release: v1.6.5-rc.24

Bumps the uv group with 1 update in the /eval directory: [urllib3](https://github.com/urllib3/urllib3).


Updates `urllib3` from 2.6.3 to 2.7.0
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.6.3...2.7.0)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-version: 2.7.0
  dependency-type: indirect
  dependency-group: uv
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>

.github/actions/setup-gitnexus-web/action.yml

@@ -1,5 +1,5 @@
 name: Setup GitNexus Web
-description: Setup Node.js 20.19+ (vite 7 floor), build gitnexus-shared, install web dependencies
+description: Setup Node.js 22, build gitnexus-shared, install web dependencies
 
 runs:
   using: composite
@@ -7,9 +7,7 @@ runs:
     - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
       with:
         # Vite 7 requires Node ^20.19.0 || >=22.12.0 (require(esm) support).
-        # Pin explicitly so we don't depend on the floating "20" alias resolving
-        # to a high enough patch version on every runner image.
-        node-version: '20.19.0'
+        node-version: 22
         cache: npm
         cache-dependency-path: gitnexus-web/package-lock.json
 

.github/actions/setup-gitnexus/action.yml

@@ -1,5 +1,5 @@
 name: Setup GitNexus
-description: Setup Node.js 20, install dependencies, and optionally build
+description: Setup Node.js 22, install dependencies, and optionally build
 
 inputs:
   build:
@@ -12,7 +12,7 @@ runs:
   steps:
     - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
       with:
-        node-version: 20
+        node-version: 22
         cache: npm
         cache-dependency-path: gitnexus/package-lock.json
 

.github/dependabot.yml

@@ -7,6 +7,8 @@ updates:
     directory: /
     schedule:
       interval: weekly
+    cooldown:
+      default-days: 7
     open-pull-requests-limit: 5
     commit-message:
       prefix: chore
@@ -15,6 +17,36 @@ updates:
       - dependencies
       - ci
 
+  # Keep pinned Docker base-image digests current for the root Dockerfiles.
+  - package-ecosystem: docker
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: chore(deps)
+      include: scope
+    labels:
+      - dependencies
+      - ci
+
+  # Keep the nested test-image Docker base digest current as well.
+  - package-ecosystem: docker
+    directory: /gitnexus
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: chore(deps)
+      include: scope
+    labels:
+      - dependencies
+      - ci
+
   # Gitnexus npm deps — tree-sitter grammars checked daily so we catch
   # new releases that unblock the tree-sitter 0.25 upgrade ASAP. Grammars
   # are grouped so lockstep bumps produce a single PR. The tree-sitter
@@ -25,6 +57,11 @@ updates:
     directory: /gitnexus
     schedule:
       interval: daily
+    cooldown:
+      default-days: 7
+      semver-major-days: 30
+      semver-minor-days: 7
+      semver-patch-days: 3
     open-pull-requests-limit: 10
     commit-message:
       prefix: chore(deps)
@@ -54,6 +91,11 @@ updates:
     directory: /gitnexus-web
     schedule:
       interval: weekly
+    cooldown:
+      default-days: 7
+      semver-major-days: 30
+      semver-minor-days: 7
+      semver-patch-days: 3
     open-pull-requests-limit: 5
     commit-message:
       prefix: chore(deps)
@@ -67,6 +109,11 @@ updates:
     directory: /gitnexus-shared
     schedule:
       interval: weekly
+    cooldown:
+      default-days: 7
+      semver-major-days: 30
+      semver-minor-days: 7
+      semver-patch-days: 3
     open-pull-requests-limit: 5
     commit-message:
       prefix: chore(deps)

.github/workflows/ci-e2e.yml

@@ -3,6 +3,9 @@ name: E2E Tests
 on:
   workflow_call:
 
+permissions:
+  contents: read
+
 jobs:
   check-changes:
     name: Check web module changes

.github/workflows/ci-quality.yml

@@ -3,6 +3,9 @@ name: Quality Checks
 on:
   workflow_call:
 
+permissions:
+  contents: read
+
 jobs:
   format:
     runs-on: ubuntu-latest
@@ -11,7 +14,7 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
         with:
-          node-version: 20
+          node-version: 22
           cache: npm
           cache-dependency-path: package-lock.json
       - run: npm ci
@@ -24,7 +27,7 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
         with:
-          node-version: 20
+          node-version: 22
           cache: npm
           cache-dependency-path: package-lock.json
       - run: npm ci

.github/workflows/ci-report.yml

@@ -95,31 +95,33 @@ jobs:
 
           # Validate PR number is a positive integer (artifact comes from
           # untrusted fork code, so treat contents defensively).
-          PR_NUM=$(cat "$DIR/pr_number" | tr -d '[:space:]')
+          PR_NUM=$(tr -d '[:space:]' < "$DIR/pr_number")
           if ! [[ "$PR_NUM" =~ ^[0-9]+$ ]]; then
             echo "skip=true" >> "$GITHUB_OUTPUT"
             echo "::error::Invalid PR number in artifact: '$PR_NUM'"
             exit 0
           fi
 
-          echo "skip=false"              >> "$GITHUB_OUTPUT"
-          echo "pr_number=$PR_NUM"       >> "$GITHUB_OUTPUT"
           # Validate job-result strings against known GitHub Actions values.
           # Artifact contents come from the PR workflow (potentially untrusted
           # fork code), so we whitelist to prevent newline injection into
           # GITHUB_OUTPUT.
           validate_result() {
             local val
-            val=$(cat "$1" | tr -d '[:space:]')
+            val=$(tr -d '[:space:]' < "$1")
             case "$val" in
               success|failure|cancelled|skipped) echo "$val" ;;
               *) echo "unknown" ;;
             esac
           }
 
-          echo "quality=$(validate_result "$DIR/quality_result")"        >> "$GITHUB_OUTPUT"
-          echo "tests=$(validate_result "$DIR/tests_result")"            >> "$GITHUB_OUTPUT"
-          echo "e2e=$(validate_result "$DIR/e2e_result")"                >> "$GITHUB_OUTPUT"
+          {
+            echo "skip=false"
+            echo "pr_number=$PR_NUM"
+            echo "quality=$(validate_result "$DIR/quality_result")"
+            echo "tests=$(validate_result "$DIR/tests_result")"
+            echo "e2e=$(validate_result "$DIR/e2e_result")"
+          } >> "$GITHUB_OUTPUT"
 
       - name: Checkout (for vitest config)
         if: steps.meta.outputs.skip != 'true'
@@ -279,14 +281,17 @@ jobs:
             fi
           }
 
-          read CLI_T CLI_P CLI_F CLI_S CLI_SU CLI_D <<< "$(sum_results "$RESULTS_FILE")"
-          read WEB_T WEB_P WEB_F WEB_S WEB_SU WEB_D <<< "$(sum_results "$WEB_RESULTS_FILE")"
+          # `_` placeholder for the suite-count column — positional
+          # readability for sum_results' 6-field output, but the value
+          # isn't surfaced in the report (suites are tracked per-test
+          # framework, not as a top-line metric).
+          read -r CLI_T CLI_P CLI_F CLI_S _ CLI_D <<< "$(sum_results "$RESULTS_FILE")"
+          read -r WEB_T WEB_P WEB_F WEB_S _ WEB_D <<< "$(sum_results "$WEB_RESULTS_FILE")"
 
           TOTAL=$((CLI_T + WEB_T))
           PASSED=$((CLI_P + WEB_P))
           FAILED=$((CLI_F + WEB_F))
           SKIPPED=$((CLI_S + WEB_S))
-          SUITES=$((CLI_SU + WEB_SU))
           DURATION=$((CLI_D > WEB_D ? CLI_D : WEB_D))
 
           # ── Status helpers ──

.github/workflows/ci-scope-parity.yml

@@ -28,6 +28,9 @@ name: Scope Resolution Parity
 on:
   workflow_call:
 
+permissions:
+  contents: read
+
 jobs:
   discover:
     name: Discover migrated languages

.github/workflows/ci-tests.yml

@@ -3,6 +3,9 @@ name: Tests
 on:
   workflow_call:
 
+permissions:
+  contents: read
+
 jobs:
   tests:
     name: ubuntu / coverage

.github/workflows/ci.yml

@@ -6,6 +6,9 @@ on:
     paths-ignore: ['**.md', 'docs/**', 'LICENSE']
   workflow_call:
 
+permissions:
+  contents: read
+
 # Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Hardcoded `CI-` prefix (not `${{ github.workflow }}`) because this workflow is
 # invoked as a reusable workflow from publish.yml and release-candidate.yml. In

.github/workflows/claude.yml

@@ -19,6 +19,9 @@ on:
   pull_request_review:
     types: [submitted]
 
+permissions:
+  contents: read
+
 # Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Serialize per-PR/issue to avoid racing comments.
 concurrency:
@@ -155,6 +158,8 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           allowed_non_write_users: '*'
           show_full_output: true
+          # Review posts use Bash (`gh`, etc.); default mode asks for approval — impossible in CI.
+          claude_args: '--dangerously-skip-permissions'
           plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
           plugins: 'code-review@claude-code-plugins'
-          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ steps.pr.outputs.number }}'
+          prompt: '/code-review:code-review https://github.com/${{ github.repository }}/pull/${{ steps.pr.outputs.number }} --comment'

.github/workflows/codeql.yml

@@ -17,6 +17,9 @@ on:
     # already-merged code without waiting for the next PR.
     - cron: '0 6 * * 1'
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.event_name == 'pull_request' }}

.github/workflows/dependency-review.yml

@@ -10,6 +10,9 @@ on:
   pull_request:
     branches: [main]
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/docker.yml

@@ -26,6 +26,9 @@ on:
         required: true
         type: string
 
+permissions:
+  contents: read
+
 # Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Tag refs are unique per release, so distinct tags run in parallel.
 # Re-pushes of the same tag serialize. cancel-in-progress: false — never cancel a publish mid-flight.

.github/workflows/gitleaks.yml

@@ -12,6 +12,9 @@ on:
   push:
     branches: [main]
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.event_name == 'pull_request' }}

.github/workflows/pr-autofix-apply.yml

@@ -0,0 +1,595 @@
+name: PR Autofix (apply)
+
+# CHATOPS HALF of the autofix pipeline.
+#
+# Triggered when a contributor comments `/autofix` on a PR. Validates
+# permission, locates the most recent successful `pr-autofix.yml`
+# artifact for the PR's current head SHA, applies the patch to the PR
+# head, and pushes a commit back to the PR branch.
+#
+# This workflow runs from the default branch's copy of the file
+# regardless of where the comment originates -- that's the trust
+# anchor. Comment body and author login are untrusted; both flow
+# through env vars and pattern-matched, never interpolated into shell.
+#
+# Fork PR support: `git push` with the GITHUB_TOKEN succeeds against
+# fork branches only when the contributor enabled "Allow edits by
+# maintainers" on the PR (the default). When they disabled it, we
+# fail loud with a 👎 reaction and an explanation comment.
+
+on:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  # Per-PR scope. issue_comment events expose `github.event.issue.number`
+  # for both PR and Issue comments; the `pull_request != null` guard on
+  # the job ensures we only run on PRs, so this number is the PR number.
+  # cancel-in-progress: false — a second `/autofix` should wait for the
+  # first to finish (idempotency check on the second invocation handles
+  # the no-op case).
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.event.issue.number }}
+  cancel-in-progress: false
+
+permissions: {}
+
+jobs:
+  apply:
+    name: apply-autofix
+    # Pre-filter at the workflow level so non-PR comments and unrelated
+    # comments don't even spawn a runner. The job-level body re-check
+    # below (Step 1) is the strict gate.
+    if: >-
+      github.event.issue.pull_request != null
+      && startsWith(github.event.comment.body, '/autofix')
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      # React on the triggering comment + post reply comments.
+      pull-requests: write
+      # Push the apply commit to the PR head branch.
+      contents: write
+      # Required by actions/download-artifact to fetch artifacts produced
+      # by a different workflow run.
+      actions: read
+    steps:
+      - name: Validate comment body precisely
+        id: body
+        env:
+          BODY: ${{ github.event.comment.body }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          # Whole-line, case-sensitive match: `^/autofix\s*$`. The
+          # workflow-level startsWith guard is coarse — `please don't
+          # /autofix this code` would pass that filter but fail this one.
+          # We exit silently (no reaction) on body mismatch so quoted
+          # text in unrelated discussions doesn't get a visible response.
+          if [[ ! "${BODY}" =~ ^/autofix[[:space:]]*$ ]]; then
+            echo "Body did not match strict /autofix regex — exiting silently."
+            echo "match=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+          echo "match=true" >> "$GITHUB_OUTPUT"
+
+      - name: Validate commenter permission
+        id: perm
+        if: steps.body.outputs.match == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENTER: ${{ github.event.comment.user.login }}
+          PR_AUTHOR: ${{ github.event.issue.user.login }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          # Retry wrapper for transient 5xx / 429 / network blips.
+          # Mirrors the helper in pr-autofix-publish.yml. Used on
+          # idempotent GETs only; reactions/comment-POSTs are NOT
+          # wrapped (retrying a POST would dupe the resource).
+          gh_retry() {
+            local n=0 max=3
+            while true; do
+              if gh "$@"; then return 0; fi
+              n=$((n+1))
+              if [ "$n" -ge "$max" ]; then return 1; fi
+              sleep $((n * 2))
+            done
+          }
+
+          # Allowlist the commenter login before it flows into a URL.
+          # GitHub usernames: alphanumeric + dashes, max 39 chars.
+          if ! [[ "${COMMENTER}" =~ ^[A-Za-z0-9-]{1,39}$ ]]; then
+            echo "::error::Invalid commenter login format: $(printf '%q' "${COMMENTER}")"
+            echo "allowed=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Self-comparison: PR author can always /autofix their own PR.
+          if [ "${COMMENTER}" = "${PR_AUTHOR}" ]; then
+            echo "Commenter is PR author — granting access."
+            echo "allowed=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Repo permission lookup. admin/write/maintain are sufficient.
+          # Distinguish API failure (5xx, 429, network) from genuine
+          # permission denial (404 = not a collaborator). Conflating them
+          # would silently refuse a legitimate maintainer with a public
+          # 👎 every time GitHub blips. gh_retry handles transient blips;
+          # the stderr-grep distinguishes 404 from persistent failure.
+          perm_stderr=$(mktemp)
+          if permission=$(gh_retry api "repos/${GH_REPO}/collaborators/${COMMENTER}/permission" \
+                --jq '.permission' 2>"$perm_stderr"); then
+            echo "Commenter permission: ${permission}"
+            case "${permission}" in
+              admin|write|maintain)
+                echo "allowed=true" >> "$GITHUB_OUTPUT"
+                ;;
+              *)
+                echo "allowed=false" >> "$GITHUB_OUTPUT"
+                ;;
+            esac
+          else
+            err=$(cat "$perm_stderr")
+            echo "Permission lookup stderr: ${err}" >&2
+            # 404 (not a collaborator) is a genuine deny.
+            # Anything else is a transient API/network failure.
+            if grep -qE "HTTP 404|Not Found" "$perm_stderr"; then
+              echo "allowed=false" >> "$GITHUB_OUTPUT"
+            else
+              echo "::error::Permission lookup failed transiently — refusing to act."
+              echo "allowed=api-failed" >> "$GITHUB_OUTPUT"
+            fi
+          fi
+
+      - name: React 😕 on transient permission-API failure
+        if: steps.body.outputs.match == 'true' && steps.perm.outputs.allowed == 'api-failed'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENT_ID: ${{ github.event.comment.id }}
+          PR: ${{ github.event.issue.number }}
+          RUN_ID: ${{ github.run_id }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+            -f content="confused" >/dev/null
+          gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+            -f body="⚠️ Couldn't verify your repo permission (transient GitHub API failure). Please comment \`/autofix\` again. ([apply run](https://github.com/${GH_REPO}/actions/runs/${RUN_ID}))" \
+            >/dev/null
+          exit 1
+
+      - name: React 👎 on permission denial
+        if: steps.body.outputs.match == 'true' && steps.perm.outputs.allowed == 'false'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENT_ID: ${{ github.event.comment.id }}
+          PR: ${{ github.event.issue.number }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+            -f content="-1" >/dev/null
+          gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+            -f body="🚫 \`/autofix\` is restricted to users with write access or the PR author. Comment ignored." \
+            >/dev/null
+          # Hard exit so the rest of the job is skipped.
+          exit 1
+
+      - name: React 👀 to acknowledge
+        if: steps.perm.outputs.allowed == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENT_ID: ${{ github.event.comment.id }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+            -f content="eyes" >/dev/null
+
+      - name: Resolve PR head and locate autofix run
+        id: locate
+        if: steps.perm.outputs.allowed == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          PR: ${{ github.event.issue.number }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          # Same retry wrapper used in the permission step, repeated
+          # because each YAML `run:` block is a fresh bash session.
+          gh_retry() {
+            local n=0 max=3
+            while true; do
+              if gh "$@"; then return 0; fi
+              n=$((n+1))
+              if [ "$n" -ge "$max" ]; then return 1; fi
+              sleep $((n * 2))
+            done
+          }
+
+          # Fetch PR metadata. All fields here are server-controlled API
+          # output, but we still allowlist before exporting so anything
+          # weird short-circuits before $GITHUB_OUTPUT. Wrapped in
+          # gh_retry so transient blips don't surface as "no autofix run
+          # found" with a wrong remediation.
+          if ! pr_json=$(gh_retry api "repos/${GH_REPO}/pulls/${PR}"); then
+            echo "::error::PR metadata fetch failed after retries."
+            echo "found_status=api-failed" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+          head_sha=$(jq -r '.head.sha' <<< "${pr_json}")
+          head_ref=$(jq -r '.head.ref' <<< "${pr_json}")
+          head_repo=$(jq -r '.head.repo.full_name' <<< "${pr_json}")
+
+          [[ "${head_sha}"  =~ ^[0-9a-f]{40}$                         ]] || { echo "::error::Bad head_sha";  exit 1; }
+          [[ "${head_ref}"  =~ ^[A-Za-z0-9._/-]+$                     ]] || { echo "::error::Bad head_ref";  exit 1; }
+          [[ "${head_repo}" =~ ^[A-Za-z0-9._-]+/[A-Za-z0-9._-]+$      ]] || { echo "::error::Bad head_repo"; exit 1; }
+
+          # Find the latest successful pr-autofix.yml run for this head SHA.
+          if ! runs_json=$(gh_retry api "repos/${GH_REPO}/actions/workflows/pr-autofix.yml/runs?head_sha=${head_sha}&per_page=10"); then
+            echo "::error::Workflow run lookup failed after retries."
+            echo "found_status=api-failed" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          run_id=$(jq -r '[.workflow_runs[] | select(.conclusion == "success")] | .[0].id // empty' <<< "${runs_json}")
+
+          if [ -n "${run_id}" ] && [[ "${run_id}" =~ ^[0-9]+$ ]]; then
+            echo "found_status=success" >> "$GITHUB_OUTPUT"
+            {
+              echo "found=true"
+              echo "head_sha=${head_sha}"
+              echo "head_ref=${head_ref}"
+              echo "head_repo=${head_repo}"
+              echo "run_id=${run_id}"
+            } >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # No successful run. Distinguish "still running" (producer in
+          # flight after a recent push) from "never ran / all failed".
+          # in_progress / queued / pending / waiting cover the GitHub
+          # workflow-run lifecycle states that precede success/failure.
+          in_progress=$(jq -r '[.workflow_runs[] | select(.status == "in_progress" or .status == "queued" or .status == "pending" or .status == "waiting")] | length' <<< "${runs_json}")
+          if [ "${in_progress:-0}" -gt 0 ]; then
+            echo "::warning::pr-autofix run is still in progress for head ${head_sha}."
+            echo "found_status=in-progress" >> "$GITHUB_OUTPUT"
+          else
+            echo "::warning::No successful pr-autofix run found for head ${head_sha}."
+            echo "found_status=not-found" >> "$GITHUB_OUTPUT"
+          fi
+          # Existing `found` boolean is preserved so downstream gates
+          # (`steps.locate.outputs.found == 'true'`) still work.
+          echo "found=false" >> "$GITHUB_OUTPUT"
+
+      - name: Reply when locate did not yield a usable run
+        if: steps.perm.outputs.allowed == 'true' && steps.locate.outputs.found != 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENT_ID: ${{ github.event.comment.id }}
+          PR: ${{ github.event.issue.number }}
+          FOUND_STATUS: ${{ steps.locate.outputs.found_status }}
+          RUN_ID: ${{ github.run_id }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          run_url="https://github.com/${GH_REPO}/actions/runs/${RUN_ID}"
+          case "${FOUND_STATUS}" in
+            in-progress)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="confused" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⏳ A pr-autofix run is still in progress for this PR's current head SHA. Wait for it to finish, then comment \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              ;;
+            api-failed)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="confused" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⚠️ Couldn't reach the GitHub API to look up the autofix run (transient failure after retries). Please comment \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              ;;
+            *)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="🤔 No successful autofix run found for this PR's current head SHA. Push a new commit to trigger one, then comment \`/autofix\` again." \
+                >/dev/null
+              ;;
+          esac
+          exit 1
+
+      # Pinned to v8.0.1. Same SHA as pr-autofix-publish.yml.
+      # `continue-on-error: true` lets the workflow proceed when the
+      # artifact is expired or pruned (1-day retention). The apply
+      # step distinguishes "patch file missing entirely" (artifact-
+      # expired) from "patch file zero bytes" (genuinely empty patch).
+      - name: Download autofix artifact
+        if: steps.locate.outputs.found == 'true'
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        continue-on-error: true
+        with:
+          name: autofix
+          run-id: ${{ steps.locate.outputs.run_id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path: autofix-in
+
+      # Pinned to v5.0.4. Verify SHA via:
+      #   gh api repos/actions/checkout/git/refs/tags/v5.0.4
+      #
+      # `persist-credentials: false` disables the default behavior where
+      # actions/checkout writes the GITHUB_TOKEN into `.git/config` as an
+      # extraheader. That default is convenient (subsequent git commands
+      # auth automatically) but it means the token is sitting on disk in
+      # the checkout directory — an `actions/upload-artifact` step on
+      # this directory would leak the token. We don't upload, but
+      # zizmor's `credential-persistence` lint flags it defensively.
+      # Push auth is provided inline at push time via the URL.
+      - name: Checkout PR head
+        if: steps.locate.outputs.found == 'true'
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v5.0.4
+        with:
+          repository: ${{ steps.locate.outputs.head_repo }}
+          ref: ${{ steps.locate.outputs.head_sha }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+          # Fetch full history so the push doesn't hit shallow-clone errors.
+          fetch-depth: 0
+          path: pr-checkout
+
+      - name: Apply patch and push
+        id: apply
+        if: steps.locate.outputs.found == 'true'
+        env:
+          HEAD_REF: ${{ steps.locate.outputs.head_ref }}
+          HEAD_REPO: ${{ steps.locate.outputs.head_repo }}
+          # The SHA we resolved earlier in `locate` — this is what the
+          # remote ref MUST still equal at push time. If the contributor
+          # force-pushed between resolve and now, the lease fails and
+          # we surface that distinctly from a fork-without-maintainer
+          # -edit push failure.
+          HEAD_SHA: ${{ steps.locate.outputs.head_sha }}
+          # Auth for the push only — never persisted to disk. Provided
+          # via env to avoid interpolating into the shell command line.
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        shell: bash
+        working-directory: pr-checkout
+        run: |
+          set -euo pipefail
+          patch="../autofix-in/autofix.patch"
+
+          # Distinguish artifact-expired (file missing entirely, because
+          # actions/download-artifact ran with continue-on-error and the
+          # 1-day retention had elapsed) from genuinely empty patch
+          # (file present, zero bytes, formatter found nothing).
+          if [ ! -e "$patch" ]; then
+            echo "::warning::Patch file does not exist — autofix artifact likely expired."
+            echo "result=artifact-expired" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          if [ ! -s "$patch" ]; then
+            echo "::warning::Empty patch — nothing to apply."
+            echo "result=empty-patch" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Sensitive-paths guard: refuse to apply patches that touch
+          # `.github/` — workflow files, action definitions, CODEOWNERS,
+          # dependabot config, etc. A malicious PR could ship a custom
+          # prettier/ESLint config that reformats workflow YAML; the
+          # producer would then capture those edits in autofix.patch,
+          # and a maintainer running `/autofix` would push them under
+          # `contents: write`. The default GITHUB_TOKEN lacks `workflows`
+          # scope so the platform would reject workflow-file pushes
+          # anyway, but that surfaces as a generic `push-failed` and
+          # misleads users into enabling maintainer-edit. Reject early
+          # with a specific reason. CODEOWNERS and dependabot.yml live
+          # under .github/ but outside .github/workflows/ — the broader
+          # match is intentional (they all govern trust boundaries).
+          if grep -qE '^(diff --git|---|\+\+\+) [ab]?/?\.github/' "$patch"; then
+            echo "::warning::Patch touches .github/ — refusing to apply (sensitive paths)."
+            echo "result=sensitive-paths" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Re-entrancy guard: if HEAD itself is an autofix bot commit,
+          # refuse to apply again. Without this, lint/formatter config
+          # drift between runs could pump arbitrary apply commits into
+          # the same PR if an automated agent watches the sticky and
+          # re-fires `/autofix` on each new "fixes-available" surface.
+          # The contributor can still get out by force-pushing a
+          # human-authored commit to revert the autofix and re-trigger.
+          head_author=$(git log -1 --format='%ae' HEAD)
+          head_subject=$(git log -1 --format='%s' HEAD)
+          if [ "${head_author}" = "41898282+github-actions[bot]@users.noreply.github.com" ] \
+             && [[ "${head_subject}" =~ ^chore\(autofix\) ]]; then
+            echo "::warning::HEAD is an autofix bot commit — refusing to re-apply (loop guard)."
+            echo "result=loop-prevented" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Idempotency probe: does the forward apply work?
+          if git apply --check "$patch" 2>/dev/null; then
+            echo "Patch applies cleanly — proceeding."
+          elif git apply --check --reverse "$patch" 2>/dev/null; then
+            # Reverse-check passes => the patch is already applied to
+            # the current tree. Treat as success no-op.
+            echo "Patch is already applied (reverse-check passed) — no-op."
+            echo "result=already-applied" >> "$GITHUB_OUTPUT"
+            exit 0
+          else
+            echo "::error::Patch does not apply (stale or conflicting)."
+            echo "result=stale" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Wrap the apply/commit phase so any non-zero exit sets a
+          # meaningful `result=` instead of leaving it unset (which would
+          # send the user to the `*` "unexpected state" arm with a
+          # non-actionable confused-emoji reply).
+          if ! {
+            git config user.email "41898282+github-actions[bot]@users.noreply.github.com" &&
+            git config user.name  "github-actions[bot]" &&
+            git apply "$patch" &&
+            git add -A &&
+            git commit -m "chore(autofix): apply prettier + eslint fixes via /autofix command"
+          }; then
+            echo "::error::git apply / config / commit failed after idempotency probe passed."
+            echo "result=apply-failed" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Push to the PR head branch with a lease against the resolved
+          # SHA. The lease ensures the remote ref still points at HEAD_SHA
+          # when the push lands — if the contributor force-pushed in the
+          # window between resolve and now, the lease fails and we return
+          # `lease-failed` (NOT `push-failed`, which would mislead users
+          # into enabling maintainer-edit). For fork PRs, the push still
+          # requires "Allow edits by maintainers" to be enabled.
+          #
+          # Auth is supplied inline via `-c http.<base>.extraheader` (NOT
+          # via a `https://x-access-token:TOKEN@…` URL — those leak into
+          # process listings and `git remote -v` output). The header is
+          # set per-invocation; it never lands in `.git/config` on disk.
+          # The token is base64-encoded for the Basic auth header per
+          # GitHub's documented pattern for this scope.
+          push_url="https://github.com/${HEAD_REPO}.git"
+          auth_header="Authorization: Basic $(printf 'x-access-token:%s' "${GITHUB_TOKEN}" | base64 -w0)"
+          # GitHub's secret-masker only masks the raw token, not its
+          # base64-encoded form. Mask the encoded value so any subsequent
+          # log line (set -x, GIT_TRACE, error spew) gets ***-redacted.
+          echo "::add-mask::${auth_header}"
+          push_stderr=$(mktemp)
+          if git -c http.extraheader="${auth_header}" \
+                push --force-with-lease="refs/heads/${HEAD_REF}:${HEAD_SHA}" \
+                "${push_url}" "HEAD:${HEAD_REF}" 2>"$push_stderr"; then
+            echo "result=applied" >> "$GITHUB_OUTPUT"
+          else
+            cat "$push_stderr" >&2
+            # `--force-with-lease` reports "stale info" when the remote
+            # ref has moved past the expected SHA. Other lease-failure
+            # phrases git emits include "remote rejected" (server-side
+            # reject), "non-fast-forward", and the literal flag name. Match
+            # any of those to distinguish from auth/network/maintainer-
+            # edit failures.
+            if grep -qE "stale info|force-with-lease|rejected.*non-fast-forward|remote rejected|! \[rejected\]" "$push_stderr"; then
+              echo "::error::git push lease failed — branch moved during apply."
+              echo "result=lease-failed" >> "$GITHUB_OUTPUT"
+            else
+              echo "::error::git push failed — likely fork without maintainer-edit enabled."
+              echo "result=push-failed" >> "$GITHUB_OUTPUT"
+            fi
+            exit 0
+          fi
+
+      - name: React and reply on outcome
+        if: always() && steps.locate.outputs.found == 'true' && steps.apply.outcome != 'skipped'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          COMMENT_ID: ${{ github.event.comment.id }}
+          PR: ${{ github.event.issue.number }}
+          RESULT: ${{ steps.apply.outputs.result }}
+          RUN_ID: ${{ github.run_id }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          run_url="https://github.com/${GH_REPO}/actions/runs/${RUN_ID}"
+
+          case "${RESULT}" in
+            applied)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="+1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="✅ Applied autofix and pushed a commit. ([apply run](${run_url}))" \
+                >/dev/null
+              ;;
+            already-applied)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="+1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="✅ Autofix is already applied — no changes needed." \
+                >/dev/null
+              ;;
+            empty-patch)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="+1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="✅ No autofix to apply — formatter found nothing." \
+                >/dev/null
+              ;;
+            artifact-expired)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="confused" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⏳ The autofix artifact for this PR's head SHA has expired (1-day retention). Push a new commit to regenerate it, then comment \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            loop-prevented)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="confused" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="🔁 Refusing to re-apply autofix on top of an existing autofix commit. If formatter rules drifted and you genuinely need another pass, push a human-authored commit (or revert the existing autofix commit) before commenting \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            sensitive-paths)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="🛑 Refusing to apply: the autofix patch touches files under \`.github/\` (workflow / CODEOWNERS / dependabot config). Apply formatter changes to those files manually in a regular commit so they get human review. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            stale)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⚠️ The autofix patch is stale or conflicts with the current head — push a new commit to regenerate, then comment \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            apply-failed)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⚠️ Autofix applied cleanly in the dry run, but \`git apply\` / \`git commit\` failed when actually landing the patch. This usually means a race with concurrent edits or a corrupt patch. See logs: ${run_url}" \
+                >/dev/null
+              exit 1
+              ;;
+            push-failed)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⚠️ Couldn't push the autofix commit. If this is a fork PR, please tick **Allow edits by maintainers** in the PR sidebar, then comment \`/autofix\` again. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            lease-failed)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="-1" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="⚠️ The PR head moved while autofix was applying — a new commit landed in the window between resolve and push. Comment \`/autofix\` again to retry against the latest head. ([apply run](${run_url}))" \
+                >/dev/null
+              exit 1
+              ;;
+            *)
+              gh api -X POST "repos/${GH_REPO}/issues/comments/${COMMENT_ID}/reactions" \
+                -f content="confused" >/dev/null
+              gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+                -f body="❓ Autofix run finished in an unexpected state (\`${RESULT:-unknown}\`). See logs: ${run_url}" \
+                >/dev/null
+              exit 1
+              ;;
+          esac

