URL')).toBeVisible({ timeout: 5_000 });
-    await expect(page.getByText('Local Folder')).toBeVisible();
-    await page.screenshot({ path: testInfo.outputPath('inline-analyze-form.png') });
-  });
-});
@@ -1,10 +1,9 @@
 import { test, expect, type TestInfo } from '@playwright/test';

 /**
- * E2E tests for the GitNexus web UI — exploring view features.
- *
+ * E2E tests for the GitNexus web UI.
 * Requires:
- *   - gitnexus serve running on localhost:4747 with at least one indexed repo
+ *   - gitnexus serve running on localhost:4747
 *   - gitnexus-web dev server running on localhost:5173
 *
 * Skipped when servers aren't available (CI without services, etc.).
@@ -13,82 +12,77 @@ import { test, expect, type TestInfo } from '@playwright/test';

 const BACKEND_URL = process.env.BACKEND_URL ?? 'http://localhost:4747';
 const FRONTEND_URL = process.env.FRONTEND_URL ?? 'http://localhost:5173';
-
+// Skip all tests if the gitnexus server or Vite dev server isn't reachable
 test.beforeAll(async () => {
-  if (process.env.E2E) return;
+  if (process.env.E2E) return; // force-run
  try {
    const [backendRes, frontendRes] = await Promise.allSettled([
      fetch(`${BACKEND_URL}/api/repos`),
      fetch(FRONTEND_URL),
    ]);
-    if (
-      backendRes.status === 'rejected' ||
-      (backendRes.status === 'fulfilled' && !backendRes.value.ok)
-    ) {
+    if (backendRes.status === 'rejected' || (backendRes.status === 'fulfilled' && !backendRes.value.ok)) {
      test.skip(true, 'gitnexus serve not available on :4747');
      return;
    }
-    if (
-      frontendRes.status === 'rejected' ||
-      (frontendRes.status === 'fulfilled' && !frontendRes.value.ok)
-    ) {
+    if (frontendRes.status === 'rejected' || (frontendRes.status === 'fulfilled' && !frontendRes.value.ok)) {
      test.skip(true, 'Vite dev server not available on :5173');
      return;
    }
-    // Check there's at least one indexed repo
-    if (backendRes.status === 'fulfilled') {
-      const repos = await backendRes.value.json();
-      if (!repos.length) {
-        test.skip(true, 'No indexed repos — run gitnexus analyze first');
-        return;
-      }
-    }
  } catch {
    test.skip(true, 'servers not available');
  }
 });

-/**
- * Wait for the server-detection flow to complete.
- *
- * The app auto-detects the server, then either:
- *   - shows the landing screen when indexed repos exist, or
- *   - goes straight into analyze onboarding when there are zero repos.
- *
- * For these tests we require at least one indexed repo, so pick the first
- * landing card when present and then wait for the exploring view.
- */
-async function waitForGraphLoaded(page: import('@playwright/test').Page, testInfo: TestInfo) {
+/** Shared helper: connect to the local server and wait for the graph to load */
+async function connectAndWaitForGraph(page: import('@playwright/test').Page, testInfo: TestInfo) {
+  // Signal to the app that we are running under Playwright (used to skip heavy Ladybug loads).
+  await page.addInitScript(() => {
+    (window as unknown as { __PLAYWRIGHT_TEST__?: boolean }).__PLAYWRIGHT_TEST__ = true;
+  });
+
  await page.goto('/');

-  const landingCard = page.locator('[data-testid="landing-repo-card"]').first();
-  try {
-    await landingCard.waitFor({ state: 'visible', timeout: 15_000 });
-    await landingCard.click();
-  } catch {
-    // Landing screen may not appear (e.g. ?server auto-connect)
-  }
+  // Wait for the app to fully render before interacting
+  const serverTab = page.getByRole('button', { name: 'Server' });
+  await expect(serverTab).toBeVisible({ timeout: 15_000 });
+  await page.screenshot({ path: testInfo.outputPath('step-1-landing.png') });