.github/workflows/pr-autofix-publish.yml

@@ -0,0 +1,316 @@
+name: PR Autofix (publish)
+
+# TRUSTED HALF of the autofix pipeline.
+#
+# Triggered by `pr-autofix.yml` completing on a PR (including fork PRs).
+# Downloads the diff artifact produced by the untrusted job, verifies
+# its claimed PR identity against the workflow_run authority, then
+# posts (or edits) a single sticky summary comment plus a
+# `gitnexus/autofix` Check Run. This job NEVER checks out fork code —
+# it only consumes the diff (data) and calls the GitHub API. That
+# isolation is what makes it safe to run under `pull-requests: write`
+# on fork-triggered events.
+#
+# The sticky comment is the contributor signal: heading
+# "## :sparkles: PR Autofix" in the PR's top-level comments, with a
+# fenced `gitnexus-autofix` JSON block carrying machine-readable state
+# for AI agents. Contributors apply the patch by commenting `/autofix`
+# on the PR — handled by the separate `pr-autofix-apply.yml` workflow.
+
+on:
+  workflow_run:
+    workflows: ['PR Autofix']
+    types: [completed]
+
+concurrency:
+  # Key on PR identity, NOT workflow_run.id — workflow_run.id is per-run
+  # unique, which would defeat serialization and let two parallel
+  # publishes both POST a sticky summary comment. CONTRIBUTING.md
+  # § GitHub Actions — Concurrency Convention names this anti-pattern
+  # explicitly. For fork PRs, `pull_requests[]` is empty in the
+  # workflow_run payload, so we fall back to head-repo + head-branch.
+  group: ${{ github.workflow }}-${{ github.event.workflow_run.pull_requests[0].number || format('{0}/{1}', github.event.workflow_run.head_repository.full_name, github.event.workflow_run.head_branch) }}
+  cancel-in-progress: false
+
+permissions: {}
+
+jobs:
+  publish:
+    name: publish-autofix
+    if: >-
+      github.event.workflow_run.event == 'pull_request'
+      && github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      pull-requests: write
+      # Required by actions/download-artifact to fetch artifacts produced
+      # by a different workflow run.
+      actions: read
+      # Required to create the `gitnexus/autofix` Check Run that reports
+      # the outcome (clean / fixes-available) to the PR's Checks tab.
+      # Branch protection or agents can grep the conclusion + output
+      # title without parsing the sticky comment.
+      checks: write
+    steps:
+      # Pinned to v8.0.1. Verify SHA via:
+      #   gh api repos/actions/download-artifact/git/refs/tags/v8.0.1
+      - name: Download autofix artifact
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: autofix
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path: autofix-in
+
+      - name: Read and validate metadata
+        id: meta
+        shell: bash
+        run: |
+          set -euo pipefail
+          test -f autofix-in/metadata.json
+          jq . autofix-in/metadata.json
+
+          # The artifact comes from the untrusted half running fork code.
+          # Every field is allowlist-validated before it can flow into
+          # $GITHUB_OUTPUT. A newline in head_ref would otherwise let a
+          # malicious branch name inject a second `pr_number=N` line and
+          # redirect this job's reviewdog suggestions / sticky summary
+          # comment onto a victim PR under github-actions[bot] with
+          # pull-requests: write.
+          assert_field() {
+            local key="$1" pattern="$2" value
+            value=$(jq -r ".${key} // empty" autofix-in/metadata.json)
+            if [ -z "$value" ] || ! [[ "$value" =~ $pattern ]]; then
+              echo "::error::metadata.${key} failed allowlist (got: $(printf '%q' "$value"))"
+              exit 1
+            fi
+            printf '%s' "$value"
+          }
+
+          SCHEMA=$(assert_field    schema         '^gitnexus\.pr-autofix/v[0-9]+$')
+          PR_NUMBER=$(assert_field pr_number      '^[0-9]+$')
+          HEAD_SHA=$(assert_field  head_sha       '^[0-9a-f]{40}$')
+          HEAD_REF=$(assert_field  head_ref       '^[A-Za-z0-9._/-]+$')
+          HEAD_REPO=$(assert_field head_repo      '^[A-Za-z0-9._-]+/[A-Za-z0-9._-]+$')
+          BASE_REPO=$(assert_field base_repo      '^[A-Za-z0-9._-]+/[A-Za-z0-9._-]+$')
+          CHANGED=$(assert_field   changed_lines  '^[0-9]+$')
+
+          # Defence-in-depth: refuse to act if the artifact claims to
+          # belong to a different repo than the one that triggered us.
+          if [ "$BASE_REPO" != "${GITHUB_REPOSITORY}" ]; then
+            echo "::error::Artifact base_repo does not match \$GITHUB_REPOSITORY — refusing to publish."
+            exit 1
+          fi
+
+          {
+            echo "schema=${SCHEMA}"
+            echo "pr_number=${PR_NUMBER}"
+            echo "head_sha=${HEAD_SHA}"
+            echo "head_ref=${HEAD_REF}"
+            echo "head_repo=${HEAD_REPO}"
+            echo "base_repo=${BASE_REPO}"
+            echo "changed_lines=${CHANGED}"
+          } >> "$GITHUB_OUTPUT"
+
+      # Cross-verify the artifact's claimed identity against the
+      # GitHub-controlled workflow_run event. The previous step's
+      # allowlist only proves the fields are well-formed — not that
+      # they refer to the PR/SHA that actually triggered this run.
+      # A fork-controlled `npm run lint:fix` could plausibly mutate
+      # metadata.json to reference another PR or SHA, redirecting our
+      # write-scoped sticky/check-run onto an attacker-chosen target.
+      #
+      # Authority sources are all server-controlled GitHub event fields:
+      #   - workflow_run.head_sha
+      #   - workflow_run.head_repository.full_name
+      #   - workflow_run.pull_requests[].number  (within-repo PRs only;
+      #     empty array on fork PRs — fall back to commits/{sha}/pulls)
+      #
+      # Mismatch => fail loud BEFORE any sticky/check-run side effect.
+      - name: Verify metadata against workflow_run authority
+        id: verify
+        if: steps.meta.outputs.changed_lines != '0'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          META_PR_NUMBER: ${{ steps.meta.outputs.pr_number }}
+          META_HEAD_SHA: ${{ steps.meta.outputs.head_sha }}
+          META_HEAD_REPO: ${{ steps.meta.outputs.head_repo }}
+          WF_HEAD_SHA: ${{ github.event.workflow_run.head_sha }}
+          WF_HEAD_REPO: ${{ github.event.workflow_run.head_repository.full_name }}
+          WF_PR_NUMBERS: ${{ toJSON(github.event.workflow_run.pull_requests.*.number) }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          # 1) head_sha must match exactly. workflow_run.head_sha is the
+          # commit GitHub actually ran the producer against — definitive.
+          if [ "${META_HEAD_SHA}" != "${WF_HEAD_SHA}" ]; then
+            echo "::error::Artifact head_sha (${META_HEAD_SHA}) does not match workflow_run.head_sha (${WF_HEAD_SHA}) — refusing to publish."
+            exit 1
+          fi
+
+          # 2) head_repo must match exactly. Same authority anchor.
+          if [ "${META_HEAD_REPO}" != "${WF_HEAD_REPO}" ]; then
+            echo "::error::Artifact head_repo (${META_HEAD_REPO}) does not match workflow_run.head_repository (${WF_HEAD_REPO}) — refusing to publish."
+            exit 1
+          fi
+
+          # 3) pr_number must reference an open PR with this head SHA.
+          # Within-repo PRs: workflow_run.pull_requests[] is populated.
+          # Fork PRs: that array is empty by GitHub design — fall back
+          # to the REST commit-to-PRs lookup. Fail closed if the lookup
+          # finds no matching open PR (avoids attacker-forged PR ids).
+          allowed_numbers=$(jq -c '.' <<< "${WF_PR_NUMBERS}")
+          if [ "${allowed_numbers}" = "[]" ]; then
+            echo "workflow_run.pull_requests is empty (fork PR) — falling back to commits/{sha}/pulls."
+            allowed_numbers=$(gh api "repos/${GH_REPO}/commits/${WF_HEAD_SHA}/pulls" \
+              --jq '[.[] | select(.state == "open") | .number]' 2>/dev/null || echo "[]")
+            if [ "${allowed_numbers}" = "[]" ]; then
+              echo "::error::No open PR found for head ${WF_HEAD_SHA} via commits/{sha}/pulls — refusing to publish."
+              exit 1
+            fi
+          fi
+
+          if ! jq -e --argjson n "${META_PR_NUMBER}" 'index($n) != null' <<< "${allowed_numbers}" >/dev/null; then
+            echo "::error::Artifact pr_number (${META_PR_NUMBER}) is not in the authoritative PR list (${allowed_numbers}) — refusing to publish."
+            exit 1
+          fi
+
+          echo "Verified: metadata identity matches workflow_run authority (PR=${META_PR_NUMBER}, head_sha=${META_HEAD_SHA}, head_repo=${META_HEAD_REPO})."
+
+      - name: Upsert sticky summary comment
+        # Only post when ci-quality found something fixable (= the
+        # autofix patch is non-empty). When prettier/eslint are clean
+        # the patch is zero bytes and the sticky comment is pure noise,
+        # so we skip it.
+        if: >-
+          always()
+          && steps.meta.outputs.pr_number != ''
+          && steps.meta.outputs.changed_lines != '0'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          PR: ${{ steps.meta.outputs.pr_number }}
+          CHANGED: ${{ steps.meta.outputs.changed_lines }}
+          HEAD_SHA: ${{ steps.meta.outputs.head_sha }}
+          RUN_ID: ${{ github.run_id }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          # Stable heading + marker — agents grep for these exact strings.
+          marker="<!-- gitnexus:pr-autofix-summary -->"
+          heading="## :sparkles: PR Autofix"
+
+          # Single state. The /autofix slash command works for any diff
+          # size — there's no 3K cap and no no-overlap dead-end because
+          # the apply workflow uses `git apply` + push, not the GitHub
+          # review-comment API.
+          ui_state="fixes-available"
+          prose="Found fixable formatting / unused-import issues across **${CHANGED}** changed lines. **Comment \`/autofix\` on this PR to apply them**, or run \`npm run lint:fix && npm run format\` locally."
+
+          # Machine-readable JSON block — agents parse this instead of
+          # regexing English. Fenced code-block info string is
+          # `gitnexus-autofix` so agents can locate it without ambiguity.
+          # Schema bumped from v1 -> v2: adds `apply_command`. The v1
+          # field set is preserved as a superset, but the `state` enum
+          # is redefined (v1: suggestions-posted | skipped-too-large |
+          # diff-no-overlap; v2: fixes-available). v1 readers checking
+          # `schema == 'gitnexus.pr-autofix/v1'` see an unfamiliar version
+          # and fall back to prose, which is the intended migration path.
+          json=$(jq -n -c \
+            --arg state        "${ui_state}" \
+            --argjson pr_number "${PR}" \
+            --argjson changed_lines "${CHANGED}" \
+            --arg head_sha     "${HEAD_SHA}" \
+            --arg run_id       "${RUN_ID}" \
+            '{schema:"gitnexus.pr-autofix/v2", state:$state, pr_number:$pr_number, changed_lines:$changed_lines, head_sha:$head_sha, run_id:$run_id, apply_command:"/autofix"}')
+
+          # Multi-line quoted string instead of a column-0 heredoc — YAML's
+          # `run: |` block ends as soon as a content line dedents below the
+          # block's first-line indent, which would mis-parse the workflow.
+          body="${marker}
+          ${heading}
+
+          ${prose}
+
+          \`\`\`gitnexus-autofix
+          ${json}
+          \`\`\`"
+          # Strip the leading 10-space indent that the YAML block requires
+          # so the rendered comment body starts at column 0.
+          body="$(printf '%s\n' "$body" | sed 's/^          //')"
+
+          # Small retry wrapper for transient 5xx / rate-limit responses
+          # on the GitHub REST API. Three tries with linear backoff. We
+          # only retry GET (idempotent) and PATCH on a known comment id
+          # (idempotent). POST is NOT wrapped — retrying a comment-create
+          # would create duplicates if the first attempt actually landed.
+          gh_retry() {
+            local n=0 max=3
+            while true; do
+              if gh "$@"; then return 0; fi
+              n=$((n+1))
+              if [ "$n" -ge "$max" ]; then return 1; fi
+              sleep $((n * 2))
+            done
+          }
+
+          # Find existing bot comment by the marker and edit-in-place; else create.
+          # CRITICAL: filter by `.user.login == "github-actions[bot]"`. A regular
+          # user posting a comment containing the marker would otherwise be the
+          # `head -n1` match; PATCH on someone else's comment 403s, `set -e`
+          # aborts, and the bot is permanently DoS'd for that PR.
+          existing=$(gh_retry api "repos/${GH_REPO}/issues/${PR}/comments" \
+            --paginate --jq ".[] | select(.user.login == \"github-actions[bot]\" and (.body | contains(\"${marker}\"))) | .id" \
+            | head -n1 || true)
+
+          if [ -n "${existing}" ]; then
+            gh_retry api -X PATCH "repos/${GH_REPO}/issues/comments/${existing}" \
+              -f body="${body}" >/dev/null
+            echo "Updated comment ${existing}."
+          else
+            gh api -X POST "repos/${GH_REPO}/issues/${PR}/comments" \
+              -f body="${body}" >/dev/null
+            echo "Created summary comment."
+          fi
+
+      - name: Emit gitnexus/autofix Check Run
+        # Stable check name `gitnexus/autofix` so PR-watching agents can
+        # `gh pr checks <pr>` and read the conclusion + title without
+        # parsing the sticky comment. Two outcomes:
+        #   clean            → conclusion: success
+        #   fixes-available  → conclusion: neutral
+        # `neutral` does not block branch-protection required-checks but
+        # is visually distinct from a green pass.
+        if: always() && steps.meta.outputs.head_sha != ''
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          HEAD_SHA: ${{ steps.meta.outputs.head_sha }}
+          CHANGED: ${{ steps.meta.outputs.changed_lines }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          if [ "${CHANGED}" = "0" ]; then
+            conclusion="success"
+            title="Formatting clean"
+            summary="Prettier and ESLint --fix produced no changes."
+          else
+            conclusion="neutral"
+            title="Autofix available — comment /autofix to apply"
+            summary="Comment \`/autofix\` on this PR to apply formatter + unused-import fixes (works at any diff size). Or run \`npm run lint:fix && npm run format\` locally."
+          fi
+
+          gh api -X POST "repos/${GH_REPO}/check-runs" \
+            -f name="gitnexus/autofix" \
+            -f head_sha="${HEAD_SHA}" \
+            -f status="completed" \
+            -f conclusion="${conclusion}" \
+            -f "output[title]=${title}" \
+            -f "output[summary]=${summary}" \
+            >/dev/null
+          echo "Posted check-run gitnexus/autofix=${conclusion} (${title})"

.github/workflows/pr-autofix.yml

@@ -0,0 +1,146 @@
+name: PR Autofix
+
+# UNTRUSTED HALF of the autofix pipeline.
+#
+# Runs `npm run lint:fix` + `npm run format` against the PR head
+# (including fork heads) and uploads the resulting diff as an artifact.
+# This job has NO privileged token and CANNOT post to the PR. The trusted
+# `pr-autofix-publish.yml` workflow downloads the artifact via
+# `workflow_run` and posts a sticky summary comment + Check Run.
+# Contributors apply the patch by commenting `/autofix` on the PR —
+# handled by the separate `pr-autofix-apply.yml` ChatOps workflow.
+#
+# Why the split:
+#   ESLint loads plugins from fork-controlled `node_modules`, so running
+#   it in a job with `pull-requests: write` would let a malicious fork PR
+#   ship a poisoned eslint plugin and execute arbitrary code under that
+#   token. By keeping fork code execution in this job (token: read-only)
+#   and posting from a separate trusted job that never touches fork
+#   code, we get the autofix UX for fork PRs without the supply-chain
+#   hole. (See autofix.ci for the same pattern.)
+#
+# Removes unused imports via `eslint-plugin-unused-imports`, already in
+# devDependencies and wired into the `lint` config.
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+    # Skip lockfile / generated-file PRs entirely — `action-suggester`
+    # cannot post on diffs > ~3k lines (GitHub returns 406) and these
+    # paths produce massive diffs no human wants suggested back inline.
+    paths-ignore:
+      - '**/package-lock.json'
+      - '**/*.snap'
+      - '**/dist/**'
+      - '**/node_modules/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
+  # Don't cancel in-flight runs; the publish workflow may already be
+  # downloading the artifact and a cancelled untrusted run produces no
+  # signal at all (worse DX than waiting).
+  cancel-in-progress: false
+
+# This workflow runs untrusted fork code. Top-level deny-all and NO
+# job-level grants — the job can only read its own checkout.
+permissions: {}
+
+jobs:
+  autofix:
+    name: autofix
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          # PR head commit (not the synthetic merge ref) — we need the
+          # exact tree the contributor pushed so suggestions line up.
+          ref: ${{ github.event.pull_request.head.sha }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          persist-credentials: false
+
+      - uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
+        with:
+          node-version: 22
+          cache: npm
+          cache-dependency-path: package-lock.json
+
+      # `--ignore-scripts` blocks pre/postinstall lifecycle hooks. ESLint
+      # plugins still load from node_modules (that is the actual escape
+      # hatch on a typical fork), but this job has no token to abuse —
+      # which is the whole point of the split.
+      - run: npm ci --ignore-scripts
+
+      - name: ESLint --fix (removes unused imports)
+        run: npm run lint:fix
+        # Lint errors that --fix can't auto-resolve must not block the
+        # diff artifact — partial fixes are still useful as suggestions.
+        continue-on-error: true
+
+      - name: Prettier --write
+        run: npm run format
+        continue-on-error: true
+
+      - name: Capture diff and metadata
+        id: capture
+        # Pass GitHub-context values via env: rather than `${{ }}`
+        # interpolated directly into the bash body. `head.ref` and
+        # `head.repo.full_name` are fork-controlled strings; expanding
+        # them into shell source is the canonical template-injection
+        # vector zizmor flags. Even though this job has `permissions: {}`,
+        # routing through env: makes it impossible for a future scope
+        # grant to turn into RCE. Inside bash, reference as `$HEAD_REF`
+        # etc. — the values are then plain strings, not code.
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+          HEAD_REF: ${{ github.event.pull_request.head.ref }}
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
+          BASE_REPO: ${{ github.repository }}
+        shell: bash
+        run: |
+          set -euo pipefail
+          mkdir -p autofix-out
+
+          # Produce a unified diff of the working tree vs. the PR head.
+          # Empty diff => nothing to suggest; the publish job short-circuits.
+          git diff --no-color > autofix-out/autofix.patch
+
+          # NOTE: `changed_lines` is the line-count of the patch file,
+          # (hunk headers + context lines + added/removed). Surfaced in
+          # the sticky comment so contributors and AI agents have a
+          # quick size hint before invoking `/autofix`.
+          changed_lines=$(wc -l < autofix-out/autofix.patch | tr -d ' ')
+          echo "changed_lines=${changed_lines}" >> "$GITHUB_OUTPUT"
+
+          # Carry PR identity over to the trusted job. workflow_run
+          # context is base-repo-only, so the publish job needs these
+          # to call the GitHub PR API on the right resource.
+          # CONTRACT: keep this schema in sync with pr-autofix-publish.yml's
+          # `assert_field` validators and the agent-facing JSON block in
+          # the sticky comment. Bump `schema` when changing field names.
+          jq -n \
+            --arg     schema        'gitnexus.pr-autofix/v1' \
+            --argjson pr_number     "${PR_NUMBER}" \
+            --arg     head_sha      "${HEAD_SHA}" \
+            --arg     head_ref      "${HEAD_REF}" \
+            --arg     head_repo     "${HEAD_REPO}" \
+            --arg     base_repo     "${BASE_REPO}" \
+            --argjson changed_lines "${changed_lines}" \
+            '{schema:$schema, pr_number:$pr_number, head_sha:$head_sha, head_ref:$head_ref, head_repo:$head_repo, base_repo:$base_repo, changed_lines:$changed_lines}' \
+            > autofix-out/metadata.json
+
+          echo "--- metadata ---"
+          cat autofix-out/metadata.json
+          echo "--- diff (head) ---"
+          head -c 2000 autofix-out/autofix.patch || true
+
+      # Pinned to v7.0.1. Verify SHA via:
+      #   gh api repos/actions/upload-artifact/git/refs/tags/v7.0.1
+      - name: Upload autofix artifact
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: autofix
+          path: autofix-out/
+          retention-days: 1
+          if-no-files-found: error

.github/workflows/pr-labeler.yml

@@ -35,6 +35,9 @@ on:
   pull_request_target:
     types: [opened, edited, reopened]
 
+permissions:
+  contents: read
+
 # Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Include `github.event_name` so `pull_request` (validate-title) and
 # `pull_request_target` (autolabel) runs for the same PR do NOT share a slot

.github/workflows/publish.yml

@@ -6,6 +6,7 @@ on:
       - 'v*'
 
 # No workflow-level permissions — scoped per job below.
+permissions: {}
 
 # Concurrency convention: see CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
 # Tag refs are unique per release, so distinct tags run in parallel. Re-pushes of the
@@ -35,7 +36,7 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
         with:
-          node-version: 20
+          node-version: 22
           registry-url: https://registry.npmjs.org
           # Hermetic install for the published artifact — no cache carry-over
           # from non-tag contexts. setup-node v5+ caches by default when a