+  // Click "Server" tab and wait for the input to appear
+  await serverTab.click();
+  const serverInput = page.locator('input[name="server-url-input"]');
+  await expect(serverInput).toBeVisible({ timeout: 15_000 });
+  await page.screenshot({ path: testInfo.outputPath('step-2-server-tab.png') });
+  await serverInput.fill(BACKEND_URL);
+  await page.screenshot({ path: testInfo.outputPath('step-3-url-filled.png') });
+
+  await page.getByRole('button', { name: /Connect/ }).click();
+
+  // Wait for graph to load — status bar shows "Ready"
  await expect(page.locator('[data-testid="status-ready"]')).toBeVisible({ timeout: 30_000 });
  await expect(page.getByText(/\d+ nodes/).first()).toBeVisible();
-  await page.screenshot({ path: testInfo.outputPath('graph-loaded.png') });
+  await page.screenshot({ path: testInfo.outputPath('step-4-graph-loaded.png') });
 }

 test.describe('Server Connection & Graph Loading', () => {
-  test('selects a repo from landing and loads graph', async ({ page }, testInfo) => {
-    await waitForGraphLoaded(page, testInfo);
-    await page.screenshot({ path: testInfo.outputPath('graph-loaded-full.png'), fullPage: true });
+  test('connects to server and loads graph', async ({ page }, testInfo) => {
+    await connectAndWaitForGraph(page, testInfo);
+    await page.screenshot({ path: testInfo.outputPath('graph-loaded.png'), fullPage: true });
  });
 });

 test.describe('Nexus AI', () => {
  test('panel opens and agent initializes without error', async ({ page }, testInfo) => {
-    await waitForGraphLoaded(page, testInfo);
+    await connectAndWaitForGraph(page, testInfo);

+    // Click Nexus AI button to open the panel
    await page.getByRole('button', { name: 'Nexus AI' }).click();
+
+    // Should see the Nexus AI tab content
    await expect(page.getByText('Ask me anything')).toBeVisible({ timeout: 15_000 });
+
    await page.screenshot({ path: testInfo.outputPath('nexus-ai-panel.png'), fullPage: true });

+    // "Database not ready" should NOT be visible
    const errorBanner = page.getByText('Database not ready');
    expect(await errorBanner.isVisible().catch(() => false)).toBe(false);
  });
@@ -96,16 +90,17 @@ test.describe('Nexus AI', () => {

 test.describe('Processes Panel', () => {
  test('shows process list and View button works', async ({ page }, testInfo) => {
-    await waitForGraphLoaded(page, testInfo);
+    await connectAndWaitForGraph(page, testInfo);

+    // Open Nexus AI panel, switch to Processes tab
    await page.getByRole('button', { name: 'Nexus AI' }).click();
    await page.getByText('Processes').click();

-    await expect(page.locator('[data-testid="process-list-loaded"]')).toBeVisible({
-      timeout: 15_000,
-    });
+    // Should show process count — wait for data-testid instead of fixed timeout
+    await expect(page.locator('[data-testid="process-list-loaded"]')).toBeVisible({ timeout: 15_000 });
    await page.screenshot({ path: testInfo.outputPath('processes-panel.png'), fullPage: true });

+    // Hover first process item to reveal View button, then click it
    const processRow = page.locator('[data-testid="process-row"]').first();
    await expect(processRow).toBeVisible({ timeout: 10_000 });
    await processRow.hover();
@@ -113,22 +108,21 @@ test.describe('Processes Panel', () => {
    const viewBtn = processRow.locator('[data-testid="process-view-button"]');
    await viewBtn.waitFor({ state: 'visible', timeout: 5_000 });
    await viewBtn.click();
+    // Wait for modal to appear
    await expect(page.locator('[data-testid="process-modal"]')).toBeVisible({ timeout: 5_000 });
-    await page.screenshot({
-      path: testInfo.outputPath('process-view-clicked.png'),
-      fullPage: true,
-    });
+    await page.screenshot({ path: testInfo.outputPath('process-view-clicked.png'), fullPage: true });
  });

  test('lightbulb highlights nodes in graph', async ({ page }, testInfo) => {
-    await waitForGraphLoaded(page, testInfo);
+    await connectAndWaitForGraph(page, testInfo);

    await page.getByRole('button', { name: 'Nexus AI' }).click();
    await page.getByText('Processes').click();
-    await expect(page.locator('[data-testid="process-list-loaded"]')).toBeVisible({
-      timeout: 15_000,
-    });
+    await expect(page.locator('[data-testid="process-list-loaded"]')).toBeVisible({ timeout: 15_000 });