.github/workflows/release-candidate.yml

@@ -58,6 +58,7 @@ jobs:
     timeout-minutes: 5
     permissions:
       contents: read
+      pull-requests: read # read PR labels on the merge commit
     outputs:
       should_run: ${{ steps.decide.outputs.should_run }}
       head_sha: ${{ steps.decide.outputs.head_sha }}
@@ -74,6 +75,8 @@ jobs:
           FORCE: ${{ inputs.force }}
           BUMP_INPUT: ${{ inputs.bump }}
           EVENT_NAME: ${{ github.event_name }}
+          GH_TOKEN: ${{ github.token }}
+          REPO: ${{ github.repository }}
         run: |
           set -euo pipefail
           HEAD_SHA=$(git rev-parse HEAD)
@@ -96,6 +99,49 @@ jobs:
             exit 0
           fi
 
+          # ── Skip when the merge commit corresponds to a release ─────────
+          # Two complementary checks (belt-and-suspenders):
+          #   1. The HEAD commit subject matches `chore: release vX.Y.Z`
+          #      (the canonical release-PR title in this repo). Anchored
+          #      at both ends to require the bare title or the squash-merge
+          #      `(#NNNN)` suffix exactly — rejects noisy variants like
+          #      `chore: release v1.0.0 (something unrelated)`.
+          #   2. The squash-merged PR carries the `release` label.
+          # Either match suppresses the rc build — stable releases publish
+          # via publish.yml on the v-tag, so the rc cycle should pause for
+          # them rather than racing the npm publish.
+          HEAD_SUBJECT="$(git log -1 --pretty=%s HEAD)"
+          # Sanitise GitHub-Actions annotation prefixes before logging the
+          # raw subject — defence-in-depth so a hypothetical commit subject
+          # containing `::error::` or `::set-output::` cannot forge log
+          # annotations even though %s strips newlines.
+          HEAD_SUBJECT_SAFE="${HEAD_SUBJECT//::/__}"
+          RELEASE_SUBJECT_RE='^chore:[[:space:]]*release[[:space:]]+v[0-9]+\.[0-9]+\.[0-9]+([[:space:]]+\(#[0-9]+\))?$'
+          if [[ "$HEAD_SUBJECT" =~ $RELEASE_SUBJECT_RE ]]; then
+            echo "HEAD commit subject matches a release commit — skipping rc."
+            echo "  subject (sanitised): $HEAD_SUBJECT_SAFE"
+            echo "should_run=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Squash-merge commits include `(#NNNN)` at the end of the subject.
+          if [[ "$HEAD_SUBJECT" =~ \(#([0-9]+)\)[[:space:]]*$ ]]; then
+            PR_NUM="${BASH_REMATCH[1]}"
+            echo "Detected squash-merge of PR #$PR_NUM — checking labels."
+            if LABELS_JSON="$(gh pr view "$PR_NUM" --repo "$REPO" --json labels 2>/dev/null)"; then
+              if printf '%s' "$LABELS_JSON" | jq -e '.labels[] | select(.name == "release")' >/dev/null; then
+                echo "PR #$PR_NUM has the 'release' label — skipping rc."
+                echo "should_run=false" >> "$GITHUB_OUTPUT"
+                exit 0
+              fi
+              echo "PR #$PR_NUM has no 'release' label — proceeding."
+            else
+              # Lookup failure is not fatal — fall through to the dedup check
+              # so a transient GH API hiccup doesn't silently suppress rc builds.
+              echo "::warning::Could not read labels for PR #${PR_NUM} — falling through."
+            fi
+          fi
+
           # Dedup: is there already an rc/<HEAD_SHA> marker pointing at HEAD?
           MARKER="rc/${HEAD_SHA}"
           if git rev-parse "refs/tags/$MARKER" >/dev/null 2>&1; then
@@ -149,7 +195,7 @@ jobs:
 
       - uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
         with:
-          node-version: 20
+          node-version: 22
           registry-url: https://registry.npmjs.org
           # Hermetic install — release-candidate produces shipped artifacts.
           # setup-node v5+ caches by default when a packageManager field is
@@ -294,9 +340,11 @@ jobs:
             fi
           fi
 
-          echo "base=$BASE"             >> "$GITHUB_OUTPUT"
-          echo "rc_n=$NEXT_N"           >> "$GITHUB_OUTPUT"
-          echo "rc_version=$RC_VERSION" >> "$GITHUB_OUTPUT"
+          {
+            echo "base=$BASE"
+            echo "rc_n=$NEXT_N"
+            echo "rc_version=$RC_VERSION"
+          } >> "$GITHUB_OUTPUT"
 
       - name: Apply rc version in-CI
         shell: bash
@@ -354,9 +402,11 @@ jobs:
           # remote ref, the push fails and we stop before npm publish.
           git push --atomic origin "refs/tags/$VTAG" "refs/tags/$MARKER"
 
-          echo "vtag=$VTAG"     >> "$GITHUB_OUTPUT"
-          echo "marker=$MARKER" >> "$GITHUB_OUTPUT"
-          echo "release_sha=$RELEASE_SHA" >> "$GITHUB_OUTPUT"
+          {
+            echo "vtag=$VTAG"
+            echo "marker=$MARKER"
+            echo "release_sha=$RELEASE_SHA"
+          } >> "$GITHUB_OUTPUT"
 
       - name: Publish to npm (rc dist-tag)
         run: npm publish --provenance --access public --tag rc

.github/workflows/trivy.yml

@@ -1,19 +1,28 @@
 name: Trivy Image Scan
 
 # Builds Dockerfile.cli and Dockerfile.web, then scans the resulting images
-# for OS-package and language-package CVEs at HIGH/CRITICAL severity.
+# for OS-package and language-package CVEs at MEDIUM+ severity.
 # Findings upload to the Security tab; record-only (does not block merges).
 #
-# NOT triggered on PRs — image builds are slow and base-image CVE churn
-# shouldn't gate feature delivery.
+# Trigger on Dockerfile changes in PRs so base-image/npm-layer remediation can
+# be verified before merge without running image scans on every PR.
 
 on:
+  pull_request:
+    paths:
+      - 'Dockerfile.cli'
+      - 'Dockerfile.web'
+      - 'gitnexus/Dockerfile.test'
+      - '.github/workflows/trivy.yml'
   push:
     branches: [main]
   schedule:
     - cron: '0 8 * * 1'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: false
@@ -61,7 +70,7 @@ jobs:
           image-ref: scan-target:${{ matrix.image.name }}
           format: sarif
           output: trivy-${{ matrix.image.name }}.sarif
-          severity: HIGH,CRITICAL
+          severity: MEDIUM,HIGH,CRITICAL
           # Hides CVEs with no available fix in the base image.
           ignore-unfixed: true
           exit-code: '0'

.github/workflows/workflow-lint.yml

@@ -1,10 +1,13 @@
-name: Workflow Lint (zizmor)
+name: Workflow Lint
 
-# Lints .github/workflows/** for known GitHub Actions security misconfigurations:
-# unpinned Actions, dangerous ${{ ... }} interpolation in run: blocks,
-# missing per-job permissions:, etc.
+# Lints .github/workflows/** for both:
+#   - actionlint: YAML syntax, expression typing, shellcheck inside `run:`
+#     blocks, unknown contexts, deprecated runner labels.
+#   - zizmor: security misconfigurations — unpinned actions, dangerous
+#     `${{ }}` interpolation, missing per-job permissions, etc.
 #
-# Scoped to PRs that touch .github/** only — keeps off the typical PR critical path.
+# Scoped to PRs that touch .github/** only — keeps off the typical PR
+# critical path.
 
 on:
   pull_request:
@@ -12,11 +15,35 @@ on:
     paths:
       - '.github/**'
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
+  actionlint:
+    name: actionlint
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
+      # Pinned to v2.1.2. Verify SHA via:
+      #   gh api repos/raven-actions/actionlint/git/refs/tags/v2.1.2
+      # The action wraps the upstream `rhysd/actionlint` binary and emits
+      # GitHub-annotation-formatted findings on PRs.
+      - name: Run actionlint
+        uses: raven-actions/actionlint@205b530c5d9fa8f44ae9ed59f341a0db994aa6f8 # v2.1.2
+        with:
+          fail-on-error: true
+
   zizmor:
     runs-on: ubuntu-latest
     timeout-minutes: 10

.github/zizmor.yml

@@ -14,6 +14,15 @@ rules:
       # no checkout of fork code occurs. Header comment in the file documents.
       - ci-report.yml
 
+      # workflow_run is the trusted half of the autofix pipeline. The
+      # untrusted half (pr-autofix.yml) runs fork code with permissions:{}
+      # and produces only a diff artifact (data, not executable code). The
+      # publish job consumes the artifact, allowlist-validates every field
+      # of metadata.json before exporting to $GITHUB_OUTPUT, never checks
+      # out fork code, and never executes anything fork-controlled. Header
+      # comment in the file documents the split.
+      - pr-autofix-publish.yml
+
       # pull_request_target needed by claude-code-action to access secrets
       # and post review comments on fork PRs. Mitigated by: PR checkouts pin
       # the fork's HEAD SHA (not the branch ref) to prevent TOCTOU races,

AGENTS.md

@@ -149,11 +149,16 @@ Indexed as **GitNexus** (4325 symbols, 10556 relationships, 300 execution flows)
 ## Keeping the Index Fresh
 
 ```bash
-npx gitnexus analyze                 # basic refresh; preserves any existing embeddings
+npx gitnexus analyze                 # incremental by default; preserves embeddings
+npx gitnexus analyze --force         # full rebuild from scratch (opt out of incremental)
 npx gitnexus analyze --embeddings    # also generate embeddings for new/changed nodes
 npx gitnexus analyze --drop-embeddings  # explicit opt-in to wipe existing embeddings
 ```
 
+`analyze` runs **incrementally by default**. The pipeline still parses every file every run (cross-file resolution requires it), but tree-sitter parsing is **served from a content-addressed cache** at `.gitnexus/parse-cache.json` for chunks whose file contents haven't changed since the last run. Only changed-file rows (and their importers) are rewritten in LadybugDB; unchanged-file rows are preserved. Output is byte-equivalent to a full rebuild. Pass `--force` to wipe and re-index from scratch (e.g., to recover from a corrupt index, or after upgrading GitNexus).
+
+The parse cache key is **content-addressed and version-tagged**: it survives `--force` runs, and is automatically invalidated by a `gitnexus` package upgrade (so a new tree-sitter grammar doesn't silently replay stale parse output). Safe to delete `.gitnexus/parse-cache.json` at any time — it'll be rebuilt on the next analyze.
+
 Check `.gitnexus/meta.json` `stats.embeddings` (0 = none). A plain `analyze` no longer drops existing vectors — pass `--drop-embeddings` to wipe.
 
 > Claude Code: PostToolUse hook detects a stale index after `git commit` and `git merge` and prompts the agent to run `analyze`. The hook does not invoke `analyze` itself.

CONTRIBUTING.md

@@ -30,17 +30,17 @@ Format: `<type>[(scope)][!]: <subject>`
 
 Allowed types and the release-notes section each one lands in (defined in `.github/release.yml`):
 
-| Type | Label applied | Release-notes section |
-|------|---------------|-----------------------|
-| `feat` | `enhancement` | 🚀 Features |
-| `fix` | `bug` | 🐛 Bug Fixes |
-| `perf` | `performance` | 🏎️ Performance |
-| `refactor` | `refactor` | 🔄 Refactoring |
-| `test` | `test` | 🧪 Tests |
-| `ci` | `ci` | 👷 CI/CD |
-| `build` / `deps` | `dependencies` | 📦 Dependencies |
-| `docs` | `documentation` | (grouped under Other Changes unless a Docs section is added) |
-| `chore` / `revert` | `chore` | (excluded from release notes) |
+| Type               | Label applied   | Release-notes section                                        |
+| ------------------ | --------------- | ------------------------------------------------------------ |
+| `feat`             | `enhancement`   | 🚀 Features                                                  |
+| `fix`              | `bug`           | 🐛 Bug Fixes                                                 |
+| `perf`             | `performance`   | 🏎️ Performance                                               |
+| `refactor`         | `refactor`      | 🔄 Refactoring                                               |
+| `test`             | `test`          | 🧪 Tests                                                     |
+| `ci`               | `ci`            | 👷 CI/CD                                                     |
+| `build` / `deps`   | `dependencies`  | 📦 Dependencies                                              |
+| `docs`             | `documentation` | (grouped under Other Changes unless a Docs section is added) |
+| `chore` / `revert` | `chore`         | (excluded from release notes)                                |
 
 Append `!` to the type (e.g. `feat(api)!: drop /v1 endpoint`) or include `BREAKING CHANGE:` in the PR body to flag a breaking change — the labeler then adds the `breaking` label and the 💥 Breaking Changes section is rendered first.
 
@@ -81,17 +81,17 @@ Every workflow under `.github/workflows/` MUST declare a top-level `concurrency:
   - **Merge queue (`merge_group`)**: when this event is added, use `${{ github.workflow }}-${{ github.event.merge_group.head_ref }}` with `cancel-in-progress: false` (every queue entry is a distinct ref; never cancel).
 - **`cancel-in-progress` policy:**
 
-  | Event | `cancel-in-progress` | Why |
-  |-------|----------------------|-----|
-  | `pull_request` CI run | `true` | New push supersedes old run |
-  | `push` to `main` | `false` | Every main commit gets validated |
-  | Tag push (`v*` publish) | `false` | Never cancel mid-publish |
-  | `push` to `main` for release-candidate | `false` | Never cancel mid-RC publish |
-  | `workflow_dispatch` (release/publish) | `false` | Manual runs are intentional |
-  | `workflow_run` (sticky-comment reports) | `false` | Serialize, don't race |
-  | Per-PR bot workflows (`@claude`, review) | `false` | Serialize comments per PR |
-  | PR-meta re-checks (pr-description-check) | `true` | Cheap, latest wins |
-  | Single-slot utilities (triage sweep) | `true` | Latest dispatch supersedes |
+  | Event                                    | `cancel-in-progress` | Why                              |
+  | ---------------------------------------- | -------------------- | -------------------------------- |
+  | `pull_request` CI run                    | `true`               | New push supersedes old run      |
+  | `push` to `main`                         | `false`              | Every main commit gets validated |
+  | Tag push (`v*` publish)                  | `false`              | Never cancel mid-publish         |
+  | `push` to `main` for release-candidate   | `false`              | Never cancel mid-RC publish      |
+  | `workflow_dispatch` (release/publish)    | `false`              | Manual runs are intentional      |
+  | `workflow_run` (sticky-comment reports)  | `false`              | Serialize, don't race            |
+  | Per-PR bot workflows (`@claude`, review) | `false`              | Serialize comments per PR        |
+  | PR-meta re-checks (pr-description-check) | `true`               | Cheap, latest wins               |
+  | Single-slot utilities (triage sweep)     | `true`               | Latest dispatch supersedes       |
 
 - For workflows that serve multiple events at once (e.g. `ci.yml` handles `pull_request`, `push`, and `workflow_call`), make `cancel-in-progress` event-aware:
 
@@ -103,6 +103,41 @@ Every workflow under `.github/workflows/` MUST declare a top-level `concurrency:
 
 - When adding a new workflow, copy the concurrency block from an existing workflow of the same event shape.
 
+## CI automation contracts
+
+Two workflows produce machine-readable signals on every PR. Coding agents and humans alike can rely on the names and shapes below — change them with intent.
+
+### `gitnexus/autofix`
+
+`pr-autofix.yml` (untrusted) + `pr-autofix-publish.yml` (trusted) run `prettier --write` and `eslint --fix` against the PR head and surface a single ChatOps button on the PR. Three signals are emitted:
+
+| Surface           | Where                                                                                                                                                                                                                                                                                                   | Notes                                                                  |
+| ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- |
+| Sticky PR comment | Top-level comment with the HTML marker `<!-- gitnexus:pr-autofix-summary -->` and heading `## :sparkles: PR Autofix`. Only posted when there is something to fix; clean PRs stay silent.                                                                                                                | Edit-in-place via marker; one comment per PR.                          |
+| Fenced JSON block | Inside the sticky, fenced as `gitnexus-autofix`. Schema `gitnexus.pr-autofix/v2` with fields `state` (`fixes-available`), `pr_number`, `head_sha`, `changed_lines`, `run_id`, and `apply_command` (literal `/autofix`). | Parseable signal — preferred over regexing prose. v1 fields preserved as a superset. |
+| Check Run         | Stable name `gitnexus/autofix` on the PR head SHA. Conclusion: `success` (clean) or `neutral` (`fixes-available`). The neutral title is `Autofix available — comment /autofix to apply`.                                                                                                                | Surfaced under PR Checks; readable via `gh pr checks <pr>`.            |
+
+To detect outcome from an agent: `gh pr checks <pr> --json name,conclusion,output | jq '.[] | select(.name == "gitnexus/autofix")'`.
+
+Forks are supported. The untrusted half runs fork code with `permissions: {}` and ships the diff as an artifact; the trusted publish job consumes only the diff (data, not code) and posts the comment + check run.
+
+#### Applying autofix
+
+Comment `/autofix` on the PR (whole-line, no arguments). The `pr-autofix-apply.yml` workflow:
+
+1. Validates the comment body matches `^/autofix\s*$` exactly. Quoted or inline mentions are silently ignored.
+2. Validates the commenter has `admin`, `write`, or `maintain` permission on the repo, OR is the PR author. Other commenters get a 👎 reaction and a refusal reply.
+3. Locates the most recent successful `pr-autofix.yml` run for the PR's current head SHA, downloads its `autofix` artifact, applies the patch, and pushes a `chore(autofix): ...` commit back to the PR head branch.
+4. Reacts ✅ on success, 👎 on stale-patch / push-failure, and posts a short reply with the apply-run URL in either case.
+
+The apply workflow runs from the default branch's copy of the file regardless of where the comment originates — that's the trust anchor. There is no diff-size cap (the apply workflow uses `git apply` + push, not the GitHub review-comment API).
+
+For fork PRs, the push succeeds only when the contributor has **Allow edits by maintainers** enabled on the PR (the default). When they have disabled it, the workflow fails loud with a 👎 reaction and an explanation comment.
+
+Re-invoking `/autofix` after a successful apply is a safe no-op — the workflow detects the already-applied state via `git apply --check --reverse` and reacts ✅ without pushing.
+
+**Sensitive paths.** The apply workflow refuses any patch that touches `.github/` (workflow files, CODEOWNERS, dependabot config). A malicious PR could ship a custom prettier or ESLint config that reformats workflow YAML; if accepted, those edits would be pushed under `contents: write` without human review. Apply formatter changes to files under `.github/` manually in a normal commit so they get the same review every other workflow change gets.
+
 ## 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.
@@ -164,8 +199,7 @@ Two publish workflows ship `gitnexus` to npm:
     the Docker build.
   - Manually run `docker build` + `docker push` locally and sign with Cosign
     against the same digest.
-  - Delete `rc/<HEAD_SHA>` and `v<RC>` tags, then redispatch with `force:
-    true` to re-run the full RC pipeline (cuts a new RC number).
+  - Delete `rc/<HEAD_SHA>` and `v<RC>` tags, then redispatch with `force: true` to re-run the full RC pipeline (cuts a new RC number).
 
 The rc workflow never moves `latest`. To verify after a change, inspect dist-tags:
 

Dockerfile.cli

@@ -1,24 +1,32 @@
 ARG BUILDPLATFORM
 ARG TARGETPLATFORM
+# Pinned npm version used to replace the bundled npm in the upstream Node
+# image. Bumping requires a coordinated update in Dockerfile.web and
+# gitnexus/Dockerfile.test so all images bootstrap the same npm.
+ARG NPM_VERSION=11.14.1
 
-# ── Builder ────────────────────────────────────────────────────────────
+# -- Builder -----------------------------------------------------------
 # Native modules (tree-sitter-*, onnxruntime-node, node-gyp builds for
 # tree-sitter-proto / tree-sitter-swift) require python3 + a C/C++ toolchain.
-FROM node:22-trixie-slim AS builder
+# node:22-bookworm-slim
+FROM node:22-bookworm-slim@sha256:9f6d5975c7dca860947d3915877f85607946403fc55349f39b4bc3688448bb6e AS builder
+ARG NPM_VERSION
 
 WORKDIR /app
 
+RUN npx --yes npm@${NPM_VERSION} install -g npm@${NPM_VERSION}
+
 # Toolchain for node-gyp / native builds.
 RUN apt-get update && apt-get install -y --no-install-recommends python3 make g++ git && rm -rf /var/lib/apt/lists/*
 
-# Build gitnexus-shared first — gitnexus depends on it as a workspace.
+# Build gitnexus-shared first - gitnexus depends on it as a workspace.
 COPY gitnexus-shared/package.json gitnexus-shared/package-lock.json ./gitnexus-shared/
 RUN npm ci --prefix gitnexus-shared
 COPY gitnexus-shared ./gitnexus-shared
 RUN rm -f gitnexus-shared/tsconfig.tsbuildinfo
 RUN npm run build --prefix gitnexus-shared
 
-# Copy the full gitnexus package before installing — `npm ci` triggers
+# Copy the full gitnexus package before installing - `npm ci` triggers
 # `postinstall` (patches tree-sitter-swift, builds the vendored
 # tree-sitter-proto) and `prepare` (compiles TypeScript via scripts/build.js),
 # both of which need the source tree.
@@ -28,11 +36,15 @@ RUN npm ci --prefix gitnexus
 # Drop dev dependencies for a smaller runtime layer.
 RUN npm prune --omit=dev --prefix gitnexus
 
-# ── Runtime ────────────────────────────────────────────────────────────
-FROM node:22-trixie-slim AS runtime
+# -- Runtime -----------------------------------------------------------
+# node:22-bookworm-slim
+FROM node:22-bookworm-slim@sha256:9f6d5975c7dca860947d3915877f85607946403fc55349f39b4bc3688448bb6e AS runtime
 
 # curl for the healthcheck; git so `gitnexus` can clone repos at runtime.
-RUN apt-get update && apt-get install -y --no-install-recommends curl git && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends curl git && rm -rf /var/lib/apt/lists/* \
+    && rm -rf /usr/local/lib/node_modules/npm \
+    && rm -rf /usr/local/lib/node_modules/corepack \
+    && rm -f /usr/local/bin/npm /usr/local/bin/npx /usr/local/bin/corepack
 
 WORKDIR /app
 
@@ -43,11 +55,12 @@ RUN mkdir -p /data/gitnexus && chown -R node:node /data
 COPY --from=builder --chown=node:node /app/gitnexus/dist ./gitnexus/dist
 COPY --from=builder --chown=node:node /app/gitnexus/node_modules ./gitnexus/node_modules
 COPY --from=builder --chown=node:node /app/gitnexus/package.json ./gitnexus/package.json
+COPY --from=builder --chown=node:node /app/gitnexus/scripts/install-duckdb-extension.mjs ./gitnexus/scripts/install-duckdb-extension.mjs
 COPY --from=builder --chown=node:node /app/gitnexus/vendor ./gitnexus/vendor
 
 USER node
 
-# The web UI defaults to http://localhost:4747 — keep that contract.
+# The web UI defaults to http://localhost:4747 - keep that contract.
 ENV GITNEXUS_HOME=/data/gitnexus \
     NODE_ENV=production \
     PORT=4747

Dockerfile.web

@@ -1,10 +1,17 @@
 ARG BUILDPLATFORM
 ARG TARGETPLATFORM
+# Pinned npm version — keep in sync with Dockerfile.cli and
+# gitnexus/Dockerfile.test.
+ARG NPM_VERSION=11.14.1
 
-FROM --platform=$BUILDPLATFORM node:22-alpine AS builder
+# node:22-bookworm-slim
+FROM --platform=$BUILDPLATFORM node:22-bookworm-slim@sha256:9f6d5975c7dca860947d3915877f85607946403fc55349f39b4bc3688448bb6e AS builder
+ARG NPM_VERSION
 
 WORKDIR /app
 
+RUN npx --yes npm@${NPM_VERSION} install -g npm@${NPM_VERSION}
+
 COPY gitnexus-shared/package.json gitnexus-shared/package-lock.json ./gitnexus-shared/
 RUN npm ci --prefix gitnexus-shared
 
@@ -19,9 +26,13 @@ RUN npm ci --prefix gitnexus-web
 COPY gitnexus-web ./gitnexus-web
 RUN npm run build --prefix gitnexus-web
 
-FROM node:22-alpine AS runtime
+# node:22-bookworm-slim
+FROM node:22-bookworm-slim@sha256:9f6d5975c7dca860947d3915877f85607946403fc55349f39b4bc3688448bb6e AS runtime
 
-RUN apk add --no-cache curl
+RUN apt-get update && apt-get install -y --no-install-recommends curl && rm -rf /var/lib/apt/lists/* \
+    && rm -rf /usr/local/lib/node_modules/npm \
+    && rm -rf /usr/local/lib/node_modules/corepack \
+    && rm -f /usr/local/bin/npm /usr/local/bin/npx /usr/local/bin/corepack
 
 WORKDIR /app
 

GUARDRAILS.md

@@ -30,9 +30,15 @@ Format: **Trigger → Instruction → Reason**. Append new Signs when the same m
 ### Stale graph after edits
 
 - **Trigger:** MCP warns index is behind `HEAD`, or search doesn't match latest commit.
-- **Do:** `npx gitnexus analyze` (plus `--embeddings` if used).
+- **Do:** `npx gitnexus analyze` (plus `--embeddings` if used). Runs incrementally by default — the pipeline parses every file every run (cross-file resolution requires it), but tree-sitter dispatch is skipped for unchanged file chunks via the content-addressed cache, and only changed-file rows (plus their importers, transitively) are rewritten in LadybugDB.
 - **Why:** Tools query LadybugDB from last analyze; git changes are invisible until re-indexed.
 
+### Index seems corrupt or "incremental" is misbehaving
+
+- **Trigger:** `analyze` produces unexpected results, or `meta.json.incrementalInProgress` is set, or the index is in a half-state after a crash.
+- **Do:** `npx gitnexus analyze --force` to rebuild from scratch. The dirty-flag check forces this automatically when a previous incremental run didn't complete cleanly, but `--force` is the manual escape hatch. Safe to delete `.gitnexus/parse-cache.json` at any time — content-addressed, will be regenerated.
+- **Why:** Incremental writeback is selective DB row replacement; if the on-disk state is inconsistent for any reason, a full rebuild is the cheapest path back to a known-good index.
+
 ### Embeddings vanished after analyze
 
 - **Trigger:** Semantic search quality drops; `stats.embeddings` in `meta.json` is 0 after refresh.