+    await page.screenshot({ path: testInfo.outputPath('before-highlight.png'), fullPage: true });
+
+    // Hover first process to reveal lightbulb
    const processRow = page.locator('[data-testid="process-row"]').first();
    await expect(processRow).toBeVisible({ timeout: 10_000 });
    await processRow.hover();
@@ -136,6 +130,7 @@ test.describe('Processes Panel', () => {
    const lightbulb = processRow.locator('[data-testid="process-highlight-button"]');
    await lightbulb.waitFor({ state: 'visible', timeout: 5_000 });
    await lightbulb.click();
+    // Wait for highlight to apply — the process row gets amber styling when focused
    await expect(processRow).toHaveClass(/bg-amber-950/, { timeout: 5_000 });
    await page.screenshot({ path: testInfo.outputPath('after-highlight.png'), fullPage: true });
  });
@@ -143,23 +138,28 @@ test.describe('Processes Panel', () => {

 test.describe('Turn Off All Highlights', () => {
  test('selecting a node dims others, button clears it', async ({ page }, testInfo) => {
-    await waitForGraphLoaded(page, testInfo);
+    await connectAndWaitForGraph(page, testInfo);

+    // Wait for graph to fully render by checking for canvas element
    await expect(page.locator('canvas').first()).toBeVisible({ timeout: 10_000 });

+    await page.screenshot({ path: testInfo.outputPath('before-select.png'), fullPage: true });
+
+    // Click a file in the file tree to select a node
    const fileItem = page.getByText('package.json').first();
    await expect(fileItem).toBeVisible({ timeout: 10_000 });
    await fileItem.click();

+    // Wait for highlight toggle to show "Turn off" (indicates highlights are active)
    const highlightToggle = page.locator('[data-testid="ai-highlights-toggle"]');
-    await expect(highlightToggle).toHaveAttribute('title', 'Turn off all highlights', {
-      timeout: 5_000,
-    });
+    await expect(highlightToggle).toHaveAttribute('title', 'Turn off all highlights', { timeout: 5_000 });
+    await page.screenshot({ path: testInfo.outputPath('node-selected.png'), fullPage: true });

+    // Click the toggle to clear all highlights
    await highlightToggle.click();
-    await expect(highlightToggle).toHaveAttribute('title', 'Turn on AI highlights', {
-      timeout: 5_000,
-    });
+
+    // Verify highlights are now off — button title changes to "Turn on"
+    await expect(highlightToggle).toHaveAttribute('title', 'Turn on AI highlights', { timeout: 5_000 });
    await page.screenshot({ path: testInfo.outputPath('highlights-cleared.png'), fullPage: true });
  });
 });
@@ -4,12 +4,9 @@
    <meta charset="UTF-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
    <title>GitNexus</title>
-    <link rel="preconnect" href="https://fonts.googleapis.com" />
-    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
-    <link
-      href="https://fonts.googleapis.com/css2?family=JetBrains+Mono:wght@400;500;600&family=Outfit:wght@300;400;500;600;700&display=swap"
-      rel="stylesheet"
-    />
+    <link rel="preconnect" href="https://fonts.googleapis.com">
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+    <link href="https://fonts.googleapis.com/css2?family=JetBrains+Mono:wght@400;500;600&family=Outfit:wght@300;400;500;600;700&display=swap" rel="stylesheet">
  </head>
  <body>
    <div id="root"></div>
@@ -18,7 +18,9 @@
    "test:e2e:report": "playwright show-report"
  },
  "dependencies": {
-    "gitnexus-shared": "file:../gitnexus-shared",
+    "@huggingface/transformers": "^3.0.0",
+    "@isomorphic-git/lightning-fs": "^4.6.2",
+    "@ladybugdb/wasm-core": "^0.15.1",
    "@langchain/anthropic": "^1.3.10",
    "@langchain/core": "^1.1.15",
    "@langchain/google-genai": "^2.1.10",
@@ -28,6 +30,8 @@
    "@sigma/edge-curve": "^3.1.0",
    "@tailwindcss/vite": "^4.1.18",
    "axios": "^1.13.2",
+    "buffer": "^6.0.3",
+    "comlink": "^4.4.2",
    "d3": "^7.9.0",
    "dompurify": "^3.3.3",
    "graphology": "^0.26.0",
@@ -36,10 +40,13 @@
    "graphology-layout-forceatlas2": "^0.10.1",
    "graphology-layout-noverlap": "^0.4.2",
    "graphology-utils": "^2.3.0",
+    "isomorphic-git": "^1.36.1",
+    "jszip": "^3.10.1",
    "langchain": "^1.2.10",
    "lru-cache": "^11.2.4",
    "lucide-react": "^0.562.0",
    "mermaid": "^11.12.2",
+    "minisearch": "^7.2.0",
    "mnemonist": "^0.39.0",
    "pandemonium": "^2.4.0",
    "react": "^18.3.1",
@@ -51,6 +58,9 @@
    "sigma": "^3.0.2",
    "tailwindcss": "^4.1.18",
    "uuid": "^13.0.0",
+    "vite-plugin-top-level-await": "^1.6.0",
+    "vite-plugin-wasm": "^3.5.0",
+    "web-tree-sitter": "^0.20.8",
    "zod": "^3.25.76"
  },
  "devDependencies": {
@@ -60,6 +70,7 @@
    "@testing-library/react": "^16.3.2",
    "@testing-library/user-event": "^14.6.1",
    "@types/dompurify": "^3.0.5",
+    "@types/jszip": "^3.4.0",
    "@types/node": "^24.10.1",
    "@types/react": "^18.3.5",
    "@types/react-dom": "^18.3.0",
@@ -71,6 +82,7 @@
    "tree-sitter-wasms": "^0.1.13",
    "typescript": "^5.4.5",
    "vite": "^5.2.0",
+    "vite-plugin-static-copy": "^3.1.4",
    "vitest": "^3.2.4",
    "wait-on": "^8.0.5"
  }
@@ -40,6 +40,9 @@ export default defineConfig({
      use: { browserName: 'chromium' },
    },
  ],
-  reporter: [['list'], ['html', { open: 'never', outputFolder: 'playwright-report' }]],
+  reporter: [
+    ['list'],
+    ['html', { open: 'never', outputFolder: 'playwright-report' }],
+  ],
  outputDir: 'test-results',
 });
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
copilot-swe-agent[bot]andmagyargergo	1d7782e4e1	fix(cobol): single-quote CALL/COPY, sequence number stripping, PERFORM keyword filtering Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/afed41bd-98b4-48e8-a9e5-ebf0b97deaa8	2026-03-24 17:10:16 +00:00
copilot-swe-agent[bot]andmagyargergo	7ce1371ad8	Initial plan: review COBOL processor completeness Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/afed41bd-98b4-48e8-a9e5-ebf0b97deaa8	2026-03-24 16:59:25 +00:00
copilot-swe-agent[bot]	ae437dc30e	Initial plan	2026-03-24 16:48:12 +00:00