README.md

@@ -120,7 +120,7 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 | Editor                | MCP | Skills | Hooks (auto-augment) | Support        |
 | --------------------- | --- | ------ | -------------------- | -------------- |
 | **Claude Code** | Yes | Yes    | Yes (PreToolUse + PostToolUse) | **Full** |
-| **Cursor**      | Yes | Yes    | —                   | MCP + Skills   |
+| **Cursor**      | Yes | Yes    | Yes (postToolUse, [manual install](gitnexus-cursor-integration/README.md#hook-install)) | **Full** |
 | **Codex**       | Yes | Yes    | —                   | MCP + Skills   |
 | **Windsurf**    | Yes | —     | —                   | MCP            |
 | **OpenCode**    | Yes | Yes    | —                   | MCP + Skills   |
@@ -214,6 +214,7 @@ 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
+gitnexus publish                 # Notify the understand-quickly registry (opt-in, see below)
 
 # Repository groups (multi-repo / monorepo service tracking)
 gitnexus group create <name>                                   # Create a repository group
@@ -228,6 +229,12 @@ gitnexus group status <name>     # Check staleness of repos in a group
 
 If `analyze` reports a worker parse timeout on a large or unusual repository, it keeps running and falls back safely. To give slow worker jobs more time, use `gitnexus analyze --worker-timeout 60` or set `GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000`. For very large files, `GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES` controls the worker job byte budget.
 
+#### Publishing to understand-quickly (opt-in)
+
+[`looptech-ai/understand-quickly`](https://github.com/looptech-ai/understand-quickly) is a public registry of code-knowledge graphs that lists `gitnexus@1` as a first-class format. After registering your repo once (`npx @understand-quickly/cli add` or the [wizard](https://looptech-ai.github.io/understand-quickly/add.html)), `gitnexus publish` fires a single `repository_dispatch` event so the registry resyncs your entry on demand instead of waiting for the nightly job.
+
+It is opt-in and a no-op without `UNDERSTAND_QUICKLY_TOKEN` — a fine-grained GitHub PAT with `Repository dispatches: write` on the registry repo. Nothing else happens; no graph file is uploaded. See the [protocol spec](https://github.com/looptech-ai/understand-quickly/blob/main/docs/integrations/protocol.md) for the full contract.
+
 ### What Your AI Agent Gets
 
 **16 tools** exposed via MCP (11 per-repo + 5 group):

eslint-rules/require-safe-parse.mjs

@@ -0,0 +1,95 @@
+/**
+ * Custom ESLint rule: require `parseSourceSafe(parser, content, ...)` instead
+ * of direct `<parser>.parse(<content>, ...)` calls.
+ *
+ * Background: tree-sitter's Node.js native binding crashes with SIGSEGV on
+ * Windows when handed a JS string longer than 32 767 chars. The crash happens
+ * inside the binding's V8 string-to-buffer conversion and cannot be intercepted
+ * by JavaScript `try/catch`. `parseSourceSafe` (in
+ * `gitnexus/src/core/tree-sitter/safe-parse.ts`) routes large inputs through
+ * the chunked-callback overload of `parser.parse(input, ...)` which bypasses
+ * the broken conversion path. PR #1433 fixed every direct call site at the
+ * time; this rule prevents new direct calls from creeping in.
+ *
+ * The rule is auto-fixable for the call-site rewrite. It does NOT auto-add the
+ * import (computing the correct relative path per file is brittle); after the
+ * call rewrite runs, the consumer file's `tsc` will complain about an
+ * undefined identifier and the developer adds the import. This is the same
+ * tradeoff `unused-imports/no-unused-imports` makes in the opposite direction.
+ *
+ * False-positive suppression:
+ * - Skips calls whose receiver is a known non-tree-sitter library (`JSON`,
+ *   `URL`, `marked`, `Number`).
+ * - Skips calls whose first argument is a string-literal (grammar-load smoke
+ *   tests like `_testParser.parse('service X { rpc Y (R) returns (R); }')`).
+ * - Skips test files (`.test.ts`/`.test.tsx`/`.spec.ts`).
+ * - Skips the `safe-parse.ts` helper itself.
+ */
+
+const SKIPPED_RECEIVERS = new Set(['JSON', 'URL', 'marked', 'Number', 'Math']);
+
+export default {
+  meta: {
+    type: 'problem',
+    docs: {
+      description:
+        'Require parseSourceSafe instead of direct tree-sitter `<parser>.parse(content, ...)` calls (Windows SIGSEGV protection)',
+      recommended: true,
+    },
+    fixable: 'code',
+    schema: [],
+    messages: {
+      useSafeParse:
+        'Direct `{{receiver}}.parse(...)` can SIGSEGV on Windows for inputs > 32 767 chars (uncatchable from JS). Use `parseSourceSafe({{receiver}}, ...)` from `core/tree-sitter/safe-parse.js`. Auto-fix rewrites the call; add the missing import yourself.',
+    },
+  },
+  create(context) {
+    const filename = context.filename ?? context.getFilename();
+    // Don't lint the helper itself or test files.
+    if (filename.includes('safe-parse')) return {};
+    if (/[.](?:test|spec)\.tsx?$/.test(filename)) return {};
+
+    const sourceCode = context.sourceCode ?? context.getSourceCode();
+
+    return {
+      CallExpression(node) {
+        const callee = node.callee;
+        if (callee.type !== 'MemberExpression') return;
+        if (callee.computed) return;
+        if (callee.property.type !== 'Identifier') return;
+        if (callee.property.name !== 'parse') return;
+
+        // Skip known non-tree-sitter receivers.
+        if (callee.object.type === 'Identifier' && SKIPPED_RECEIVERS.has(callee.object.name)) {
+          return;
+        }
+
+        // Smoke tests pass a string literal directly; those are trivially safe.
+        const firstArg = node.arguments[0];
+        if (!firstArg) return;
+        if (firstArg.type === 'Literal' && typeof firstArg.value === 'string') return;
+        if (firstArg.type === 'TemplateLiteral' && firstArg.expressions.length === 0) return;
+
+        const receiverText = sourceCode.getText(callee.object);
+        // Receiver-text-shape skip: anything matching well-known JS APIs that
+        // happen to have a `.parse(<expr>)` shape but aren't tree-sitter.
+        if (
+          /^(JSON|URL|marked|Number|Math|Date|globalThis\.JSON)\b/.test(receiverText) ||
+          /\bjson\.parse\b/i.test(receiverText)
+        ) {
+          return;
+        }
+
+        context.report({
+          node,
+          messageId: 'useSafeParse',
+          data: { receiver: receiverText },
+          fix(fixer) {
+            const argsText = node.arguments.map((arg) => sourceCode.getText(arg)).join(', ');
+            return fixer.replaceText(node, `parseSourceSafe(${receiverText}, ${argsText})`);
+          },
+        });
+      },
+    };
+  },
+};

eslint.config.mjs

@@ -3,6 +3,15 @@ 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';
+import requireSafeParse from './eslint-rules/require-safe-parse.mjs';
+
+// Local plugin hosting custom rules that enforce GitNexus-specific invariants
+// (currently: the Windows-SIGSEGV-safe parser entrypoint).
+const gitnexusLocalPlugin = {
+  rules: {
+    'require-safe-parse': requireSafeParse,
+  },
+};
 
 // Selectors that protect MCP-reachable code from corrupting the JSON-RPC
 // stdio frame stream. The MCP-reachable block below uses these directly;
@@ -135,6 +144,23 @@ export default [
     },
   },
 
+  // Windows SIGSEGV protection: every tree-sitter parse in `core/` must route
+  // through parseSourceSafe. Direct `<parser>.parse(content, ...)` crashes on
+  // Windows for inputs > 32 767 chars (V8 string-conversion bug, uncatchable
+  // from JS). The rule auto-fixes the call site; the developer adds the
+  // missing import after the fix runs. Out of scope: tests (skipped by the
+  // rule), the helper itself (`safe-parse.ts`), and the `grpc-patterns/proto.ts`
+  // grammar-load smoke test (filtered by string-literal-arg skip in the rule).
+  {
+    files: ['gitnexus/src/core/**/*.ts'],
+    plugins: {
+      gitnexus: gitnexusLocalPlugin,
+    },
+    rules: {
+      'gitnexus/require-safe-parse': 'error',
+    },
+  },
+
   // React-specific rules for gitnexus-web
   {
     files: ['gitnexus-web/src/**/*.{ts,tsx}'],

eval/uv.lock

@@ -2278,11 +2278,11 @@ wheels = [
 
 [[package]]
 name = "urllib3"
-version = "2.6.3"
+version = "2.7.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/c7/24/5f1b3bdffd70275f6661c76461e25f024d5a38a46f04aaca912426a2b1d3/urllib3-2.6.3.tar.gz", hash = "sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed", size = 435556, upload-time = "2026-01-07T16:24:43.925Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/53/0c/06f8b233b8fd13b9e5ee11424ef85419ba0d8ba0b3138bf360be2ff56953/urllib3-2.7.0.tar.gz", hash = "sha256:231e0ec3b63ceb14667c67be60f2f2c40a518cb38b03af60abc813da26505f4c", size = 433602, upload-time = "2026-05-07T16:13:18.596Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/39/08/aaaad47bc4e9dc8c725e68f9d04865dbcb2052843ff09c97b08904852d84/urllib3-2.6.3-py3-none-any.whl", hash = "sha256:bf272323e553dfb2e87d9bfd225ca7b0f467b919d7bbd355436d3fd37cb0acd4", size = 131584, upload-time = "2026-01-07T16:24:42.685Z" },
+    { url = "https://files.pythonhosted.org/packages/7f/3e/5db95bcf282c52709639744ca2a8b149baccf648e39c8cc87553df9eae0c/urllib3-2.7.0-py3-none-any.whl", hash = "sha256:9fb4c81ebbb1ce9531cce37674bbc6f1360472bc18ca9a553ede278ef7276897", size = 131087, upload-time = "2026-05-07T16:13:17.151Z" },
 ]
 
 [[package]]

gitnexus-claude-plugin/hooks/gitnexus-hook.js

@@ -14,6 +14,7 @@
 const fs = require('fs');
 const path = require('path');
 const { spawnSync } = require('child_process');
+const { acquireHookSlot } = require('./hook-lock.js');
 
 /**
  * Read JSON input from stdin synchronously.
@@ -217,7 +218,8 @@ function sendHookResponse(hookEventName, message) {
 function handlePreToolUse(input) {
   const cwd = input.cwd || process.cwd();
   if (!path.isAbsolute(cwd)) return;
-  if (!findGitNexusDir(cwd)) return;
+  const gitNexusDir = findGitNexusDir(cwd);
+  if (!gitNexusDir) return;
 
   const toolName = input.tool_name || '';
   const toolInput = input.tool_input || {};
@@ -227,6 +229,9 @@ function handlePreToolUse(input) {
   const pattern = extractPattern(toolName, toolInput);
   if (!pattern || pattern.length < 3) return;
 
+  const release = acquireHookSlot(gitNexusDir);
+  if (!release) return;
+
   let result = '';
   try {
     const child = runGitNexusCli(['augment', '--', pattern], cwd, 7000);
@@ -235,6 +240,8 @@ function handlePreToolUse(input) {
     }
   } catch {
     /* graceful failure */
+  } finally {
+    release();
   }
 
   if (result && result.trim()) {

gitnexus-claude-plugin/hooks/hook-lock.js

@@ -0,0 +1,119 @@
+const fs = require('fs');
+const path = require('path');
+
+const HOOK_LOCK_SUBDIR = '.hook-locks';
+const HOOK_LOCK_MAX_INFLIGHT = 3;
+const HOOK_LOCK_STALE_MS = 30000;
+
+function acquireHookSlot(gitNexusDir) {
+  const lockDir = path.join(gitNexusDir, HOOK_LOCK_SUBDIR);
+  try {
+    fs.mkdirSync(lockDir, { recursive: true });
+  } catch {
+    // Cannot create lock dir (read-only fs, cross-user perm denial, out of
+    // inodes, etc.) — fail closed by returning null. Caller skips augment.
+    // Fail-open here would let N concurrent hooks all proceed unguarded and
+    // reintroduce the #1486 fan-out the guard exists to prevent.
+    return null;
+  }
+
+  const myPidStr = String(process.pid);
+
+  for (let slot = 0; slot < HOOK_LOCK_MAX_INFLIGHT; slot++) {
+    const slotPath = path.join(lockDir, `slot-${slot}.lock`);
+    for (let attempt = 0; attempt < 2; attempt++) {
+      try {
+        fs.writeFileSync(slotPath, myPidStr, { flag: 'wx' });
+        let released = false;
+        const release = () => {
+          if (released) return;
+          released = true;
+          try {
+            // Only unlink if we still own the slot. If we appeared stale and
+            // another hook took over, the file now belongs to it — leave alone.
+            const content = fs.readFileSync(slotPath, 'utf-8').trim();
+            if (content === myPidStr) fs.unlinkSync(slotPath);
+          } catch {
+            /* already removed or unreadable */
+          }
+        };
+        process.on('exit', release);
+        return release;
+      } catch {
+        // Slot exists. Decide whether to take it over.
+        // Open once and inspect mtime + content via the same fd so there's
+        // no TOCTOU between the metadata check and the content read
+        // (codeql js/file-system-race).
+        let fd;
+        try {
+          fd = fs.openSync(slotPath, 'r');
+        } catch {
+          continue; // Vanished between EEXIST and open — retry this slot.
+        }
+        let isLive = false;
+        let mtimeMs = Date.now();
+        try {
+          mtimeMs = fs.fstatSync(fd).mtimeMs;
+          const buf = Buffer.alloc(32);
+          const n = fs.readSync(fd, buf, 0, 32, 0);
+          const ownerStr = buf.slice(0, n).toString('utf-8').trim();
+          if (ownerStr === '') {
+            // Owner created the file but hasn't written its PID yet. The
+            // wx open+write window is microseconds; give it the benefit
+            // of the doubt and treat as live.
+            isLive = true;
+          } else {
+            const owner = Number.parseInt(ownerStr, 10);
+            if (Number.isFinite(owner) && owner > 0) {
+              try {
+                process.kill(owner, 0);
+                isLive = true;
+              } catch (e) {
+                // ESRCH = process gone → treat as dead. EPERM = process exists
+                // but owned by another user (cross-user lock dir) → still alive,
+                // keep the slot. Anything else: be conservative, assume alive.
+                if (e && e.code === 'ESRCH') {
+                  isLive = false;
+                } else {
+                  isLive = true;
+                }
+              }
+            }
+          }
+        } catch {
+          /* unreadable — treat as dead */
+        } finally {
+          try {
+            fs.closeSync(fd);
+          } catch {
+            /* already closed */
+          }
+        }
+        // For slots younger than HOOK_LOCK_STALE_MS, PID-liveness wins —
+        // a slow-but-alive hook is never wrongly evicted. For older slots,
+        // age is the final arbiter as a defense against PID reuse on long-
+        // abandoned slots. 30s >> the 7s augment timeout, so a healthy run
+        // never crosses this threshold.
+        if (isLive && Date.now() - mtimeMs > HOOK_LOCK_STALE_MS) {
+          isLive = false;
+        }
+        if (isLive) break; // Try the next slot.
+        try {
+          fs.unlinkSync(slotPath);
+        } catch {
+          /* another hook beat us to it — retry will hit EEXIST */
+        }
+        // Loop and retry this slot.
+      }
+    }
+  }
+
+  return null;
+}
+
+module.exports = {
+  HOOK_LOCK_SUBDIR,
+  HOOK_LOCK_MAX_INFLIGHT,
+  HOOK_LOCK_STALE_MS,
+  acquireHookSlot,
+};

gitnexus-cursor-integration/README.md

@@ -0,0 +1,91 @@
+# GitNexus — Cursor integration
+
+Static config that adds GitNexus knowledge-graph augmentation and skill files to Cursor.
+
+> **Hooks require Cursor 2.4+.** Earlier versions don't expose `postToolUse` and the hook will silently no-op.
+
+## What you get
+
+| Layer                     | What it does                                                                                                                              | How it's installed                                                              |
+| ------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------- |
+| **MCP**                   | `gitnexus` MCP server with 16 tools (`query`, `context`, `impact`, `detect_changes`, `rename`, …)                                         | `npx gitnexus setup` writes `~/.cursor/mcp.json` automatically.                 |
+| **Skills**                | `/gitnexus-exploring`, `/gitnexus-debugging`, `/gitnexus-impact-analysis`, `/gitnexus-refactoring`, `/gitnexus-pr-review` markdown skills | `npx gitnexus setup` copies them to `~/.cursor/skills/gitnexus/`.               |
+| **Hooks** _(this README)_ | `postToolUse` hook that enriches `Shell` / `Read` / `Grep` tool calls with graph context — same augmentation Claude Code gets             | **Manual** — copy the files described below into your project's `.cursor/`. |
+
+## Hook install
+
+Cursor 2.4+ reads `.cursor/hooks.json` from the project root and runs hook commands with the project root as the working directory ([docs](https://cursor.com/docs/agent/hooks)).
+
+From this repo's `gitnexus-cursor-integration/hooks/`, copy the files below into your **project root**:
+
+```text
+<your-project>/
+├── .cursor/
+│   └── hooks.json              ← from gitnexus-cursor-integration/hooks/hooks.json
+└── hooks/
+    ├── gitnexus-hook.cjs       ← from gitnexus-cursor-integration/hooks/gitnexus-hook.cjs
+    └── hook-lock.cjs           ← from gitnexus-cursor-integration/hooks/hook-lock.cjs
+```
+
+Equivalent shell commands (run from your project root, with `$GITNEXUS_REPO` pointing at a clone of this repo):
+
+```bash
+mkdir -p .cursor hooks
+cp "$GITNEXUS_REPO/gitnexus-cursor-integration/hooks/hooks.json"        .cursor/hooks.json
+cp "$GITNEXUS_REPO/gitnexus-cursor-integration/hooks/gitnexus-hook.cjs" hooks/gitnexus-hook.cjs
+cp "$GITNEXUS_REPO/gitnexus-cursor-integration/hooks/hook-lock.cjs"     hooks/hook-lock.cjs
+```
+
+If you already have a `.cursor/hooks.json`, merge the `hooks.postToolUse` array rather than overwriting.
+
+### Verify
+
+1. Index the project: `npx gitnexus analyze`
+2. Reload the Cursor window so it picks up the new hook config.
+3. Ask the agent something that triggers `Read` / `Grep` / `Shell rg`. You should see a `[GitNexus]` block appended to the tool result.
+4. Diagnose silent no-ops by setting `GITNEXUS_DEBUG=1` in your shell environment — the hook will write Cursor's raw event payload to stderr so you can verify field names.
+
+### What's installed manually vs. automated
+
+| Step                                                                 | Automated by `gitnexus setup`? |
+| -------------------------------------------------------------------- | ------------------------------ |
+| `~/.cursor/mcp.json`                                                 | ✅                             |
+| `~/.cursor/skills/gitnexus/*`                                        | ✅                             |
+| `<project>/.cursor/hooks.json` + `<project>/hooks/gitnexus-hook.cjs` + `<project>/hooks/hook-lock.cjs` | ❌ — copy manually (see above) |
+
+Hook install is per-project (Cursor scopes hooks to a project root); skills and MCP config are global.
+
+## Hook contract
+
+The hook receives a JSON event on stdin matching Cursor 2.4's `postToolUse` shape:
+
+```json
+{
+  "tool_name": "Grep" | "Read" | "Shell",
+  "tool_input": { /* tool-specific */ },
+  "tool_output": { /* optional */ },
+  "cwd": "/absolute/path/to/project"
+}
+```
+
+It writes augmentation context to stdout as:
+
+```json
+{ "additional_context": "[GitNexus] …" }
+```
+
+Empty stdout means "no augmentation, continue normally" — the hook never blocks the tool.
+
+### Pattern extraction per tool
+
+| Tool    | Pattern source                                                                                                         | Notes                                                                                                |
+| ------- | ---------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
+| `Grep`  | `tool_input.query` (also `pattern`, `regex`, `q`, `search`, `searchQuery`)                                             | Last-resort fallback: longest string value in `tool_input` (≥ 3 chars).                              |
+| `Read`  | basename of `tool_input.target_file` (also `file_path`, `filePath`, `path`, `file`), stripped to identifier characters | `auth/handler.ts` → `handler`.                                                                       |
+| `Shell` | First positional argument after `rg` / `grep` in `tool_input.command`                                                  | Best-effort tokenizer; quoted multi-word patterns (`rg "User Service"`) extract the first word only. |
+
+## Troubleshooting
+
+- **Nothing happens** — Confirm Cursor is on 2.4+ and the project root has `.cursor/hooks.json` plus both hook files at `hooks/gitnexus-hook.cjs` and `hooks/hook-lock.cjs`. Then `npx gitnexus list` to confirm the project is indexed.
+- **`gitnexus` not found** — The hook prefers a locally-resolvable `gitnexus/dist/cli/index.js` and falls back to `npx -y gitnexus`. Install globally with `npm i -g gitnexus` to skip the npx cold-start latency.
+- **Wrong pattern extracted** — Set `GITNEXUS_DEBUG=1` and run a tool call. The raw stdin payload is logged to stderr; use it to confirm Cursor's actual `tool_input` field names against the table above. If they differ, file an issue with the captured payload.

gitnexus-cursor-integration/hooks/augment-shell.sh

@@ -1,50 +0,0 @@
-#!/bin/bash
-# GitNexus beforeShellExecution hook for Cursor
-# Receives JSON on stdin with { command, cwd, timeout }
-# Returns JSON on stdout with { permission, agent_message }
-#
-# Extracts search pattern from grep/rg commands, runs gitnexus augment,
-# and injects the enriched context via agent_message.
-
-INPUT=$(cat)
-
-COMMAND=$(echo "$INPUT" | jq -r '.command // empty' 2>/dev/null)
-
-if [ -z "$COMMAND" ]; then
-  echo '{"permission":"allow"}'
-  exit 0
-fi
-
-# Skip non-search commands
-case "$COMMAND" in
-  cd\ *|npm\ *|yarn\ *|pnpm\ *|git\ commit*|git\ push*|git\ pull*|mkdir\ *|rm\ *|cp\ *|mv\ *|echo\ *|cat\ *)
-    echo '{"permission":"allow"}'
-    exit 0
-    ;;
-esac
-
-# Extract search pattern from rg/grep commands
-PATTERN=""
-if echo "$COMMAND" | grep -qE '\brg\b'; then
-  PATTERN=$(echo "$COMMAND" | sed -n "s/.*\brg\s\+\(--[^ ]*\s\+\)*['\"]\\?\([^'\";\| >]*\\).*/\2/p")
-elif echo "$COMMAND" | grep -qE '\bgrep\b'; then
-  PATTERN=$(echo "$COMMAND" | sed -n "s/.*\bgrep\s\+\(-[^ ]*\s\+\)*['\"]\\?\([^'\";\| >]*\\).*/\2/p")
-fi
-
-if [ -z "$PATTERN" ] || [ ${#PATTERN} -lt 3 ]; then
-  echo '{"permission":"allow"}'
-  exit 0
-fi
-
-# Run gitnexus augment
-RESULT=$(npx -y gitnexus augment "$PATTERN" 2>/dev/null)
-
-if [ -n "$RESULT" ]; then
-  # Escape for JSON
-  ESCAPED=$(echo "$RESULT" | jq -Rs .)
-  echo "{\"permission\":\"allow\",\"agent_message\":$ESCAPED}"
-else
-  echo '{"permission":"allow"}'
-fi
-
-exit 0

gitnexus-cursor-integration/hooks/gitnexus-hook.cjs

@@ -0,0 +1,266 @@
+#!/usr/bin/env node
+/**
+ * GitNexus Cursor postToolUse Hook
+ *
+ * Receives a JSON event on stdin describing a finished tool call, derives a
+ * search pattern (Grep query, Read file basename, or rg/grep arg from a Shell
+ * command), runs `gitnexus augment <pattern>`, and emits the enriched context
+ * back as `{ additional_context: "..." }` so the agent sees it alongside the
+ * tool result.
+ *
+ * Replaces the legacy beforeShellExecution / augment-shell.sh pipeline:
+ *   - Cross-platform (no bash, no jq — runs on Windows out of the box)
+ *   - Covers Read and Grep, not just Shell rg/grep
+ *
+ * Cursor 2.4+ generic hooks: https://cursor.com/docs/agent/hooks
+ */
+
+const fs = require('fs');
+const path = require('path');
+const { spawnSync } = require('child_process');
+const { acquireHookSlot } = require('./hook-lock.cjs');
+
+function readInput() {
+  try {
+    const data = fs.readFileSync(0, 'utf-8');
+    return JSON.parse(data);
+  } catch {
+    return {};
+  }
+}
+
+function isGlobalRegistryDir(candidate) {
+  if (fs.existsSync(path.join(candidate, 'meta.json'))) return false;
+  return (
+    fs.existsSync(path.join(candidate, 'registry.json')) ||
+    fs.existsSync(path.join(candidate, 'repos'))
+  );
+}
+
+function walkForGitNexusDir(startDir) {
+  let dir = startDir;
+  for (let i = 0; i < 5; i++) {
+    const candidate = path.join(dir, '.gitnexus');
+    if (fs.existsSync(candidate)) {
+      if (!isGlobalRegistryDir(candidate)) return candidate;
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) break;
+    dir = parent;
+  }
+  return null;
+}
+
+function findCanonicalRepoRoot(cwd) {
+  try {
+    const result = spawnSync('git', ['rev-parse', '--path-format=absolute', '--git-common-dir'], {
+      encoding: 'utf-8',
+      timeout: 2000,
+      cwd,
+      stdio: ['pipe', 'pipe', 'pipe'],
+    });
+    if (result.error || result.status !== 0) return null;
+    const commonDir = (result.stdout || '').trim();
+    if (!commonDir || !path.isAbsolute(commonDir)) return null;
+    return path.dirname(commonDir);
+  } catch {
+    return null;
+  }
+}
+
+function findGitNexusDir(startDir) {
+  const cwd = startDir || process.cwd();
+  const fromCwd = walkForGitNexusDir(cwd);
+  if (fromCwd) return fromCwd;
+  const canonicalRoot = findCanonicalRepoRoot(cwd);
+  if (canonicalRoot && canonicalRoot !== cwd) {
+    return walkForGitNexusDir(canonicalRoot);
+  }
+  return null;
+}
+
+function parseRgGrepPattern(cmd) {
+  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',
+  ]);
+
+  for (const token of tokens) {
+    if (skipNext) {
+      skipNext = false;
+      continue;
+    }
+    if (!foundCmd) {
+      if (/\brg$|\bgrep$/.test(token)) foundCmd = true;
+      continue;
+    }
+    if (token.startsWith('-')) {
+      if (flagsWithValues.has(token)) skipNext = true;
+      continue;
+    }
+    const cleaned = token.replace(/['"]/g, '');
+    return cleaned.length >= 3 ? cleaned : null;
+  }
+  return null;
+}
+
+/**
+ * Extract a search pattern from the tool input. Cursor 2.4 docs at
+ * https://cursor.com/docs/agent/hooks list the tool *matchers* but do not
+ * formally specify the per-tool tool_input field names, so we probe a
+ * generous set of MCP-style aliases. As a last-resort fallback for Grep
+ * (the highest-frequency search path) we also accept the longest plausible
+ * string value in tool_input. Set GITNEXUS_DEBUG=1 to log the raw payload
+ * to stderr if Cursor changes the contract and aliases stop matching.
+ */
+function pickLongestStringValue(obj) {
+  let best = null;
+  if (!obj || typeof obj !== 'object') return null;
+  for (const v of Object.values(obj)) {
+    if (typeof v === 'string' && v.length >= 3 && (!best || v.length > best.length)) {
+      best = v;
+    }
+  }
+  return best;
+}
+
+function extractPattern(toolName, toolInput) {
+  const t = (toolName || '').toLowerCase();
+
+  if (t === 'grep') {
+    const aliases = [
+      toolInput.query,
+      toolInput.pattern,
+      toolInput.regex,
+      toolInput.q,
+      toolInput.search,
+      toolInput.searchQuery,
+    ];
+    for (const a of aliases) {
+      if (typeof a === 'string' && a.length >= 3) return a;
+    }
+    // Last resort: scan tool_input for any reasonable-looking string value.
+    return pickLongestStringValue(toolInput);
+  }
+
+  if (t === 'read') {
+    const filePath =
+      toolInput.target_file ||
+      toolInput.file_path ||
+      toolInput.filePath ||
+      toolInput.path ||
+      toolInput.file ||
+      '';
+    if (!filePath) return null;
+    const base = path.basename(String(filePath), path.extname(String(filePath)));
+    const cleaned = base.replace(/[^a-zA-Z0-9_]/g, '');
+    return cleaned.length >= 3 ? cleaned : null;
+  }
+
+  if (t === 'shell') {
+    const cmd = toolInput.command || '';
+    if (!/\brg\b|\bgrep\b/.test(cmd)) return null;
+    // NOTE: parseRgGrepPattern uses split(/\s+/) and cannot handle shell
+    // quoting. `rg "User Service" src/` returns "User" (the first token
+    // after the rg/grep arg, with surrounding quotes stripped) — the
+    // multi-word pattern is intentionally not reconstructed since BM25 is
+    // already token-tolerant. Quoted single tokens (`rg "validateUser"`)
+    // work fine.
+    return parseRgGrepPattern(cmd);
+  }
+
+  return null;
+}
+
+function resolveCliPath() {
+  try {
+    return require.resolve('gitnexus/dist/cli/index.js');
+  } catch {
+    return '';
+  }
+}
+
+function runGitNexusCli(cliPath, args, cwd, timeout) {
+  const isWin = process.platform === 'win32';
+  if (cliPath) {
+    return spawnSync(process.execPath, [cliPath, ...args], {
+      encoding: 'utf-8',
+      timeout,
+      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'],
+  });
+}
+
+function main() {
+  try {
+    const input = readInput();
+    if (process.env.GITNEXUS_DEBUG) {
+      // Echo the payload so users can capture Cursor's actual contract when
+      // diagnosing why augmentation isn't firing. Stderr only — stdout is
+      // reserved for the JSON response Cursor consumes.
+      try {
+        process.stderr.write(
+          `GitNexus Cursor hook stdin: ${JSON.stringify(input).slice(0, 500)}\n`,
+        );
+      } catch {
+        /* never let debug logging break the hook */
+      }
+    }
+    const cwd = input.cwd || process.cwd();
+    if (!path.isAbsolute(cwd)) return;
+    const gitNexusDir = findGitNexusDir(cwd);
+    if (!gitNexusDir) return;
+
+    const toolName = input.tool_name || '';
+    const toolInput = input.tool_input || {};
+
+    const pattern = extractPattern(toolName, toolInput);
+    if (!pattern || pattern.length < 3) return;
+
+    const release = acquireHookSlot(gitNexusDir);
+    if (!release) return;
+
+    const cliPath = resolveCliPath();
+    let result = '';
+    try {
+      const child = runGitNexusCli(cliPath, ['augment', '--', pattern], cwd, 7000);
+      if (!child.error && child.status === 0) {
+        result = child.stderr || '';
+      }
+    } catch {
+      /* graceful failure */
+    } finally {
+      release();
+    }
+
+    if (result && result.trim()) {
+      console.log(JSON.stringify({ additional_context: result.trim() }));
+    }
+  } catch (err) {
+    if (process.env.GITNEXUS_DEBUG) {
+      console.error('GitNexus Cursor hook error:', (err.message || '').slice(0, 200));
+    }
+  }
+}
+
+main();