Gergo Magyar	832789f288	test(cobol): exhaustive 57-test suite with strict exact assertions Complete rewrite of COBOL integration tests using ground-truth approach: dump the full graph, then assert EVERY node and EVERY edge. 57 tests across 9 sections: - Node completeness: Module(3), Function(13), Namespace(2), Property(21), Record(1), CodeElement(8), Constructor(1) — exact sorted arrays - Edge completeness: 22 tests covering every type+reason combination with exact source→target pairs - Cross-program resolution: 6 tests verifying CALL, CICS LINK/XCTL, JCL - COPY expansion: copybook data items in RPTGEN - Section hierarchy: exact paragraph membership per section - Data item ownership: exact per-module breakdown - MOVE data flow: exact read/write pairs - JCL integration: job/step/dataset containment - Grand totals: CALLS(22), CONTAINS(48), IMPORTS(1), ACCESSES(7) Fixture enhancements: - CUSTUPDT.cbl: added INIT-SECTION + PROCESSING-SECTION, PERFORM THRU - AUDITLOG.cbl: added ENTRY "AUDITLOG-BATCH" - RPTGEN.cbl: added EXEC CICS XCTL Zero fuzzy assertions — every expect uses toBe(N) or toEqual([...sorted]).	2026-03-24 16:10:29 +00:00
Gergo Magyar	41b0d8dfad	test(cobol): add 26 integration tests with exact assertions + fix CICS resolution bug Integration tests (test/integration/resolvers/cobol.test.ts): - 26 tests covering full COBOL system extraction - ALL assertions use exact toBe(N) — zero fuzzy assertions - Fixtures: CUSTUPDT.cbl, AUDITLOG.cbl, CUSTDAT.cpy, RPTGEN.cbl, RUNJOBS.jcl Bug fix (cobol-processor.ts): - CICS LINK/XCTL cross-program resolution was broken — edges were created with "resolved" reason but pointing to <unresolved> targets - Fix: use cics-link-unresolved / cics-xctl-unresolved suffix pattern matching the existing cobol-call-unresolved pattern - Second-pass resolver now patches both CALL and CICS unresolved edges All 3915 tests pass, 0 failures.	2026-03-24 15:41:00 +00:00
Gergo Magyar	9760f966cb	feat(cobol): enrich graph with EXEC SQL/CICS, ENTRY points, MOVE data flow, PERFORM THRU Maps the remaining 60% of CobolRegexResults to the graph: - EXEC SQL blocks → CodeElement nodes + ACCESSES edges to DB tables - EXEC CICS LINK/XCTL → CodeElement nodes + cross-program CALLS edges - ENTRY points → Constructor nodes (registered for cross-program resolution) - MOVE statements → ACCESSES edges (read/write data flow tracking) - PERFORM THRU → expanded CALLS edges for range targets - File declarations → Record nodes with assignment metadata - Cross-program CALL 2nd pass: resolves unresolved targets after all programs processed	2026-03-24 15:20:26 +00:00
Gergo Magyar	88c89c42e6	docs: document custom processor pattern in pipeline.ts Add comment block at the custom processor integration point documenting the pattern for future non-tree-sitter language additions.	2026-03-24 14:59:09 +00:00
Gergo Magyar	4af677e637	feat: add COBOL language support with regex extraction pipeline Standalone COBOL processor following the markdown-processor.ts pattern: - No LanguageProvider modification — COBOL uses regex, not tree-sitter - No SupportedLanguages enum change — standalone processor pattern New files: - cobol-processor.ts — orchestrator (processCobol, isCobolFile, isJclFile) - cobol/cobol-preprocessor.ts — regex state machine extraction (~888 LOC) - cobol/cobol-copy-expander.ts — COPY statement expansion with circular detection - cobol/jcl-parser.ts — JCL job/step/DD extraction - cobol/jcl-processor.ts — JCL graph node creation Extraction produces: - Module nodes (PROGRAM-ID) - Function nodes (paragraphs) - Namespace nodes (sections) - Property nodes (data items) - CALLS edges (PERFORM intra-file, CALL cross-program) - IMPORTS edges (COPY statements) - CONTAINS edges (section → paragraph hierarchy) Pipeline integration: single processCobol() call in Phase 2.6 54 new tests (33 COBOL + 21 JCL), all 3889 tests pass.	2026-03-24 14:39:25 +00:00
				`@@ -1 +0,0 @@`
				`"""Utility package for the eval harness."""`