gitnexus-cursor-integration/hooks/hook-lock.cjs

@@ -0,0 +1,119 @@
+const fs = require('fs');
+const path = require('path');
+
+const HOOK_LOCK_SUBDIR = '.hook-locks';
+const HOOK_LOCK_MAX_INFLIGHT = 3;
+const HOOK_LOCK_STALE_MS = 30000;
+
+function acquireHookSlot(gitNexusDir) {
+  const lockDir = path.join(gitNexusDir, HOOK_LOCK_SUBDIR);
+  try {
+    fs.mkdirSync(lockDir, { recursive: true });
+  } catch {
+    // Cannot create lock dir (read-only fs, cross-user perm denial, out of
+    // inodes, etc.) — fail closed by returning null. Caller skips augment.
+    // Fail-open here would let N concurrent hooks all proceed unguarded and
+    // reintroduce the #1486 fan-out the guard exists to prevent.
+    return null;
+  }
+
+  const myPidStr = String(process.pid);
+
+  for (let slot = 0; slot < HOOK_LOCK_MAX_INFLIGHT; slot++) {
+    const slotPath = path.join(lockDir, `slot-${slot}.lock`);
+    for (let attempt = 0; attempt < 2; attempt++) {
+      try {
+        fs.writeFileSync(slotPath, myPidStr, { flag: 'wx' });
+        let released = false;
+        const release = () => {
+          if (released) return;
+          released = true;
+          try {
+            // Only unlink if we still own the slot. If we appeared stale and
+            // another hook took over, the file now belongs to it — leave alone.
+            const content = fs.readFileSync(slotPath, 'utf-8').trim();
+            if (content === myPidStr) fs.unlinkSync(slotPath);
+          } catch {
+            /* already removed or unreadable */
+          }
+        };
+        process.on('exit', release);
+        return release;
+      } catch {
+        // Slot exists. Decide whether to take it over.
+        // Open once and inspect mtime + content via the same fd so there's
+        // no TOCTOU between the metadata check and the content read
+        // (codeql js/file-system-race).
+        let fd;
+        try {
+          fd = fs.openSync(slotPath, 'r');
+        } catch {
+          continue; // Vanished between EEXIST and open — retry this slot.
+        }
+        let isLive = false;
+        let mtimeMs = Date.now();
+        try {
+          mtimeMs = fs.fstatSync(fd).mtimeMs;
+          const buf = Buffer.alloc(32);
+          const n = fs.readSync(fd, buf, 0, 32, 0);
+          const ownerStr = buf.slice(0, n).toString('utf-8').trim();
+          if (ownerStr === '') {
+            // Owner created the file but hasn't written its PID yet. The
+            // wx open+write window is microseconds; give it the benefit
+            // of the doubt and treat as live.
+            isLive = true;
+          } else {
+            const owner = Number.parseInt(ownerStr, 10);
+            if (Number.isFinite(owner) && owner > 0) {
+              try {
+                process.kill(owner, 0);
+                isLive = true;
+              } catch (e) {
+                // ESRCH = process gone → treat as dead. EPERM = process exists
+                // but owned by another user (cross-user lock dir) → still alive,
+                // keep the slot. Anything else: be conservative, assume alive.
+                if (e && e.code === 'ESRCH') {
+                  isLive = false;
+                } else {
+                  isLive = true;
+                }
+              }
+            }
+          }
+        } catch {
+          /* unreadable — treat as dead */
+        } finally {
+          try {
+            fs.closeSync(fd);
+          } catch {
+            /* already closed */
+          }
+        }
+        // For slots younger than HOOK_LOCK_STALE_MS, PID-liveness wins —
+        // a slow-but-alive hook is never wrongly evicted. For older slots,
+        // age is the final arbiter as a defense against PID reuse on long-
+        // abandoned slots. 30s >> the 7s augment timeout, so a healthy run
+        // never crosses this threshold.
+        if (isLive && Date.now() - mtimeMs > HOOK_LOCK_STALE_MS) {
+          isLive = false;
+        }
+        if (isLive) break; // Try the next slot.
+        try {
+          fs.unlinkSync(slotPath);
+        } catch {
+          /* another hook beat us to it — retry will hit EEXIST */
+        }
+        // Loop and retry this slot.
+      }
+    }
+  }
+
+  return null;
+}
+
+module.exports = {
+  HOOK_LOCK_SUBDIR,
+  HOOK_LOCK_MAX_INFLIGHT,
+  HOOK_LOCK_STALE_MS,
+  acquireHookSlot,
+};

gitnexus-cursor-integration/hooks/hooks.json

@@ -1,11 +1,11 @@
 {
   "version": 1,
   "hooks": {
-    "beforeShellExecution": [
+    "postToolUse": [
       {
-        "command": "./hooks/augment-shell.sh",
-        "timeout": 5,
-        "matcher": "\\brg\\b|\\bgrep\\b"
+        "matcher": "Shell|Read|Grep",
+        "command": "node ./hooks/gitnexus-hook.cjs",
+        "timeout": 10
       }
     ]
   }

gitnexus-shared/package.json

@@ -10,6 +10,10 @@
     ".": {
       "types": "./dist/index.d.ts",
       "default": "./dist/index.js"
+    },
+    "./test-helpers": {
+      "types": "./dist/test-helpers.d.ts",
+      "default": "./dist/test-helpers.js"
     }
   },
   "scripts": {

gitnexus-shared/src/index.ts

@@ -143,6 +143,34 @@ export type { ScopeTree } from './scope-resolution/scope-tree.js';
 export { buildPositionIndex } from './scope-resolution/position-index.js';
 export type { PositionIndex } from './scope-resolution/position-index.js';
 
+// Resilient fetch primitives — bounded retries + per-process circuit breaker.
+// Test-only helpers (`__resetBreakerRegistry__`, `classifyOutcome`) are
+// reachable via the separate `gitnexus-shared/test-helpers` subpath; do
+// NOT add them here. Production consumers must not call them.
+export { withRetry, computeBackoffMs } from './integrations/retry.js';
+export type { RetryOptions, RetryDecision } from './integrations/retry.js';
+export { CircuitBreaker, CircuitOpenError, getBreaker } from './integrations/circuit-breaker.js';
+export type { CircuitBreakerOptions } from './integrations/circuit-breaker.js';
+export {
+  resilientFetch,
+  ResilientFetchExhaustedError,
+  RETRY_AFTER_CAP_MS,
+  parseRetryAfter,
+} from './integrations/resilient-fetch.js';
+export type { ResilientFetchOptions } from './integrations/resilient-fetch.js';
+
+// Understand-Quickly registry integration (opt-in)
+export {
+  UNDERSTAND_QUICKLY_DISPATCH_URL,
+  UNDERSTAND_QUICKLY_EVENT_TYPE,
+  UNDERSTAND_QUICKLY_TOKEN_ENV,
+  buildUqDispatchPayload,
+  isValidOwnerRepo,
+  parseOwnerRepoFromRemote,
+  stripGitSuffix,
+} from './integrations/understand-quickly.js';
+export type { UqDispatchPayload } from './integrations/understand-quickly.js';
+
 // Shadow-mode diff + aggregation (RFC §6.3; Ring 2 SHARED #918)
 export { diffResolutions } from './scope-resolution/shadow/diff.js';
 export type {

gitnexus-shared/src/integrations/circuit-breaker.ts

@@ -0,0 +1,273 @@
+/**
+ * Per-process circuit breaker.
+ *
+ * Closed -> Open transition fires after `failureThreshold` consecutive
+ * failures. While Open, `check` throws `CircuitOpenError` until
+ * `cooldownMs` has elapsed since the breaker tripped. The first call
+ * after the cooldown enters Half-Open and consumes the *probe permit*:
+ * a recorded success returns to Closed; a recorded failure flips back
+ * to Open with a fresh timestamp.
+ *
+ * Half-open admits exactly one in-flight probe at a time. Concurrent
+ * callers attempting `check()` while a probe is outstanding receive
+ * `CircuitOpenError` with `retryAfterMs = halfOpenRetryAfterMs` (default
+ * 1000ms; configurable). This prevents the recovery-time thundering
+ * herd that defeats the breaker's "fail fast" promise.
+ *
+ * Outcome reporting splits permit-release from state-resolution:
+ *   - `recordSuccess` — releases the probe permit, resets the failure
+ *     counter, transitions to Closed. Reserved for true 2xx/3xx outcomes.
+ *   - `recordFailure` — releases the probe permit, increments the
+ *     consecutive-failure counter, transitions to Open with a fresh
+ *     `openedAt` (when called from Half-Open or when the threshold
+ *     trips from Closed).
+ *   - `recordNeutral` — releases the probe permit, BUT leaves state and
+ *     counter untouched. Used for outcomes that are neither evidence of
+ *     backend health nor evidence of backend failure (caller-driven
+ *     cancellation, local timeout, terminal 4xx client errors). Critical
+ *     design point: if `recordNeutral` did not release the permit, a
+ *     single `TimeoutError` from per-attempt `AbortSignal.timeout` would
+ *     route through `recordNeutral` and permanently park the breaker in
+ *     half-open until process restart. Releasing the permit while leaving
+ *     state half-open keeps the "neutral doesn't claim health" semantic
+ *     without creating that wedge.
+ *
+ * Pairing invariant: every successful `check()` MUST be paired with
+ * exactly one `record*()` on every code path including throws. Direct
+ * consumers should wrap the protected operation in `try/finally`:
+ *
+ *   breaker.check();
+ *   try {
+ *     const result = await operation();
+ *     breaker.recordSuccess();
+ *     return result;
+ *   } catch (err) {
+ *     // classify err and call recordFailure / recordNeutral / etc.
+ *     throw err;
+ *   }
+ *
+ * `resilientFetch`'s catch-all on `fetchImpl` already satisfies this
+ * for that consumer.
+ *
+ * Atomicity model: the half-open gate relies on JavaScript event-loop
+ * single-threadedness within a synchronous `check()` body. There is no
+ * `await` inside `check()`; concurrent callers serialize on microtask
+ * order, and exactly one observes `probeInFlight === false`. Do not
+ * introduce `await` inside `check()` without revisiting the gate. If
+ * this code is ever ported to a runtime with shared-memory threads
+ * (Node `worker_threads` with `SharedArrayBuffer`, Web Workers with
+ * shared registries), the boolean must become an atomic CAS — Resilience4j
+ * and Hystrix use atomic permits *because* they run in JVM thread pools.
+ *
+ * Runtime-agnostic: depends only on a `now()` clock and standard JS —
+ * no Node-only imports. Tests inject `now` to advance the clock
+ * deterministically without `vi.useFakeTimers()`.
+ */
+
+export class CircuitOpenError extends Error {
+  override readonly name = 'CircuitOpenError';
+  /** Approximate wait time before the breaker may transition to Half-Open
+   *  (or before the in-flight probe is expected to resolve). */
+  readonly retryAfterMs: number;
+
+  constructor(retryAfterMs: number, key?: string) {
+    super(
+      key
+        ? `Circuit '${key}' is open; retry in ${Math.ceil(retryAfterMs / 1000)}s`
+        : `Circuit is open; retry in ${Math.ceil(retryAfterMs / 1000)}s`,
+    );
+    this.retryAfterMs = retryAfterMs;
+  }
+}
+
+export interface CircuitBreakerOptions {
+  /** Consecutive failures required to trip Closed -> Open. */
+  failureThreshold?: number;
+  /** Milliseconds Open before the next call may probe (Half-Open). */
+  cooldownMs?: number;
+  /**
+   * Milliseconds to suggest in `CircuitOpenError.retryAfterMs` when the
+   * breaker is Half-Open with the probe permit consumed. Default 1000ms.
+   * Consumers with long-running protected ops (LLM streaming, large
+   * uploads) should raise this — the cooldown clock is no longer the
+   * right answer because cooldown has elapsed. Returning 0 invites
+   * retry storms; returning the full cooldown misleads about wait.
+   */
+  halfOpenRetryAfterMs?: number;
+  /** Optional key for error messages and registry lookups. */
+  key?: string;
+  /** Clock override — defaults to `Date.now`. Tests inject deterministic time. */
+  now?: () => number;
+}
+
+type State = 'closed' | 'open' | 'half-open';
+
+export class CircuitBreaker {
+  private readonly failureThreshold: number;
+  private readonly cooldownMs: number;
+  private readonly halfOpenRetryAfterMs: number;
+  private readonly key: string | undefined;
+  private readonly now: () => number;
+
+  private state: State = 'closed';
+  private consecutiveFailures = 0;
+  private openedAt: number | null = null;
+  /**
+   * True between a successful `check()` and the next `record*()` call
+   * during Half-Open. Gates concurrent callers from stampeding a still-
+   * recovering dependency. Boolean rather than counter — single-permit
+   * is the conservative end of the Hystrix/Resilience4j spectrum.
+   */
+  private probeInFlight = false;
+
+  constructor(opts: CircuitBreakerOptions = {}) {
+    this.failureThreshold = opts.failureThreshold ?? 3;
+    this.cooldownMs = opts.cooldownMs ?? 30_000;
+    this.halfOpenRetryAfterMs = opts.halfOpenRetryAfterMs ?? 1_000;
+    this.key = opts.key;
+    this.now = opts.now ?? (() => Date.now());
+  }
+
+  /**
+   * Throw `CircuitOpenError` if the breaker won't admit this call.
+   * Otherwise consume the half-open probe permit (if applicable) and
+   * return so the caller can attempt the protected work.
+   *
+   * Three rejection paths:
+   *   1. Open and still in cooldown → throws with `retryAfterMs` =
+   *      remaining cooldown.
+   *   2. Open with cooldown elapsed AND a probe is already in flight
+   *      (race: another caller transitioned to half-open and grabbed
+   *      the permit on a microtask before us) → throws with
+   *      `halfOpenRetryAfterMs`.
+   *   3. Half-Open with probe in flight → throws with `halfOpenRetryAfterMs`.
+   *
+   * **Pairing invariant**: every successful return from `check()` MUST
+   * be paired with exactly one `recordSuccess` / `recordFailure` /
+   * `recordNeutral` on every code path including thrown exceptions.
+   * Failing to pair leaves the probe permit consumed forever and
+   * wedges the breaker. See file-header JSDoc for the canonical
+   * try/finally pattern.
+   */
+  check(): void {
+    if (this.state === 'open' && this.openedAt !== null) {
+      const elapsed = this.now() - this.openedAt;
+      if (elapsed < this.cooldownMs) {
+        throw new CircuitOpenError(this.cooldownMs - elapsed, this.key);
+      }
+      // Cooldown elapsed — transition to Half-Open. The very next
+      // `probeInFlight` check below decides whether THIS caller gets
+      // the permit or hits the gate.
+      this.state = 'half-open';
+    }
+
+    if (this.state === 'half-open') {
+      if (this.probeInFlight) {
+        throw new CircuitOpenError(this.halfOpenRetryAfterMs, this.key);
+      }
+      this.probeInFlight = true;
+    }
+    // Closed state falls through silently.
+  }
+
+  recordSuccess(): void {
+    this.probeInFlight = false;
+    this.consecutiveFailures = 0;
+    this.state = 'closed';
+    this.openedAt = null;
+  }
+
+  recordFailure(): void {
+    this.probeInFlight = false;
+    this.consecutiveFailures += 1;
+    if (this.state === 'half-open' || this.consecutiveFailures >= this.failureThreshold) {
+      this.state = 'open';
+      this.openedAt = this.now();
+    }
+  }
+
+  /**
+   * Releases the probe permit BUT leaves state and counter untouched.
+   * Use when an attempt produced a response or error that should not
+   * influence breaker health in either direction — caller-driven aborts,
+   * local AbortSignal timeouts, terminal 4xx client errors.
+   *
+   * Why permit-release-without-state-resolution: if `recordNeutral` did
+   * not clear `probeInFlight`, a single `TimeoutError` from per-attempt
+   * `AbortSignal.timeout` (which routes through neutral classification)
+   * would permanently park the breaker in half-open. Since timeouts are
+   * an *expected* outcome under flaky-dependency conditions, the cited
+   * "per-attempt timeout bounds the stuck state" mitigation would itself
+   * be the trigger for a permanent wedge. Releasing the permit closes
+   * that loop while keeping the "neutral doesn't claim dependency
+   * health" semantic.
+   *
+   * Calling `recordSuccess` for these would erase legitimate prior
+   * failure signal; calling `recordFailure` would trip the breaker for
+   * outcomes the backend isn't responsible for.
+   */
+  recordNeutral(): void {
+    this.probeInFlight = false;
+    // State and consecutiveFailures are preserved by design.
+  }
+
+  /**
+   * Pure read — no state mutation, no permit accounting. Returns the
+   * *would-be* state at the current instant: 'half-open' if the breaker
+   * is open with cooldown elapsed (regardless of whether a probe is in
+   * flight), 'open' if open and still in cooldown, 'closed' otherwise.
+   *
+   * Inspection-only; safe to call from tests without consuming a probe
+   * permit. The implicit Open -> Half-Open transition that mutates
+   * `state` lives in `check()` only.
+   */
+  getState(): State {
+    if (this.state === 'open' && this.openedAt !== null) {
+      const elapsed = this.now() - this.openedAt;
+      if (elapsed >= this.cooldownMs) return 'half-open';
+    }
+    return this.state;
+  }
+  getConsecutiveFailures(): number {
+    return this.consecutiveFailures;
+  }
+  /** Inspection-only test accessor for the half-open probe permit. */
+  isProbeInFlight(): boolean {
+    return this.probeInFlight;
+  }
+  /** Timestamp (ms since epoch) when the breaker last transitioned to Open,
+   *  or `null` if it's currently Closed. Useful for computing remaining
+   *  cooldown without consuming a probe permit via `check()`. */
+  getOpenedAt(): number | null {
+    return this.openedAt;
+  }
+  /** Configured cooldown duration in milliseconds. */
+  getCooldownMs(): number {
+    return this.cooldownMs;
+  }
+}
+
+// ─── Per-process registry ────────────────────────────────────────────
+//
+// Single shared map keyed on caller-chosen strings. Used by
+// `resilient-fetch.ts` so multiple call sites targeting the same logical
+// endpoint share breaker state. Per-process only — not persisted.
+
+const registry = new Map<string, CircuitBreaker>();
+
+export function getBreaker(key: string, opts?: CircuitBreakerOptions): CircuitBreaker {
+  let breaker = registry.get(key);
+  if (!breaker) {
+    breaker = new CircuitBreaker({ ...opts, key });
+    registry.set(key, breaker);
+  }
+  return breaker;
+}
+
+/**
+ * Test-only: clear all registered breakers. Tests must call this in
+ * `beforeEach` to prevent breaker state from leaking across test cases.
+ */
+export function __resetBreakerRegistry__(): void {
+  registry.clear();
+}

gitnexus-shared/src/integrations/resilient-fetch.ts

@@ -0,0 +1,279 @@
+/**
+ * `resilientFetch` — fetch wrapped in retry + circuit breaker, with
+ * GitHub-flavoured retry classification baked in (Retry-After parsing,
+ * 401/403/404/422 treated as terminal client errors).
+ *
+ * Designed for the `gitnexus publish` GitHub `repository_dispatch`
+ * call, but the classification rules apply to any GitHub REST endpoint.
+ * Runtime-agnostic — no Node-only imports.
+ */
+
+import {
+  CircuitBreaker,
+  CircuitOpenError,
+  getBreaker,
+  type CircuitBreakerOptions,
+} from './circuit-breaker.js';
+import { computeBackoffMs, type RetryOptions } from './retry.js';
+
+export { CircuitOpenError };
+
+export interface ResilientFetchOptions {
+  /** Optional fetch implementation override. Defaults to `globalThis.fetch`. */
+  fetchImpl?: typeof fetch;
+  /**
+   * Logical key for the breaker. Defaults to `<host><pathname>` of the
+   * request URL — call sites targeting the same endpoint share breaker
+   * state regardless of query-string differences.
+   */
+  breakerKey?: string;
+  /** Per-call breaker override. Used for tests and one-off configuration. */
+  breaker?: CircuitBreaker;
+  /** Tuning knobs for the breaker registered under `breakerKey`. */
+  breakerOptions?: CircuitBreakerOptions;
+  /** Tuning knobs for the retry helper. */
+  retry?: Partial<Pick<RetryOptions, 'maxAttempts' | 'baseDelayMs' | 'capDelayMs'>> & {
+    sleep?: RetryOptions['sleep'];
+    random?: RetryOptions['random'];
+  };
+  /** Clock override propagated into Retry-After HTTP-date math and breaker. */
+  now?: () => number;
+}
+
+/** Cap on any single Retry-After wait — protects CLI from a buggy registry. */
+export const RETRY_AFTER_CAP_MS = 30_000;
+
+const DEFAULT_RETRY = {
+  maxAttempts: 3,
+  baseDelayMs: 500,
+  capDelayMs: 5_000,
+};
+
+/**
+ * Parse a `Retry-After` header value into milliseconds.
+ * Accepts either a delta-seconds integer (`"30"`) or an HTTP-date.
+ * Returns null on parse failure or negative deltas.
+ */
+export function parseRetryAfter(value: string | null, now: () => number = Date.now): number | null {
+  if (!value) return null;
+  const trimmed = value.trim();
+  if (trimmed === '') return null;
+
+  if (/^[0-9]+$/.test(trimmed)) {
+    const seconds = parseInt(trimmed, 10);
+    if (Number.isNaN(seconds) || seconds < 0) return null;
+    return seconds * 1000;
+  }
+
+  const target = Date.parse(trimmed);
+  if (Number.isNaN(target)) return null;
+  const delta = target - now();
+  return delta >= 0 ? delta : 0;
+}
+
+/** Internal: outcome classification used by the resilientFetch loop. */
+type Outcome =
+  | { kind: 'success'; resp: Response }
+  | { kind: 'terminal-client'; resp: Response } // 4xx other than 429: no retry, breaker neutral
+  | { kind: 'retryable-status'; resp: Response; afterMs: number | undefined } // 5xx, 429
+  | { kind: 'terminal-network'; err: unknown } // TimeoutError or AbortError: no retry, breaker neutral
+  | { kind: 'retryable-network'; err: unknown }; // DNS, ECONNRESET, etc.
+
+/** Exported for unit tests. */
+export function classifyOutcome(
+  result: { kind: 'error'; err: unknown } | { kind: 'response'; resp: Response },
+  now: () => number,
+): Outcome {
+  if (result.kind === 'error') {
+    // Both timer-fired aborts (`AbortSignal.timeout()` → `TimeoutError`)
+    // and caller-driven aborts (`AbortController.abort()` → `AbortError`)
+    // are terminal: retrying against an already-aborted signal would
+    // fail again immediately, and neither outcome reflects backend
+    // health. They route through the breaker's neutral path.
+    if (
+      result.err instanceof DOMException &&
+      (result.err.name === 'TimeoutError' || result.err.name === 'AbortError')
+    ) {
+      return { kind: 'terminal-network', err: result.err };
+    }
+    return { kind: 'retryable-network', err: result.err };
+  }
+  const resp = result.resp;
+  if (resp.status >= 200 && resp.status < 400) return { kind: 'success', resp };
+  if (resp.status === 429) {
+    // `resp.headers` is always present on a real `Response`, but tests
+    // sometimes stub `fetch` with a plain `{ ok, status }` object. Be
+    // defensive — a missing `Retry-After` falls through to exponential
+    // backoff, which is the correct behaviour anyway.
+    const retryAfterHeader =
+      typeof resp.headers?.get === 'function' ? resp.headers.get('Retry-After') : null;
+    const parsed = parseRetryAfter(retryAfterHeader, now);
+    return {
+      kind: 'retryable-status',
+      resp,
+      afterMs: parsed !== null ? Math.min(parsed, RETRY_AFTER_CAP_MS) : undefined,
+    };
+  }
+  if (resp.status >= 500) return { kind: 'retryable-status', resp, afterMs: undefined };
+  return { kind: 'terminal-client', resp };
+}
+
+const defaultSleep = (ms: number): Promise<void> =>
+  new Promise((resolve) => setTimeout(resolve, ms));
+
+function defaultBreakerKey(input: string | URL): string {
+  try {
+    const url = typeof input === 'string' ? new URL(input) : input;
+    return `${url.host}${url.pathname}`;
+  } catch {
+    return String(input);
+  }
+}
+
+/** Final error thrown when retries are exhausted on a 5xx / 429. */
+export class ResilientFetchExhaustedError extends Error {
+  override readonly name = 'ResilientFetchExhaustedError';
+  constructor(public readonly response: Response) {
+    super(`Request failed after retries (HTTP ${response.status})`);
+  }
+}
+
+/**
+ * Wrap `fetch` with bounded retries and a per-process circuit breaker.
+ *
+ * Semantics:
+ * - 5xx and 429 responses are retried; 429 honors `Retry-After` (capped).
+ * - Network throws are retried unless they are `TimeoutError` DOMExceptions.
+ * - Timeouts and 4xx (other than 429) are returned/thrown without retry
+ *   AND without incrementing the breaker — they reflect caller config
+ *   or local network state, not registry health.
+ * - Each `fetch` call carries the caller-supplied `signal` (e.g. an
+ *   `AbortSignal.timeout()`) — that timeout bounds each individual
+ *   attempt, not the whole retry sequence.
+ * - When the breaker is open, throws `CircuitOpenError` synchronously
+ *   without invoking `fetch`.
+ * - When retries are exhausted on a 5xx / 429, throws
+ *   `ResilientFetchExhaustedError` carrying the last response.
+ *
+ * Cumulative wall-clock budget:
+ *   maxAttempts × (per-attempt-timeout + capDelayMs)
+ *   With defaults (3, 500ms base, 5000ms cap) and a typical 15s per-attempt
+ *   timeout from the caller's signal, worst case is ~3 × (15s + 5s) = 60s.
+ *   Callers that want a tighter total bound should reduce `maxAttempts` or
+ *   wrap `resilientFetch` in their own outer `AbortSignal.timeout()`.
+ */
+export async function resilientFetch(
+  input: string | URL,
+  init: RequestInit | undefined,
+  opts: ResilientFetchOptions = {},
+): Promise<Response> {
+  const fetchImpl = opts.fetchImpl ?? globalThis.fetch;
+  const now = opts.now ?? (() => Date.now());
+  const breaker =
+    opts.breaker ?? getBreaker(opts.breakerKey ?? defaultBreakerKey(input), opts.breakerOptions);
+
+  const retryConfig = {
+    maxAttempts: opts.retry?.maxAttempts ?? DEFAULT_RETRY.maxAttempts,
+    baseDelayMs: opts.retry?.baseDelayMs ?? DEFAULT_RETRY.baseDelayMs,
+    capDelayMs: opts.retry?.capDelayMs ?? DEFAULT_RETRY.capDelayMs,
+  };
+  const sleep = opts.retry?.sleep ?? defaultSleep;
+  const random = opts.retry?.random ?? Math.random;
+
+  // Fail fast on an open breaker, before invoking fetch.
+  breaker.check();
+
+  for (let attempt = 0; attempt < retryConfig.maxAttempts; attempt++) {
+    let result: { kind: 'error'; err: unknown } | { kind: 'response'; resp: Response };
+    try {
+      // CodeQL js/server-side-request-forgery — flagged because `input`
+      // is caller-supplied. Suppressed: every concrete caller passes
+      // either a hardcoded URL constant (UNDERSTAND_QUICKLY_DISPATCH_URL,
+      // OpenRouter base URL) or a value derived from configuration
+      // (env vars, saved settings, the local backend URL). User-input
+      // request fields (e.g. PR title, repo name) never flow into
+      // `input`. Validating URL shape here would push false-positive
+      // rejection onto every caller — wrong layer for the check.
+      // lgtm[js/server-side-request-forgery]
+      // codeql[js/server-side-request-forgery]
+      const resp = await fetchImpl(input, init);
+      result = { kind: 'response', resp };
+    } catch (err) {
+      result = { kind: 'error', err };
+    }
+
+    const outcome = classifyOutcome(result, now);
+
+    switch (outcome.kind) {
+      case 'success':
+        breaker.recordSuccess();
+        return outcome.resp;
+
+      case 'terminal-client':
+        // 4xx: do not count as breaker failure (the server is healthy
+        // and rejecting our request — auth, scope, or routing). But
+        // also do NOT call recordSuccess: a 401 sandwiched between
+        // 5xx responses would otherwise erase the running outage
+        // signal. The breaker's neutral path leaves state untouched.
+        breaker.recordNeutral();
+        return outcome.resp;
+
+      case 'terminal-network':
+        // Either `AbortSignal.timeout()` fired locally OR an external
+        // caller cancelled the request via AbortController. The server
+        // never had a chance to answer; this reflects the user's
+        // network or an explicit cancel, not registry health. Don't
+        // punish the breaker AND don't reset its outage signal.
+        breaker.recordNeutral();
+        throw outcome.err;
+
+      case 'retryable-status':
+        if (attempt + 1 >= retryConfig.maxAttempts) {
+          breaker.recordFailure();
+          throw new ResilientFetchExhaustedError(outcome.resp);
+        }
+        await sleep(
+          computeBackoffMs(
+            attempt,
+            retryConfig.baseDelayMs,
+            retryConfig.capDelayMs,
+            outcome.afterMs,
+            random,
+          ),
+        );
+        break;
+
+      case 'retryable-network':
+        if (attempt + 1 >= retryConfig.maxAttempts) {
+          breaker.recordFailure();
+          throw outcome.err;
+        }
+        await sleep(
+          computeBackoffMs(
+            attempt,
+            retryConfig.baseDelayMs,
+            retryConfig.capDelayMs,
+            undefined,
+            random,
+          ),
+        );
+        break;
+
+      default: {
+        // Exhaustiveness guard. If a sixth `Outcome` kind is added in
+        // future, TypeScript will refuse to assign it to `never` and
+        // this line forces the maintainer to add an explicit arm
+        // rather than silently fall through to retry/no-retry behaviour.
+        const _exhaustive: never = outcome;
+        throw new Error(`resilientFetch: unhandled outcome ${JSON.stringify(_exhaustive)}`);
+      }
+    }
+  }
+
+  // Unreachable: every iteration of the loop either returns (success
+  // / terminal-client) or throws (terminal-network / retry exhaustion).
+  // The throw is here purely so TypeScript's control-flow analysis sees
+  // the function never falls off the end without producing `Promise<Response>`.
+  /* c8 ignore next 2 */
+  throw new Error('resilientFetch: retry loop terminated unexpectedly');
+}

gitnexus-shared/src/integrations/retry.ts

@@ -0,0 +1,105 @@
+/**
+ * Bounded retry helper with full-jitter exponential backoff.
+ *
+ * Runtime-agnostic: depends only on `setTimeout`, `Math.random`, and the
+ * Promise machinery — no Node-only imports. Safe to consume from CLI,
+ * server, or browser callers.
+ *
+ * Pattern reference: gitnexus/src/core/embeddings/http-client.ts. This
+ * helper is the upgraded form: classification is caller-supplied (so
+ * 4xx-vs-5xx-vs-timeout decisions live with the protocol that knows
+ * them), backoff is exponential with full jitter, and an optional
+ * `afterMs` lets callers honor `Retry-After` headers.
+ */
+
+export interface RetryOptions {
+  /** Initial delay before the first retry attempt, in milliseconds. */
+  baseDelayMs: number;
+  /** Upper bound on any single delay, in milliseconds. */
+  capDelayMs: number;
+  /** Total attempts including the first call. Must be >= 1. */
+  maxAttempts: number;
+  /**
+   * Decide whether to retry after a thrown error.
+   * Return `{retry:false}` to terminate immediately and rethrow.
+   * Return `{retry:true}` to retry with exponential-backoff jitter.
+   * Return `{retry:true, afterMs}` to wait at least `afterMs` (still
+   * subject to `capDelayMs`) — used by callers parsing `Retry-After`.
+   */
+  isRetryable: (err: unknown, attempt: number) => RetryDecision;
+  /** Sleep override — defaults to `setTimeout`. Tests inject fake timers. */
+  sleep?: (ms: number) => Promise<void>;
+  /** Random override — defaults to `Math.random`. Tests inject seeded values. */
+  random?: () => number;
+}
+
+export type RetryDecision = { retry: false } | { retry: true; afterMs?: number };
+
+const defaultSleep = (ms: number): Promise<void> =>
+  new Promise((resolve) => setTimeout(resolve, ms));
+
+/**
+ * Compute the delay before the next retry attempt.
+ *
+ * - When the caller specifies `afterMs` (e.g., from `Retry-After`), use
+ *   `min(afterMs, capDelayMs)` so a misbehaving server can't pin the
+ *   client for an arbitrarily long wait.
+ * - Otherwise compute full-jitter exponential backoff:
+ *   `random() * min(cap, base * 2^attempt)`. Full jitter (rather than
+ *   "equal jitter") avoids retry-storm thundering herd, per AWS
+ *   guidance on backoff strategies.
+ */
+export function computeBackoffMs(
+  attempt: number,
+  baseDelayMs: number,
+  capDelayMs: number,
+  afterMs: number | undefined,
+  random: () => number,
+): number {
+  if (afterMs !== undefined) {
+    return Math.min(Math.max(0, afterMs), capDelayMs);
+  }
+  const exponential = baseDelayMs * Math.pow(2, attempt);
+  const upper = Math.min(capDelayMs, exponential);
+  return Math.floor(random() * upper);
+}
+
+/**
+ * Execute `fn` with bounded retries.
+ *
+ * The classification of "retryable" is the caller's responsibility — see
+ * `resilient-fetch.ts` for the GitHub-dispatch-specific rules. This
+ * helper is the mechanical retry loop only.
+ */
+export async function withRetry<T>(
+  fn: (attempt: number) => Promise<T>,
+  opts: RetryOptions,
+): Promise<T> {
+  if (opts.maxAttempts < 1) {
+    throw new Error(`withRetry: maxAttempts must be >= 1, got ${opts.maxAttempts}`);
+  }
+  const sleep = opts.sleep ?? defaultSleep;
+  const random = opts.random ?? Math.random;
+
+  let lastError: unknown;
+  for (let attempt = 0; attempt < opts.maxAttempts; attempt++) {
+    try {
+      return await fn(attempt);
+    } catch (err) {
+      lastError = err;
+      const decision = opts.isRetryable(err, attempt);
+      if (!decision.retry) throw err;
+      // Don't sleep after the final attempt.
+      if (attempt + 1 >= opts.maxAttempts) break;
+      const delayMs = computeBackoffMs(
+        attempt,
+        opts.baseDelayMs,
+        opts.capDelayMs,
+        decision.afterMs,
+        random,
+      );
+      if (delayMs > 0) await sleep(delayMs);
+    }
+  }
+  throw lastError;
+}

gitnexus-shared/src/integrations/understand-quickly.ts

@@ -0,0 +1,151 @@
+/**
+ * Understand-Quickly registry integration helpers.
+ *
+ * Pure, runtime-agnostic logic for opting in to publishing a GitNexus
+ * index to the [`looptech-ai/understand-quickly`](https://github.com/looptech-ai/understand-quickly)
+ * registry. Lives in `gitnexus-shared` so both the Node CLI and any
+ * future browser-side surface can construct identical dispatch payloads.
+ *
+ * Network I/O lives in the CLI command (`gitnexus/src/cli/publish.ts`)
+ * to keep this module free of Node-only imports — see the comment at
+ * the top of `gitnexus-shared/src/graph/types.ts`.
+ *
+ * The protocol contract (single dispatch event, no graph upload) is
+ * documented at:
+ *   https://github.com/looptech-ai/understand-quickly/blob/main/docs/integrations/protocol.md
+ */
+
+/**
+ * URL of the registry repo's repository_dispatch endpoint. Hardcoded
+ * because the registry is the canonical home for this integration —
+ * users who want a private registry can fork and patch.
+ */
+export const UNDERSTAND_QUICKLY_DISPATCH_URL =
+  'https://api.github.com/repos/looptech-ai/understand-quickly/dispatches';
+
+/**
+ * Event type the registry's sync workflow listens for.
+ * See `looptech-ai/understand-quickly/.github/workflows/sync.yml`.
+ */
+export const UNDERSTAND_QUICKLY_EVENT_TYPE = 'sync-entry';
+
+/** Environment variable that gates the dispatch. */
+export const UNDERSTAND_QUICKLY_TOKEN_ENV = 'UNDERSTAND_QUICKLY_TOKEN';
+
+export interface UqDispatchPayload {
+  event_type: typeof UNDERSTAND_QUICKLY_EVENT_TYPE;
+  client_payload: {
+    /** `<owner>/<repo>` shape — must match the registered entry. */
+    id: string;
+  };
+}
+
+/**
+ * Build the JSON body for the `repository_dispatch` ping. Pure — no
+ * env reads, no network. Validates that `id` looks like `owner/repo`
+ * (one slash, no whitespace, both halves non-empty) so a misconfigured
+ * caller fails loudly before the round-trip.
+ */
+export function buildUqDispatchPayload(id: string): UqDispatchPayload {
+  if (!isValidOwnerRepo(id)) {
+    throw new Error(
+      `[understand-quickly] expected id of the form "owner/repo", got "${id}". ` +
+        `The registry uses this string to look up your entry in registry.json — ` +
+        `it must match the GitHub owner/repo of the source code, not a local path.`,
+    );
+  }
+  return {
+    event_type: UNDERSTAND_QUICKLY_EVENT_TYPE,
+    client_payload: { id },
+  };
+}
+
+/**
+ * `owner/repo` validation. Conservative on purpose: GitHub's actual
+ * naming rules are looser, but we want to catch local paths
+ * (`/Users/...`), bare slugs (`my-repo`), and accidental whitespace.
+ *
+ * Matches GitHub's published slug rules:
+ *   owner: starts with alnum, then alnum/hyphen only, must end with
+ *          alnum (no trailing hyphen — GitHub rejects this at account
+ *          creation, so a `my-org-/repo` input would otherwise pass us
+ *          and 422 from GitHub). No underscore, no dot. Length cap 39.
+ *   repo:  any of alnum/dot/hyphen/underscore. Length cap 100.
+ */
+export function isValidOwnerRepo(id: string): boolean {
+  return /^[A-Za-z0-9](?:[A-Za-z0-9-]{0,37}[A-Za-z0-9])?\/[A-Za-z0-9._-]{1,100}$/.test(id);
+}
+
+/**
+ * Strip a single trailing `.git` (case-insensitive) and any trailing
+ * slashes from a URL-ish string. Bounded linear: each character is
+ * visited at most twice, no backtracking.
+ *
+ * Replaces `s.replace(/\.git\/*$/i, '').replace(/\/+$/, '')` which
+ * CodeQL's polynomial-regex check (codeql/js/polynomial-redos) flags as
+ * a worst-case O(n²) on adversarial input like "////.../x".
+ */
+export function stripGitSuffix(input: string): string {
+  let end = input.length;
+  // Trim trailing '/'.
+  while (end > 0 && input.charCodeAt(end - 1) === 0x2f) end--;
+  // Drop one trailing '.git' (case-insensitive).
+  if (end >= 4) {
+    const tail = input.slice(end - 4, end).toLowerCase();
+    if (tail === '.git') end -= 4;
+  }
+  // Trim trailing '/' that may have sat between '.git' and the rest.
+  while (end > 0 && input.charCodeAt(end - 1) === 0x2f) end--;
+  return input.slice(0, end);
+}
+
+/**
+ * Parse `owner/repo` out of a git remote URL. Mirrors the heuristic in
+ * `gitnexus/src/storage/git.ts:parseRepoNameFromUrl` but keeps both
+ * halves so we can build a registry id. Returns `null` on shapes we
+ * don't recognise.
+ *
+ * Examples:
+ *   git@github.com:looptech-ai/understand-quickly.git
+ *   https://github.com/looptech-ai/understand-quickly
+ *   ssh://git@github.com/looptech-ai/understand-quickly.git
+ */
+export function parseOwnerRepoFromRemote(url: string | null | undefined): string | null {
+  if (!url) return null;
+  const trimmed = url.trim();
+  if (!trimmed) return null;
+  // Strip a trailing `.git` (case-insensitive) and any trailing slashes
+  // so https://h/o/r and https://h/o/r.git collapse to the same id.
+  // Bounded-linear helper avoids the polynomial-regex CodeQL alert.
+  const stripped = stripGitSuffix(trimmed);
+
+  // SCP-form SSH (`git@host:owner/repo`). Capture host so we can reject
+  // non-GitHub remotes — a GitLab origin like
+  // `https://gitlab.example.com/group/sub/project.git` would otherwise
+  // silently dispatch the wrong id (LOW 9).
+  const ssh = stripped.match(/^[^@]+@([^:]+):([^/]+)\/([^/]+)$/);
+  if (ssh) {
+    const host = ssh[1].toLowerCase();
+    if (host !== 'github.com' && host !== 'www.github.com') return null;
+    return `${ssh[2]}/${ssh[3]}`;
+  }
+
+  // URL forms (https://, ssh://, git://, file://) — last two path segments.
+  const url2 = stripped.match(/^[a-zA-Z][a-zA-Z0-9+.-]*:\/\/([^/]+)\/(.+)$/);
+  if (url2) {
+    // Strip optional `userinfo@` (e.g. `ssh://git@github.com/...`).
+    const authority = url2[1];
+    const atIdx = authority.lastIndexOf('@');
+    const hostAndPort = atIdx >= 0 ? authority.slice(atIdx + 1) : authority;
+    // Strip `:port` suffix if present.
+    const colonIdx = hostAndPort.indexOf(':');
+    const host = (colonIdx >= 0 ? hostAndPort.slice(0, colonIdx) : hostAndPort).toLowerCase();
+    if (host !== 'github.com' && host !== 'www.github.com') return null;
+    const segments = url2[2].split('/').filter(Boolean);
+    if (segments.length >= 2) {
+      const [owner, repo] = segments.slice(-2);
+      return `${owner}/${repo}`;
+    }
+  }
+  return null;
+}

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

@@ -40,11 +40,27 @@ export interface MethodDispatchIndex {
   readonly mroByOwnerDefId: ReadonlyMap<DefId, readonly DefId[]>;
   /** Interfaces / traits → classes that implement them. */
   readonly implsByInterfaceDefId: ReadonlyMap<DefId, readonly DefId[]>;
+  /**
+   * Optional parallel MRO view that EXCLUDES mixin-like augmentation
+   * (e.g., PHP traits). Populated only when the input supplies
+   * `computeExtendsOnlyMro`. Used by the super-branch dispatch in
+   * `receiver-bound-calls` so that `parent::method()` walks the
+   * inheritance chain only, not the trait-augmented one. Undefined for
+   * languages without mixin-like semantics — callers should fall back
+   * to `mroFor` when this is missing.
+   */
+  readonly extendsOnlyMroByOwnerDefId?: ReadonlyMap<DefId, readonly DefId[]>;
 
   /** `mroByOwnerDefId.get`, with an empty frozen array on miss. */
   mroFor(ownerDefId: DefId): readonly DefId[];
   /** `implsByInterfaceDefId.get`, with an empty frozen array on miss. */
   implementorsOf(interfaceDefId: DefId): readonly DefId[];
+  /**
+   * `extendsOnlyMroByOwnerDefId.get`, with an empty frozen array on miss.
+   * Undefined when `extendsOnlyMroByOwnerDefId` was not populated; callers
+   * should treat this as equivalent to `mroFor` for non-mixin languages.
+   */
+  readonly extendsOnlyMroFor?: (ownerDefId: DefId) => readonly DefId[];
 }
 
 export interface MethodDispatchInput {
@@ -81,12 +97,25 @@ export interface MethodDispatchInput {
    * write-wins policy and fires at most once per unique owner.
    */
   readonly implementsOf: (ownerDefId: DefId) => readonly DefId[];
+  /**
+   * Optional: return the EXTENDS-only ancestor chain for `ownerDefId`,
+   * excluding the owner itself AND any mixin-like augmentation (e.g.,
+   * PHP traits). Languages without mixin semantics leave this undefined
+   * and the index's `extendsOnlyMroByOwnerDefId` stays unpopulated.
+   *
+   * Same contract as `computeMro`: pure, deterministic, `[]` on no parents.
+   * Called at most once per unique owner (first-write-wins).
+   */
+  readonly computeExtendsOnlyMro?: (ownerDefId: DefId) => readonly DefId[];
 }
 
 // ─── Builder ────────────────────────────────────────────────────────────────
 
 export function buildMethodDispatchIndex(input: MethodDispatchInput): MethodDispatchIndex {
   const mroByOwnerDefId = new Map<DefId, readonly DefId[]>();
+  const extendsOnlyByOwnerDefId = input.computeExtendsOnlyMro
+    ? new Map<DefId, readonly DefId[]>()
+    : undefined;
   const implsBuilding = new Map<DefId, DefId[]>();
   const implsSeen = new Map<DefId, Set<DefId>>();
 
@@ -97,6 +126,14 @@ export function buildMethodDispatchIndex(input: MethodDispatchInput): MethodDisp
       const chain = input.computeMro(ownerId);
       mroByOwnerDefId.set(ownerId, Object.freeze(chain.slice()));
     }
+    if (
+      input.computeExtendsOnlyMro !== undefined &&
+      extendsOnlyByOwnerDefId !== undefined &&
+      !extendsOnlyByOwnerDefId.has(ownerId)
+    ) {
+      const extOnly = input.computeExtendsOnlyMro(ownerId);
+      extendsOnlyByOwnerDefId.set(ownerId, Object.freeze(extOnly.slice()));
+    }
 
     for (const ifaceId of input.implementsOf(ownerId)) {
       let seen = implsSeen.get(ifaceId);
@@ -121,7 +158,7 @@ export function buildMethodDispatchIndex(input: MethodDispatchInput): MethodDisp
     implsByInterfaceDefId.set(ifaceId, Object.freeze(owners.slice()));
   }
 
-  return wrapIndex(mroByOwnerDefId, implsByInterfaceDefId);
+  return wrapIndex(mroByOwnerDefId, implsByInterfaceDefId, extendsOnlyByOwnerDefId);
 }
 
 // ─── Internal ───────────────────────────────────────────────────────────────
@@ -131,8 +168,9 @@ const EMPTY: readonly DefId[] = Object.freeze([]);
 function wrapIndex(
   mroByOwnerDefId: Map<DefId, readonly DefId[]>,
   implsByInterfaceDefId: Map<DefId, readonly DefId[]>,
+  extendsOnlyMroByOwnerDefId: Map<DefId, readonly DefId[]> | undefined,
 ): MethodDispatchIndex {
-  return {
+  const base: MethodDispatchIndex = {
     mroByOwnerDefId,
     implsByInterfaceDefId,
     mroFor(ownerDefId: DefId): readonly DefId[] {
@@ -142,4 +180,14 @@ function wrapIndex(
       return implsByInterfaceDefId.get(interfaceDefId) ?? EMPTY;
     },
   };
+  if (extendsOnlyMroByOwnerDefId !== undefined) {
+    return {
+      ...base,
+      extendsOnlyMroByOwnerDefId,
+      extendsOnlyMroFor(ownerDefId: DefId): readonly DefId[] {
+        return extendsOnlyMroByOwnerDefId.get(ownerDefId) ?? EMPTY;
+      },
+    };
+  }
+  return base;
 }

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

@@ -423,13 +423,30 @@ function applyArityFilter(
   }
 
   let anyCompatible = false;
+  let anyUnknown = false;
   for (const state of perCandidate.values()) {
     const verdict = arityFn(callsite, state.def);
     state.signals.arityVerdict = verdict;
     if (verdict === 'compatible') anyCompatible = true;
+    else if (verdict === 'unknown') anyUnknown = true;
   }
 
-  if (!anyCompatible) return;
+  // When ALL candidates are 'incompatible' (none compatible, none unknown),
+  // the call is genuinely arity-broken — drop every candidate so the
+  // registry returns no resolution. This matches the PHP variadic case
+  // f(int $req, ...$rest) called with zero args: every candidate definitively
+  // rejects, and emitting an edge to a definitively-rejected callable is
+  // a false positive. When some candidates are 'unknown' (missing metadata),
+  // keep the set so downstream evidence can break the tie — that's the
+  // original safety-fallback behavior.
+  if (!anyCompatible) {
+    if (!anyUnknown) {
+      for (const defId of perCandidate.keys()) {
+        perCandidate.delete(defId);
+      }
+    }
+    return;
+  }
 
   // Filter: when at least one compatible candidate exists, drop incompatibles.
   for (const [defId, state] of perCandidate) {

gitnexus-shared/src/test-helpers.ts

@@ -0,0 +1,13 @@
+/**
+ * Test-only helpers.
+ *
+ * Symbols here are reachable from `gitnexus-shared/test-helpers` so test
+ * suites can reset shared registries or exercise internal classifiers,
+ * but they are deliberately NOT re-exported from the main `gitnexus-shared`
+ * barrel. Production consumers should never import this module — calling
+ * `__resetBreakerRegistry__()` from a tool implementation would silently
+ * nuke every circuit breaker process-wide.
+ */
+
+export { __resetBreakerRegistry__ } from './integrations/circuit-breaker.js';
+export { classifyOutcome } from './integrations/resilient-fetch.js';

gitnexus-web/package-lock.json

@@ -8,7 +8,7 @@
       "name": "gitnexus",
       "version": "0.0.0",
       "dependencies": {
-        "@langchain/anthropic": "^1.3.28",
+        "@langchain/anthropic": "^1.3.29",
         "@langchain/core": "^1.1.44",
         "@langchain/google-genai": "^2.1.28",
         "@langchain/langgraph": "^1.2.9",
@@ -26,10 +26,10 @@
         "graphology-layout-forceatlas2": "^0.10.1",
         "graphology-layout-noverlap": "^0.4.2",
         "graphology-utils": "^2.3.0",
-        "langchain": "^1.3.4",
+        "langchain": "^1.3.5",
         "lru-cache": "^11.2.4",
-        "lucide-react": "^1.11.0",
-        "mermaid": "^11.14.0",
+        "lucide-react": "^1.14.0",
+        "mermaid": "^11.15.0",
         "mnemonist": "^0.39.0",
         "pandemonium": "^2.4.0",
         "react": "^19.2.5",
@@ -49,7 +49,7 @@
         "@testing-library/jest-dom": "^6.9.1",
         "@testing-library/react": "^16.3.2",
         "@testing-library/user-event": "^14.6.1",
-        "@types/dompurify": "^3.0.5",
+        "@types/dompurify": "^3.2.0",
         "@types/node": "^25.6.0",
         "@types/react": "^19.2.14",
         "@types/react-dom": "^19.2.3",
@@ -95,9 +95,9 @@
       }
     },
     "node_modules/@anthropic-ai/sdk": {
-      "version": "0.90.0",
-      "resolved": "https://registry.npmjs.org/@anthropic-ai/sdk/-/sdk-0.90.0.tgz",
-      "integrity": "sha512-MzZtPabJF1b0FTDl6Z6H5ljphPwACLGP13lu8MTiB8jXaW/YXlpOp+Po2cVou3MPM5+f5toyLnul9whKCy7fBg==",
+      "version": "0.91.1",
+      "resolved": "https://registry.npmjs.org/@anthropic-ai/sdk/-/sdk-0.91.1.tgz",
+      "integrity": "sha512-LAmu761tSN9r66ixvmciswUj/ZC+1Q4iAfpedTfSVLeswRwnY3n2Nb6Tsk+cLPP28aLOPWeMgIuTuCcMC6W/iw==",
       "license": "MIT",
       "dependencies": {
         "json-schema-to-ts": "^3.1.1"
@@ -528,41 +528,10 @@
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       "license": "MIT"
     },
-    "node_modules/@chevrotain/cst-dts-gen": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/cst-dts-gen/-/cst-dts-gen-12.0.0.tgz",
-      "integrity": "sha512-fSL4KXjTl7cDgf0B5Rip9Q05BOrYvkJV/RrBTE/bKDN096E4hN/ySpcBK5B24T76dlQ2i32Zc3PAE27jFnFrKg==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@chevrotain/gast": "12.0.0",
-        "@chevrotain/types": "12.0.0"
-      }
-    },
-    "node_modules/@chevrotain/gast": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/gast/-/gast-12.0.0.tgz",
-      "integrity": "sha512-1ne/m3XsIT8aEdrvT33so0GUC+wkctpUPK6zU9IlOyJLUbR0rg4G7ZiApiJbggpgPir9ERy3FRjT6T7lpgetnQ==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@chevrotain/types": "12.0.0"
-      }
-    },
-    "node_modules/@chevrotain/regexp-to-ast": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/regexp-to-ast/-/regexp-to-ast-12.0.0.tgz",
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-    },
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-      "resolved": "https://registry.npmjs.org/@chevrotain/types/-/types-12.0.0.tgz",
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-      "license": "Apache-2.0"
-    },
-    "node_modules/@chevrotain/utils": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/@chevrotain/utils/-/utils-12.0.0.tgz",
-      "integrity": "sha512-lB59uJoaGIfOOL9knQqQRfhl9g7x8/wqFkp13zTdkRu1huG9kg6IJs1O8hqj9rs6h7orGxHJUKb+mX3rPbWGhA==",
+      "version": "11.1.2",
+      "resolved": "https://registry.npmjs.org/@chevrotain/types/-/types-11.1.2.tgz",
+      "integrity": "sha512-U+HFai5+zmJCkK86QsaJtoITlboZHBqrVketcO2ROv865xfCMSFpELQoz1GkX5GzME8pTa+3kbKrZHQtI0gdbw==",
       "license": "Apache-2.0"
     },
     "node_modules/@cspotcode/source-map-support": {
@@ -1396,25 +1365,25 @@
       }
     },
     "node_modules/@langchain/anthropic": {
-      "version": "1.3.28",
-      "resolved": "https://registry.npmjs.org/@langchain/anthropic/-/anthropic-1.3.28.tgz",
-      "integrity": "sha512-gOF8oXJL8xDdYes2KXNI9vFm/9TldBBBHOjuCdt27kganVaQKzLvTw5kV6R4mjbnFagV5CWteNH7APLZYCpdwg==",
+      "version": "1.3.29",
+      "resolved": "https://registry.npmjs.org/@langchain/anthropic/-/anthropic-1.3.29.tgz",
+      "integrity": "sha512-ep1qBIcV07bajsg3fDqMd39rYwoRLOEK/6lk+MCxlm1YB5SRoKKJAZANrblQ/4RYhZJnxf95c6BSQu8VoNbVAQ==",
       "license": "MIT",
       "dependencies": {
-        "@anthropic-ai/sdk": "^0.90.0",
+        "@anthropic-ai/sdk": "^0.91.1",
         "zod": "^3.25.76 || ^4"
       },
       "engines": {
         "node": ">=20"
       },
       "peerDependencies": {
-        "@langchain/core": "^1.1.42"
+        "@langchain/core": "^1.1.45"
       }
     },
     "node_modules/@langchain/core": {
-      "version": "1.1.44",
-      "resolved": "https://registry.npmjs.org/@langchain/core/-/core-1.1.44.tgz",
-      "integrity": "sha512-RePW1IjGCHr9ua2vcby3aE8mOOz3EnwDZxMEGbNDT91kf14eqkJqxDXvaZFviGdcN9DTrxM5RPQNAHmwSm4tbg==",
+      "version": "1.1.45",
+      "resolved": "https://registry.npmjs.org/@langchain/core/-/core-1.1.45.tgz",
+      "integrity": "sha512-Y/wvuglLTMKJahkl4QD9dBIdF/z/CxZJWdTfHJF/q2jtlJtoFf6Mb5JpGxZfsi3mBY6NSG941FSLTcqhCKrhBA==",
       "license": "MIT",
       "dependencies": {
         "@cfworker/json-schema": "^4.0.2",
@@ -1679,12 +1648,12 @@
       }
     },
     "node_modules/@mermaid-js/parser": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/@mermaid-js/parser/-/parser-1.1.0.tgz",
-      "integrity": "sha512-gxK9ZX2+Fex5zu8LhRQoMeMPEHbc73UKZ0FQ54YrQtUxE1VVhMwzeNtKRPAu5aXks4FasbMe4xB4bWrmq6Jlxw==",
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/@mermaid-js/parser/-/parser-1.1.1.tgz",
+      "integrity": "sha512-VuHdsYMK1bT6X2JbcAaWAhugTRvRBRyuZgd+c22swUeI9g/ntaxF7CY7dYarhZovofCbUNO0G7JesfmNtjYOCw==",
       "license": "MIT",
       "dependencies": {
-        "langium": "^4.0.0"
+        "@chevrotain/types": "~11.1.1"
       }
     },
     "node_modules/@napi-rs/wasm-runtime": {
@@ -2800,13 +2769,14 @@
       "license": "MIT"
     },
     "node_modules/@types/dompurify": {
-      "version": "3.0.5",
-      "resolved": "https://registry.npmjs.org/@types/dompurify/-/dompurify-3.0.5.tgz",
-      "integrity": "sha512-1Wg0g3BtQF7sSb27fJQAKck1HECM6zV1EB66j8JH9i3LCjYabJa0FSdiSgsD5K/RbrsR0SiraKacLB+T8ZVYAg==",
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/@types/dompurify/-/dompurify-3.2.0.tgz",
+      "integrity": "sha512-Fgg31wv9QbLDA0SpTOXO3MaxySc4DKGLi8sna4/Utjo4r3ZRPdCt4UQee8BWr+Q5z21yifghREPJGYaEOEIACg==",
+      "deprecated": "This is a stub types definition. dompurify provides its own type definitions, so you do not need this installed.",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@types/trusted-types": "*"
+        "dompurify": "*"
       }
     },
     "node_modules/@types/estree": {
@@ -2909,8 +2879,8 @@
       "version": "2.0.7",
       "resolved": "https://registry.npmjs.org/@types/trusted-types/-/trusted-types-2.0.7.tgz",
       "integrity": "sha512-ScaPdn1dQczgbl0QFTeTOmVHFULt394XJgOQNoyVhZ6r2vLnMLJfBPd53SB52T/3G36VI1/g2MZaX0cwDuXsfw==",
-      "devOptional": true,
-      "license": "MIT"
+      "license": "MIT",
+      "optional": true
     },
     "node_modules/@types/unist": {
       "version": "3.0.3",
@@ -3642,34 +3612,6 @@
         "url": "https://github.com/sponsors/wooorm"
       }
     },
-    "node_modules/chevrotain": {
-      "version": "12.0.0",
-      "resolved": "https://registry.npmjs.org/chevrotain/-/chevrotain-12.0.0.tgz",
-      "integrity": "sha512-csJvb+6kEiQaqo1woTdSAuOWdN0WTLIydkKrBnS+V5gZz0oqBrp4kQ35519QgK6TpBThiG3V1vNSHlIkv4AglQ==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@chevrotain/cst-dts-gen": "12.0.0",
-        "@chevrotain/gast": "12.0.0",
-        "@chevrotain/regexp-to-ast": "12.0.0",
-        "@chevrotain/types": "12.0.0",
-        "@chevrotain/utils": "12.0.0"
-      },
-      "engines": {
-        "node": ">=22.0.0"
-      }
-    },
-    "node_modules/chevrotain-allstar": {
-      "version": "0.4.1",
-      "resolved": "https://registry.npmjs.org/chevrotain-allstar/-/chevrotain-allstar-0.4.1.tgz",
-      "integrity": "sha512-PvVJm3oGqrveUVW2Vt/eZGeiAIsJszYweUcYwcskg9e+IubNYKKD+rHHem7A6XVO22eDAL+inxNIGAzZ/VIWlA==",
-      "license": "MIT",
-      "dependencies": {
-        "lodash-es": "^4.17.21"
-      },
-      "peerDependencies": {
-        "chevrotain": "^12.0.0"
-      }
-    },
     "node_modules/chownr": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/chownr/-/chownr-3.0.0.tgz",
@@ -4627,6 +4569,16 @@
         "node": ">= 0.4"
       }
     },
+    "node_modules/es-toolkit": {
+      "version": "1.46.1",
+      "resolved": "https://registry.npmjs.org/es-toolkit/-/es-toolkit-1.46.1.tgz",
+      "integrity": "sha512-5eNtXOs3tbfxXOj04tjjseeWkRWaoCjdEI+96DgwzZoe6c9juL49pXlzAFTI72aWC9Y8p7168g6XIKjh7k6pyQ==",
+      "license": "MIT",
+      "workspaces": [
+        "docs",
+        "benchmarks"
+      ]
+    },
     "node_modules/esbuild": {
       "version": "0.27.0",
       "resolved": "https://registry.npmjs.org/esbuild/-/esbuild-0.27.0.tgz",
@@ -5643,53 +5595,21 @@
       "integrity": "sha512-Ls993zuzfayK269Svk9hzpeGUKob/sIgZzyHYdjQoAdQetRKpOLj+k/QQQ/6Qi0Yz65mlROrfd+Ev+1+7dz9Kw=="
     },
     "node_modules/langchain": {
-      "version": "1.3.4",
-      "resolved": "https://registry.npmjs.org/langchain/-/langchain-1.3.4.tgz",
-      "integrity": "sha512-umrD+ZC6vr0Q0U1lC5PoIMMQqgnP+7QhaIdAXCeZiSX2GPVBiVR7Ed2ZR+3MPvz1yWrRtIm17wPaovkND+wOXg==",
+      "version": "1.3.5",
+      "resolved": "https://registry.npmjs.org/langchain/-/langchain-1.3.5.tgz",
+      "integrity": "sha512-QSB8TEo6G1tWupgNt1Osm8ylLLoOMq1lLw5NeijnIwRPI5BqdBjUn4/U8usbjEJJcQnbXSK2qTKgTx7zvblnBw==",
       "license": "MIT",
       "dependencies": {
         "@langchain/langgraph": "^1.2.9",
         "@langchain/langgraph-checkpoint": "^1.0.1",
         "langsmith": ">=0.5.0 <1.0.0",
-        "uuid": "^11.1.0",
         "zod": "^3.25.76 || ^4"
       },
       "engines": {
         "node": ">=20"
       },
       "peerDependencies": {
-        "@langchain/core": "^1.1.41"
-      }
-    },
-    "node_modules/langchain/node_modules/uuid": {
-      "version": "11.1.0",
-      "resolved": "https://registry.npmjs.org/uuid/-/uuid-11.1.0.tgz",
-      "integrity": "sha512-0/A9rDy9P7cJ+8w1c9WD9V//9Wj15Ce2MPz8Ri6032usz+NfePxx5AcN3bN+r6ZL6jEo066/yNYB3tn4pQEx+A==",
-      "funding": [
-        "https://github.com/sponsors/broofa",
-        "https://github.com/sponsors/ctavan"
-      ],
-      "license": "MIT",
-      "bin": {
-        "uuid": "dist/esm/bin/uuid"
-      }
-    },
-    "node_modules/langium": {
-      "version": "4.2.2",
-      "resolved": "https://registry.npmjs.org/langium/-/langium-4.2.2.tgz",
-      "integrity": "sha512-JUshTRAfHI4/MF9dH2WupvjSXyn8JBuUEWazB8ZVJUtXutT0doDlAv1XKbZ1Pb5sMexa8FF4CFBc0iiul7gbUQ==",
-      "license": "MIT",
-      "dependencies": {
-        "@chevrotain/regexp-to-ast": "~12.0.0",
-        "chevrotain": "~12.0.0",
-        "chevrotain-allstar": "~0.4.1",
-        "vscode-languageserver": "~9.0.1",
-        "vscode-languageserver-textdocument": "~1.0.11",
-        "vscode-uri": "~3.1.0"
-      },
-      "engines": {
-        "node": ">=20.10.0",
-        "npm": ">=10.2.3"
+        "@langchain/core": "^1.1.42"
       }
     },
     "node_modules/langsmith": {
@@ -6041,9 +5961,9 @@
       }
     },
     "node_modules/lucide-react": {
-      "version": "1.11.0",
-      "resolved": "https://registry.npmjs.org/lucide-react/-/lucide-react-1.11.0.tgz",
-      "integrity": "sha512-UOhjdztXCgdBReRcIhsvz2siIBogfv/lhJEIViCpLt924dO+GDms9T7DNoucI23s6kEPpe988m5N0D2ajnzb2g==",
+      "version": "1.14.0",
+      "resolved": "https://registry.npmjs.org/lucide-react/-/lucide-react-1.14.0.tgz",
+      "integrity": "sha512-+1mdWcfSJVUsaTIjN9zoezmUhfXo5l0vP7ekBMPo3jcS/aIkxHnXqAPsByszMZx/Y8oQBRJxJx5xg+RH3urzxA==",
       "license": "ISC",
       "peerDependencies": {
         "react": "^16.5.1 || ^17.0.0 || ^18.0.0 || ^19.0.0"
@@ -6435,14 +6355,14 @@
       }
     },
     "node_modules/mermaid": {
-      "version": "11.14.0",
-      "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-11.14.0.tgz",
-      "integrity": "sha512-GSGloRsBs+JINmmhl0JDwjpuezCsHB4WGI4NASHxL3fHo3o/BRXTxhDLKnln8/Q0lRFRyDdEjmk1/d5Sn1Xz8g==",
+      "version": "11.15.0",
+      "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-11.15.0.tgz",
+      "integrity": "sha512-pTMbcf3rWdtLiYGpmoTjHEpeY8seiy6sR+9nD7LOs8KfUbHE4lOUAprTRqRAcWSQ6MQpdX+YEsxShtGsINtPtw==",
       "license": "MIT",
       "dependencies": {
         "@braintree/sanitize-url": "^7.1.1",
         "@iconify/utils": "^3.0.2",
-        "@mermaid-js/parser": "^1.1.0",
+        "@mermaid-js/parser": "^1.1.1",
         "@types/d3": "^7.4.3",
         "@upsetjs/venn.js": "^2.0.0",
         "cytoscape": "^3.33.1",
@@ -6453,27 +6373,14 @@
         "dagre-d3-es": "7.0.14",
         "dayjs": "^1.11.19",
         "dompurify": "^3.3.1",
+        "es-toolkit": "^1.45.1",
         "katex": "^0.16.25",
         "khroma": "^2.1.0",
-        "lodash-es": "^4.17.23",
         "marked": "^16.3.0",
         "roughjs": "^4.6.6",
         "stylis": "^4.3.6",
         "ts-dedent": "^2.2.0",
-        "uuid": "^11.1.0"
-      }
-    },
-    "node_modules/mermaid/node_modules/uuid": {
-      "version": "11.1.0",
-      "resolved": "https://registry.npmjs.org/uuid/-/uuid-11.1.0.tgz",
-      "integrity": "sha512-0/A9rDy9P7cJ+8w1c9WD9V//9Wj15Ce2MPz8Ri6032usz+NfePxx5AcN3bN+r6ZL6jEo066/yNYB3tn4pQEx+A==",
-      "funding": [
-        "https://github.com/sponsors/broofa",
-        "https://github.com/sponsors/ctavan"
-      ],
-      "license": "MIT",
-      "bin": {
-        "uuid": "dist/esm/bin/uuid"
+        "uuid": "^11.1.0 || ^12 || ^13 || ^14.0.0"
       }
     },
     "node_modules/micromark": {
@@ -8888,55 +8795,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/vscode-jsonrpc": {
-      "version": "8.2.0",
-      "resolved": "https://registry.npmjs.org/vscode-jsonrpc/-/vscode-jsonrpc-8.2.0.tgz",
-      "integrity": "sha512-C+r0eKJUIfiDIfwJhria30+TYWPtuHJXHtI7J0YlOmKAo7ogxP20T0zxB7HZQIFhIyvoBPwWskjxrvAtfjyZfA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">=14.0.0"
-      }
-    },
-    "node_modules/vscode-languageserver": {
-      "version": "9.0.1",
-      "resolved": "https://registry.npmjs.org/vscode-languageserver/-/vscode-languageserver-9.0.1.tgz",
-      "integrity": "sha512-woByF3PDpkHFUreUa7Hos7+pUWdeWMXRd26+ZX2A8cFx6v/JPTtd4/uN0/jB6XQHYaOlHbio03NTHCqrgG5n7g==",
-      "license": "MIT",
-      "dependencies": {
-        "vscode-languageserver-protocol": "3.17.5"
-      },
-      "bin": {
-        "installServerIntoExtension": "bin/installServerIntoExtension"
-      }
-    },
-    "node_modules/vscode-languageserver-protocol": {
-      "version": "3.17.5",
-      "resolved": "https://registry.npmjs.org/vscode-languageserver-protocol/-/vscode-languageserver-protocol-3.17.5.tgz",
-      "integrity": "sha512-mb1bvRJN8SVznADSGWM9u/b07H7Ecg0I3OgXDuLdn307rl/J3A9YD6/eYOssqhecL27hK1IPZAsaqh00i/Jljg==",
-      "license": "MIT",
-      "dependencies": {
-        "vscode-jsonrpc": "8.2.0",
-        "vscode-languageserver-types": "3.17.5"
-      }
-    },
-    "node_modules/vscode-languageserver-textdocument": {
-      "version": "1.0.12",
-      "resolved": "https://registry.npmjs.org/vscode-languageserver-textdocument/-/vscode-languageserver-textdocument-1.0.12.tgz",
-      "integrity": "sha512-cxWNPesCnQCcMPeenjKKsOCKQZ/L6Tv19DTRIGuLWe32lyzWhihGVJ/rcckZXJxfdKCFvRLS3fpBIsV/ZGX4zA==",
-      "license": "MIT"
-    },
-    "node_modules/vscode-languageserver-types": {
-      "version": "3.17.5",
-      "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.17.5.tgz",
-      "integrity": "sha512-Ld1VelNuX9pdF39h2Hgaeb5hEZM2Z3jUrrMgWQAu82jMtZp7p3vJT3BzToKtZI7NgQssZje5o0zryOrhQvzQAg==",
-      "license": "MIT"
-    },
-    "node_modules/vscode-uri": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.1.0.tgz",
-      "integrity": "sha512-/BpdSx+yCQGnCvecbyXdxHDkuk55/G3xwnC0GqY4gmQ3j+A+g8kzzgB4Nk/SINjqn6+waqw3EgbVF2QKExkRxQ==",
-      "license": "MIT"
-    },
     "node_modules/w3c-xmlserializer": {
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-5.0.0.tgz",

gitnexus-web/package.json

@@ -19,7 +19,7 @@
   },
   "dependencies": {
     "gitnexus-shared": "file:../gitnexus-shared",
-    "@langchain/anthropic": "^1.3.28",
+    "@langchain/anthropic": "^1.3.29",
     "@langchain/core": "^1.1.44",
     "@langchain/google-genai": "^2.1.28",
     "@langchain/langgraph": "^1.2.9",
@@ -36,10 +36,10 @@
     "graphology-layout-forceatlas2": "^0.10.1",
     "graphology-layout-noverlap": "^0.4.2",
     "graphology-utils": "^2.3.0",
-    "langchain": "^1.3.4",
+    "langchain": "^1.3.5",
     "lru-cache": "^11.2.4",
-    "lucide-react": "^1.11.0",
-    "mermaid": "^11.14.0",
+    "lucide-react": "^1.14.0",
+    "mermaid": "^11.15.0",
     "mnemonist": "^0.39.0",
     "pandemonium": "^2.4.0",
     "react": "^19.2.5",
@@ -59,7 +59,7 @@
     "@testing-library/jest-dom": "^6.9.1",
     "@testing-library/react": "^16.3.2",
     "@testing-library/user-event": "^14.6.1",
-    "@types/dompurify": "^3.0.5",
+    "@types/dompurify": "^3.2.0",
     "@types/node": "^25.6.0",
     "@types/react": "^19.2.14",
     "@types/react-dom": "^19.2.3",

gitnexus-web/src/core/llm/settings-service.ts

@@ -20,6 +20,7 @@ import {
   ProviderConfig,
 } from './types';
 import { DEFAULT_OPENROUTER_BASE_URL, DEFAULT_OLLAMA_BASE_URL } from '../../config/ui-constants';
+import { resilientFetch } from 'gitnexus-shared';
 
 const STORAGE_KEY = 'gitnexus-llm-settings';
 
@@ -407,7 +408,10 @@ export const getAvailableModels = (provider: LLMProvider): string[] => {
  */
 export const fetchOpenRouterModels = async (): Promise<Array<{ id: string; name: string }>> => {
   try {
-    const response = await fetch(`${DEFAULT_OPENROUTER_BASE_URL}/models`);
+    const response = await resilientFetch(`${DEFAULT_OPENROUTER_BASE_URL}/models`, undefined, {
+      breakerKey: 'openrouter-models',
+      retry: { maxAttempts: 2, baseDelayMs: 500, capDelayMs: 2_000 },
+    });
     if (!response.ok) throw new Error('Failed to fetch models');
     const data = await response.json();
     return data.data.map((model: any) => ({

gitnexus-web/src/services/backend-client.ts

@@ -7,6 +7,7 @@
  */
 
 import type { GraphNode, GraphRelationship } from 'gitnexus-shared';
+import { CircuitOpenError, ResilientFetchExhaustedError, resilientFetch } from 'gitnexus-shared';
 
 // ── Types ──────────────────────────────────────────────────────────────────
 
@@ -204,8 +205,32 @@ export function streamSSE<T = unknown>(url: string, handlers: SSEHandlers<T>): A
 
 let _backendUrl = 'http://localhost:4747';
 
+/**
+ * Validate that a backend URL is a safe http:// or https:// origin before
+ * storing it as the fetch target base (CodeQL js/client-side-request-forgery).
+ *
+ * Throws if the URL uses a non-HTTP scheme (e.g. javascript:, data:, file://).
+ * All other well-formed http/https URLs are accepted — the client intentionally
+ * supports connecting to remote GitNexus servers, not just localhost.
+ */
+export function validateBackendUrl(url: string): void {
+  let parsed: URL;
+  try {
+    parsed = new URL(url);
+  } catch {
+    // Do not echo raw input — it may contain credentials.
+    throw new Error('Invalid backend URL: must be a well-formed http:// or https:// URL');
+  }
+  if (parsed.protocol !== 'http:' && parsed.protocol !== 'https:') {
+    // Use parsed.protocol only (scheme), not the full URL, to avoid leaking credentials.
+    throw new Error(`Backend URL must use http:// or https:// (got ${parsed.protocol})`);
+  }
+}
+
 export const setBackendUrl = (url: string): void => {
-  _backendUrl = url.replace(/\/$/, '');
+  const trimmed = url.replace(/\/$/, '');
+  validateBackendUrl(trimmed);
+  _backendUrl = trimmed;
 };
 
 export const getBackendUrl = (): string => _backendUrl;
@@ -237,29 +262,91 @@ export function normalizeServerUrl(input: string): string {
 const DEFAULT_TIMEOUT_MS = 30_000;
 const PROBE_TIMEOUT_MS = 2_000;
 
+/** Idempotent HTTP methods. Other verbs (POST, PATCH, PUT, DELETE) get
+ *  a single-attempt retry budget by default to avoid duplicate side
+ *  effects on retry — a POST that 5xx'd may have already executed
+ *  server-side. Callers that have idempotency keys or otherwise know
+ *  their mutation is safe to retry can opt in via `forceRetry`. */
+const IDEMPOTENT_METHODS = new Set(['GET', 'HEAD', 'OPTIONS']);
+
 const fetchWithTimeout = async (
   url: string,
   init: RequestInit = {},
   timeoutMs: number = DEFAULT_TIMEOUT_MS,
+  /**
+   * Force a retry budget on non-idempotent methods. Default false.
+   * Pass true only when the endpoint is known-idempotent (e.g. DELETE
+   * of a known-deleted resource — second call is a 404 / no-op) AND
+   * the duplicate-side-effect window is acceptable.
+   */
+  forceRetry = false,
 ): Promise<Response> => {
-  const controller = new AbortController();
-  // Merge external signal if provided
+  // Merge the external caller signal (if any) with an
+  // `AbortSignal.timeout()` so a timer-fired abort produces a
+  // `DOMException` with `name === 'TimeoutError'` — which
+  // `resilientFetch` correctly classifies as terminal-network (no
+  // retry, no breaker hit). A manual `AbortController.abort()` would
+  // produce `name === 'AbortError'` and route through the
+  // retryable-network branch, which mis-penalizes the breaker for
+  // user-side network slowness.
+  const timeoutSignal = AbortSignal.timeout(timeoutMs);
   const externalSignal = init.signal;
-  if (externalSignal) {
-    externalSignal.addEventListener('abort', () => controller.abort());
+  const signal = externalSignal ? AbortSignal.any([timeoutSignal, externalSignal]) : timeoutSignal;
+
+  const method = (init.method ?? 'GET').toUpperCase();
+  const isIdempotent = IDEMPOTENT_METHODS.has(method);
+  const maxAttempts = isIdempotent || forceRetry ? 2 : 1;
+
+  // Key the breaker by the current backend origin so switching backend
+  // URLs (e.g. recovering from a flapping local server by pointing at
+  // a different host) gives the new origin a fresh breaker state. A
+  // single shared `'web-backend'` key would otherwise leave a user
+  // locked out for the full cooldown after one bad host trips the
+  // circuit. The malformed-URL fallback is defensive — `setBackendUrl`
+  // normalizes input, so this branch shouldn't fire in practice.
+  let breakerKey: string;
+  try {
+    breakerKey = `web-backend:${new URL(_backendUrl).origin}`;
+  } catch {
+    breakerKey = 'web-backend:invalid';
   }
-  const timer = setTimeout(() => controller.abort(), timeoutMs);
 
   try {
-    const response = await fetch(url, { ...init, signal: controller.signal });
+    // Bounded retries + 5xx/429 handling are delegated to resilientFetch.
+    // Method-aware budget: idempotent verbs retry once on transient
+    // backend failures; mutations (POST/PATCH/PUT/DELETE) default to
+    // single-attempt to avoid duplicate side effects.
+    const response = await resilientFetch(
+      url,
+      { ...init, signal },
+      {
+        breakerKey,
+        retry: { maxAttempts, baseDelayMs: 250, capDelayMs: 1500 },
+      },
+    );
     return response;
   } catch (error: unknown) {
-    if (error instanceof DOMException && error.name === 'AbortError') {
-      if (externalSignal?.aborted) {
-        throw new BackendError('Request aborted', 0, 'network');
-      }
+    if (error instanceof CircuitOpenError) {
+      throw new BackendError(
+        `GitNexus backend at ${_backendUrl} is unhealthy; retry in ${Math.ceil(error.retryAfterMs / 1000)}s`,
+        0,
+        'network',
+      );
+    }
+    if (error instanceof ResilientFetchExhaustedError) {
+      // Fall through to caller — surface the raw response so assertOk
+      // can craft the BackendError with the right code.
+      return error.response;
+    }
+    if (error instanceof DOMException && error.name === 'TimeoutError') {
       throw new BackendError(`Request to ${url} timed out after ${timeoutMs}ms`, 0, 'timeout');
     }
+    if (error instanceof DOMException && error.name === 'AbortError') {
+      // External caller-driven cancellation — `timeoutSignal` would
+      // have surfaced as TimeoutError above, so this branch covers
+      // only the externally-aborted case.
+      throw new BackendError('Request aborted', 0, 'network');
+    }
     if (error instanceof TypeError) {
       throw new BackendError(
         `Network error reaching GitNexus backend at ${_backendUrl}: ${error.message}`,
@@ -268,8 +355,6 @@ const fetchWithTimeout = async (
       );
     }
     throw error;
-  } finally {
-    clearTimeout(timer);
   }
 };
 

gitnexus-web/test/unit/backend-client-retry.test.ts

@@ -0,0 +1,110 @@
+/**
+ * Method-aware retry budget + timeout-as-TimeoutError verification for
+ * backend-client's `fetchWithTimeout`.
+ *
+ * Closes review findings on PR #1448:
+ *   - Non-idempotent POST/DELETE must NOT be retried by default —
+ *     a 5xx on `startAnalyze` could otherwise start a duplicate job.
+ *   - Timer-fired timeout must surface as `DOMException(name='TimeoutError')`,
+ *     not `AbortError`, so resilientFetch routes it through the
+ *     terminal-network branch (no retry, no breaker hit).
+ */
+
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import { getBreaker } from 'gitnexus-shared';
+import { __resetBreakerRegistry__ } from 'gitnexus-shared/test-helpers';
+import { fetchRepos, setBackendUrl, startAnalyze } from '../../src/services/backend-client';
+
+const BASE = 'http://localhost:4747';
+
+describe('backend-client retry budget (method-aware)', () => {
+  beforeEach(() => {
+    __resetBreakerRegistry__();
+    setBackendUrl(BASE);
+  });
+
+  afterEach(() => {
+    vi.unstubAllGlobals();
+  });
+
+  it('GET retries once on transient 503 (idempotent verb)', async () => {
+    let n = 0;
+    const fetchMock = vi.fn(async () => {
+      n += 1;
+      if (n === 1) return new Response('boom', { status: 503 });
+      return new Response('[]', {
+        status: 200,
+        headers: { 'Content-Type': 'application/json' },
+      });
+    });
+    vi.stubGlobal('fetch', fetchMock);
+
+    const repos = await fetchRepos();
+    expect(repos).toEqual([]);
+    // 1 retry budget on idempotent GET → 2 total fetch calls.
+    expect(fetchMock).toHaveBeenCalledTimes(2);
+  });
+
+  it('POST does NOT retry on 503 by default (non-idempotent verb)', async () => {
+    const fetchMock = vi.fn(async () => new Response('boom', { status: 503 }));
+    vi.stubGlobal('fetch', fetchMock);
+
+    await expect(startAnalyze({ path: '/tmp/repo' })).rejects.toBeTruthy();
+    // Single attempt — never duplicates a job-start POST.
+    expect(fetchMock).toHaveBeenCalledTimes(1);
+  });
+
+  it('switching backend URL after a circuit opens reaches a fresh breaker (U3)', async () => {
+    // Pre-open the breaker for host-A by directly recording 3 failures.
+    setBackendUrl('http://host-a.test:4747');
+    const aKey = 'web-backend:http://host-a.test:4747';
+    const breakerA = getBreaker(aKey);
+    breakerA.recordFailure();
+    breakerA.recordFailure();
+    breakerA.recordFailure();
+    expect(breakerA.getState()).toBe('open');
+
+    // Switch to host-B and make a request — must succeed against the
+    // new origin without tripping the host-A circuit. Under the old
+    // single-key behaviour the call would throw CircuitOpenError.
+    setBackendUrl('http://host-b.test:4747');
+    const fetchMock = vi.fn(
+      async () =>
+        new Response('[]', {
+          status: 200,
+          headers: { 'Content-Type': 'application/json' },
+        }),
+    );
+    vi.stubGlobal('fetch', fetchMock);
+
+    const repos = await fetchRepos();
+    expect(repos).toEqual([]);
+    expect(fetchMock).toHaveBeenCalledTimes(1);
+
+    // Host-A's breaker is still open in cooldown.
+    expect(breakerA.getState()).toBe('open');
+    // Host-B has its own (fresh) breaker.
+    const bKey = 'web-backend:http://host-b.test:4747';
+    expect(getBreaker(bKey).getState()).toBe('closed');
+    expect(getBreaker(bKey).getConsecutiveFailures()).toBe(0);
+  });
+
+  it('breaker not incremented when timeout fires (TimeoutError, not AbortError)', async () => {
+    // Reject directly with a TimeoutError DOMException, mimicking what
+    // `fetch` produces when its `AbortSignal.timeout()`-wired signal
+    // fires. The real-fetch path goes signal.reason → reject(reason);
+    // we shortcut that here so the test doesn't have to wait the
+    // 30-second default timeout.
+    const fetchMock = vi.fn(async () => {
+      throw new DOMException('aborted by timeout', 'TimeoutError');
+    });
+    vi.stubGlobal('fetch', fetchMock);
+
+    await expect(fetchRepos()).rejects.toMatchObject({ code: 'timeout' });
+
+    // The breaker must not have been penalized for a local timeout.
+    expect(getBreaker(`web-backend:${BASE}`).getConsecutiveFailures()).toBe(0);
+    // Timeout is terminal — no retry attempted.
+    expect(fetchMock).toHaveBeenCalledTimes(1);
+  });
+});

gitnexus-web/test/unit/server-connection.test.ts

@@ -1,5 +1,11 @@
 import { afterEach, describe, expect, it, vi } from 'vitest';
-import { fetchGraph, normalizeServerUrl, setBackendUrl } from '../../src/services/backend-client';
+import {
+  fetchGraph,
+  getBackendUrl,
+  normalizeServerUrl,
+  setBackendUrl,
+  validateBackendUrl,
+} from '../../src/services/backend-client';
 
 describe('normalizeServerUrl', () => {
   it('adds http:// to localhost', () => {
@@ -165,3 +171,61 @@ describe('fetchGraph', () => {
     });
   });
 });
+
+describe('validateBackendUrl', () => {
+  it('allows http:// URLs', () => {
+    expect(() => validateBackendUrl('http://localhost:4747')).not.toThrow();
+    expect(() => validateBackendUrl('http://127.0.0.1:4747')).not.toThrow();
+  });
+
+  it('allows https:// URLs', () => {
+    expect(() => validateBackendUrl('https://gitnexus.example.com')).not.toThrow();
+    expect(() => validateBackendUrl('https://my-server.internal:4747')).not.toThrow();
+  });
+
+  it('rejects non-http schemes', () => {
+    expect(() => validateBackendUrl('javascript:alert(1)')).toThrow('must use http:// or https://');
+    expect(() => validateBackendUrl('file:///etc/passwd')).toThrow('must use http:// or https://');
+    expect(() => validateBackendUrl('data:text/plain,evil')).toThrow(
+      'must use http:// or https://',
+    );
+  });
+
+  it('rejects malformed URLs', () => {
+    expect(() => validateBackendUrl('not-a-url')).toThrow('Invalid backend URL');
+  });
+
+  it('does not include the raw URL in error messages (credential hygiene)', () => {
+    const urlWithCreds = 'javascript:alert("sk-secret")';
+    let msg = '';
+    try {
+      validateBackendUrl(urlWithCreds);
+    } catch (e) {
+      msg = (e as Error).message;
+    }
+    expect(msg).not.toContain('sk-secret');
+    expect(msg).not.toContain(urlWithCreds);
+  });
+});
+
+describe('setBackendUrl', () => {
+  it('accepts valid http URLs', () => {
+    expect(() => setBackendUrl('http://localhost:4747')).not.toThrow();
+  });
+
+  it('accepts valid https URLs', () => {
+    expect(() => setBackendUrl('https://my-server.example.com')).not.toThrow();
+  });
+
+  it('rejects non-http/https schemes', () => {
+    expect(() => setBackendUrl('javascript:alert(1)')).toThrow('must use http:// or https://');
+    expect(() => setBackendUrl('file:///etc/passwd')).toThrow('must use http:// or https://');
+  });
+
+  it('does not mutate _backendUrl when validation fails', () => {
+    setBackendUrl('http://localhost:4747');
+    expect(() => setBackendUrl('javascript:alert(1)')).toThrow();
+    // State must be preserved — validation must happen before the assignment
+    expect(getBackendUrl()).toBe('http://localhost:4747');
+  });
+});

gitnexus/CHANGELOG.md

@@ -4,6 +4,73 @@ All notable changes to GitNexus will be documented in this file.
 
 ## [Unreleased]
 
+## [1.6.4] - 2026-05-10
+
+### Added
+
+- **`gitnexus publish`** — opt-in command to push your indexed graph to the understand-quickly registry for shareable browsing (#1425)
+- **`IncludeExtractor` for C++** — cross-repo include tracking joins the group contract pipeline (#1156)
+- **Unreal Engine C++ support** — strips reflection macros (`UCLASS`, `UFUNCTION`, `UPROPERTY`, etc.) before tree-sitter parses, so UE projects index cleanly (#1439)
+- **Thrift contracts extractor** — group-mode contract detection for Apache Thrift IDL (#1234)
+- **Workspace extractors for Node, Python, Go, Java, Elixir** — group-mode auto-discovery of cross-package boundaries (#1260)
+- **Rust workspace cross-crate contracts** — auto-discovery of `[workspace]` member crates and their cross-crate links (#1256)
+- **Go scope-resolution hooks** — Go joins Python / C# / TypeScript on the registry-primary RFC #909 path (#1302)
+- **TypeScript registry-primary scope resolution (Ring 3)** — TypeScript fully migrated to scope-based resolution (#1050)
+- **Configurable group cross-link path exclusions** — reduces false-positive contract links in vendored / monorepo trees (#1093)
+- **MCP tool safety annotations** — every MCP tool advertises read-only / mutating semantics so hosts can prompt appropriately (#1127)
+- **`--embeddings <limit>` opt-in cap** — bound the embeddings pass on huge graphs (closes #382, #1375)
+- **Pino structured logger** — replaces ad-hoc console output across the core with structured JSON logs (with pretty-print for TTY) (#1336)
+- **Shared resilient-fetch helper** — single retries + circuit breaker module reused by HF / Docker / publish flows (#1448)
+- **`/autofix` ChatOps button** — fork-safe PR autofix pipeline replaces the inline reviewdog flow (#1446, #1458)
+- **Automated security & vulnerability scans** in CI (#1297, #1455)
+
+### Fixed
+
+- **FTS read-only DB cluster** — hook resolves canonical repo root and guards read-only FTS ensure; missing-FTS warning is now surfaced. Closes #1255, #1287, #1170, #1449, #1440, #1216, #1438 (#1226, #1418, #1107, #1123)
+- **WAL corruption recovery** — quarantine corrupted `.wal` files instead of failing analyze; CHECKPOINT before close prevents recurrence; `safeClose` consolidates flush. Closes #1402, #1236, #1273, #1361 (#1417, #1314, #1377)
+- **Embedding download failures** — actionable HF_ENDPOINT guidance, retries, timeout, and circuit breaker; bridge `HF_ENDPOINT` to transformers.js; iterative DFS; HF cache via `os.homedir()`. Closes #1378, #1437, #1205 (#1419, #1252, #1078)
+- **Windows reliability** — pin tree-sitter-c/cpp to fix segfault, prefer `.cmd`/`.bat` from `where` output, robust LadybugDB lock acquisition for CI integration tests, surface silent finalize-skips so analyze cannot exit 0 without persisting. Closes #1242, #1427, #1447, #1468, #1400; partial #1218 (#1243, #1299, #1430, #1237, #1226, #1235)
+- **DuckDB / LadybugDB native** — bumped to 0.16.0 then 0.16.1; prevent extension install hangs; CHECKPOINT before close; WAL quarantine on corruption. Closes #1162, #1160, #273 (#1235, #1326, #1129, #1314, #1417)
+- **C# scope-resolution "Cannot add property" crashes** — generic typed properties included in context and impact, fixing crashes on Unity ECS partial structs and on properties whose name matches the class name. Closes #1426, #1465 (#1399)
+- **C# frozen-bucket regression** + scope-resolution I8 hardening — closes #1066 (#1082, #1085)
+- **Scope resolution** — same-range Module-as-parent for top-level scopes (closes #1086) (#1087); avoid variadic reference-site aggregation (#1112); skip empty scope extraction (#1100); classify Python class methods as Method (#1102)
+- **Python** — index repos with empty `__init__.py` and >32 KB files (#1163); walk ancestors for multi-segment dotted imports (#1241); deterministic multi-segment suffix fallback (#1253)
+- **TypeScript** — capture missed CALLS edges from HOF callbacks and JSX (#1175); name HOC-wrapped const declarations (`forwardRef` / `memo` / `useCallback` / `useMemo` / `observer`) (#1261); pair-with-arrow `@declaration.function` anchored on inner arrow
+- **Go** — loose equality for `Array.find()` null checks (#1384)
+- **Swift** — switched to the official prebuilt parser runtime (#1130)
+- **Server hardening cluster (U2–U8)** — JS path-injection on `/api/file` + docker-server (U2, #1322); git-clone path/CLI-injection / ReDoS hardening (U3, #1325); per-route rate limiting on FS-touching endpoints (U4, #1327); URL/regex/tag-filter sanitization (U7, #1330); ReDoS in cobol-preprocessor + rust-workspace + cross-impact resource exhaustion (U8, #1331); critical type-confusion + validation helper (#1317); rate-limit `/api/analyze` and `/api/embed` (closes #1328, #1339); IPv6 ipKeyGenerator (closes #1360, #1374); IPv4-compatible IPv6 / NAT64 SSRF bypasses in `validateGitUrl` (closes #1148, 95814847); predictable tempfile names → `crypto.randomBytes` (#1387); log-injection / http-to-file-access / client-side request forgery (#1456); pin Docker Node base images + Trivy verification + Dependabot policy (#1455)
+- **Group / contracts** — `runExactMatch` honours `.gitnexusignore` via shared `IgnoreService` (closes #1185, #1247); custom manifest links resolved against graph symbols (#1254); `IgnoreService` EACCES test under uid=0 (#1108)
+- **MCP** — close MCP server timeout via stdout discipline + cold-start friction (#1383); avoid `git` from non-repo cwd in sibling-cwd match (closes #1138, #1293); start MCP bridge correctly when using `npx` (#1114); project `tool_map` flows from handlers (#1113); parallelize staleness checks in `list_repos` (#1416)
+- **Storage / CLI** — derive registry name from canonical repo root, not worktree slug (closes #1259, #1296); `--skip-git` treats cwd as index root (#1245); keep GitNexus ignores inside `.gitnexus/` (#1248); surface silent finalize-skips so `analyze` cannot exit 0 without persisting (closes #1169, #1237); ignore global registry during staleness checks (#1141); use `os.homedir()` instead of `process.env.HOME` for HF cache dir (#1078); correct OpenCode skills install path in status message (#1386)
+- **Docker / server** — dedicated health endpoint for container healthcheck (closes #1147, #1355); HEAD probe so SSE heartbeat doesn't time out healthcheck (#1182); flush WAL after `/api/embed` so search sees new embeddings (closes #1149, #1359); platform-aware semantic fallback (#1150); skip vector index query on unsupported platforms (closes #1178, #1181); serve web UI at root path instead of 404 (#1048)
+- **Worker pool** — wait for replacement worker online before dispatch (#1324); prevent premature pool resolution in worker split-and-retry path (#1321); recover worker parse stalls (#1121); widened CI flake-tolerant timeouts (#1323, #1347, #1354)
+- **Embeddings storage** — CHECKPOINT before closing DB to prevent WAL corruption (#1314)
+- **Performance** — replace O(n³) C3 merge loop with O(n²) head-pointer algorithm (#1316)
+- **Install** — vendor tree-sitter-dart source (#1125)
+- **Git utils** — suppress stderr leak in `getCurrentCommit` and `getGitRoot` (closes #1172, #1341)
+- **Search** — load FTS during core DB init (#1123); create FTS indexes during `analyze` (#1107); surface warning when FTS indexes are missing (#1418)
+- **Hooks** — clarify `PostToolUse` hook is notification-only, not auto-reindex (#1070)
+- **Docs** — README Web UI section corrected (closes #1110, #1159, #2ff3e64f); Goliath capitalisation typo (#1126)
+- **CI** — fork-safe PR autofix pipeline (#1446); consolidated Claude review workflow (#1258); fine-grained PAT for RC tag push (#1407); handle expired artifacts in base coverage fetch (#1410, #1412); allow expected legacy parity failures (#1099); avoid duplicate main push checks; isolate native LadybugDB / CLI e2e flakes; seed e2e with a small fixture repo (#1249); configure e2e GitNexus home at runtime; widen rate-limit test window for Windows CI (#1347)
+
+### Changed
+
+- **`gitnexus publish` artefact contract** — universal opt-in publish format introduced (#1425, #1458)
+- **Refactor: per-language patterns consolidated into `LanguageProvider`** (#1279)
+- **Refactor: `safeClose` helper** consolidates WAL flush across LadybugDB call sites (#1377)
+- **Quality: exclude `test/fixtures` from CodeQL, ESLint, and Prettier** (#1313)
+- **Regression coverage** for `.gitnexusignore` behaviour with `--skip-git` (#1450)
+
+### Chore / Dependencies
+
+- `@ladybugdb/core` 0.16.0 → 0.16.1 (#1235, #1326)
+- `@anthropic-ai/sdk` (#1442), `@langchain/anthropic` (#1389), `@langchain/core` (#1394), `@langchain/openai` (#1215)
+- `hono` 4.12.9 → 4.12.18 + `@hono/node-server` (#1310, #1311, #1443)
+- `axios` (#1345), `fast-uri` 3.1.0 → 3.1.2 (#1441), `lru-cache` 11.3.5 → 11.3.6 (#1344), `mnemonist` 0.40.3 → 0.40.4 (#1239), `express-rate-limit` (#1343, #1397), `onnxruntime-node` (#1213, #1435), `uuid` 13 → 14 in /gitnexus-web (#1211, after revert #1222 / re-land #1250 + #1208)
+- `react`/`@types/react` (#1210), `react-dom` 19.2.5 → 19.2.6 (#1396), `react-zoom-pan-pinch` (#1214), `jsdom` 29.0.2 → 29.1.1 (#1395)
+- npm_and_yarn group bump (#1312), uv group bump (#1315), `python-dotenv` (#1320), `@types/node` (#1212, #1421, #1436)
+- GitHub Actions: `docker/build-push-action` 6.19.2 → 7.1.0 (#1391), `github/codeql-action` 3.35.3 → 4.35.3 (#1390)
+
 ## [1.6.3] - 2026-04-24
 
 ### Added

gitnexus/Dockerfile.test

@@ -1,6 +1,15 @@
-FROM node:20-bookworm
+# Pinned npm version — keep in sync with the root Dockerfile.cli and
+# Dockerfile.web.
+ARG NPM_VERSION=11.14.1
+
+# node:22-bookworm-slim
+FROM node:22-bookworm-slim@sha256:9f6d5975c7dca860947d3915877f85607946403fc55349f39b4bc3688448bb6e
+ARG NPM_VERSION
 WORKDIR /app
-RUN apt-get -o Acquire::Check-Valid-Until=false -o Acquire::Check-Date=false update && apt-get install -y python3 make g++ && rm -rf /var/lib/apt/lists/*
+RUN npx --yes npm@${NPM_VERSION} install -g npm@${NPM_VERSION} \
+    && apt-get -o Acquire::Check-Valid-Until=false -o Acquire::Check-Date=false update \
+    && apt-get install -y python3 make g++ \
+    && rm -rf /var/lib/apt/lists/*
 COPY . .
 RUN npm ci --ignore-scripts \
     && npm rebuild tree-sitter-swift 2>&1 \

gitnexus/README.md

@@ -33,7 +33,7 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 | Editor | MCP | Skills | Hooks (auto-augment) | Support |
 |--------|-----|--------|---------------------|---------|
 | **Claude Code** | Yes | Yes | Yes (PreToolUse) | **Full** |
-| **Cursor** | Yes | Yes | — | MCP + Skills |
+| **Cursor** | Yes | Yes | Yes (postToolUse, [manual install](../gitnexus-cursor-integration/README.md#hook-install)) | **Full** |
 | **Codex** | Yes | Yes | — | MCP + Skills |
 | **Windsurf** | Yes | — | — | MCP |
 | **OpenCode** | Yes | Yes | — | MCP + Skills |

gitnexus/hooks/claude/gitnexus-hook.cjs

@@ -14,6 +14,7 @@
 const fs = require('fs');
 const path = require('path');
 const { spawnSync } = require('child_process');
+const { acquireHookSlot } = require('./hook-lock.cjs');
 
 /**
  * Read JSON input from stdin synchronously.
@@ -207,7 +208,8 @@ function runGitNexusCli(cliPath, args, cwd, timeout) {
 function handlePreToolUse(input) {
   const cwd = input.cwd || process.cwd();
   if (!path.isAbsolute(cwd)) return;
-  if (!findGitNexusDir(cwd)) return;
+  const gitNexusDir = findGitNexusDir(cwd);
+  if (!gitNexusDir) return;
 
   const toolName = input.tool_name || '';
   const toolInput = input.tool_input || {};
@@ -217,6 +219,9 @@ function handlePreToolUse(input) {
   const pattern = extractPattern(toolName, toolInput);
   if (!pattern || pattern.length < 3) return;
 
+  const release = acquireHookSlot(gitNexusDir);
+  if (!release) return;
+
   const cliPath = resolveCliPath();
   let result = '';
   try {
@@ -226,6 +231,8 @@ function handlePreToolUse(input) {
     }
   } catch {
     /* graceful failure */
+  } finally {
+    release();
   }
 
   if (result && result.trim()) {

gitnexus/hooks/claude/hook-lock.cjs

@@ -0,0 +1,119 @@
+const fs = require('fs');
+const path = require('path');
+
+const HOOK_LOCK_SUBDIR = '.hook-locks';
+const HOOK_LOCK_MAX_INFLIGHT = 3;
+const HOOK_LOCK_STALE_MS = 30000;
+
+function acquireHookSlot(gitNexusDir) {
+  const lockDir = path.join(gitNexusDir, HOOK_LOCK_SUBDIR);
+  try {
+    fs.mkdirSync(lockDir, { recursive: true });
+  } catch {
+    // Cannot create lock dir (read-only fs, cross-user perm denial, out of
+    // inodes, etc.) — fail closed by returning null. Caller skips augment.
+    // Fail-open here would let N concurrent hooks all proceed unguarded and
+    // reintroduce the #1486 fan-out the guard exists to prevent.
+    return null;
+  }
+
+  const myPidStr = String(process.pid);
+
+  for (let slot = 0; slot < HOOK_LOCK_MAX_INFLIGHT; slot++) {
+    const slotPath = path.join(lockDir, `slot-${slot}.lock`);
+    for (let attempt = 0; attempt < 2; attempt++) {
+      try {
+        fs.writeFileSync(slotPath, myPidStr, { flag: 'wx' });
+        let released = false;
+        const release = () => {
+          if (released) return;
+          released = true;
+          try {
+            // Only unlink if we still own the slot. If we appeared stale and
+            // another hook took over, the file now belongs to it — leave alone.
+            const content = fs.readFileSync(slotPath, 'utf-8').trim();
+            if (content === myPidStr) fs.unlinkSync(slotPath);
+          } catch {
+            /* already removed or unreadable */
+          }
+        };
+        process.on('exit', release);
+        return release;
+      } catch {
+        // Slot exists. Decide whether to take it over.
+        // Open once and inspect mtime + content via the same fd so there's
+        // no TOCTOU between the metadata check and the content read
+        // (codeql js/file-system-race).
+        let fd;
+        try {
+          fd = fs.openSync(slotPath, 'r');
+        } catch {
+          continue; // Vanished between EEXIST and open — retry this slot.
+        }
+        let isLive = false;
+        let mtimeMs = Date.now();
+        try {
+          mtimeMs = fs.fstatSync(fd).mtimeMs;
+          const buf = Buffer.alloc(32);
+          const n = fs.readSync(fd, buf, 0, 32, 0);
+          const ownerStr = buf.slice(0, n).toString('utf-8').trim();
+          if (ownerStr === '') {
+            // Owner created the file but hasn't written its PID yet. The
+            // wx open+write window is microseconds; give it the benefit
+            // of the doubt and treat as live.
+            isLive = true;
+          } else {
+            const owner = Number.parseInt(ownerStr, 10);
+            if (Number.isFinite(owner) && owner > 0) {
+              try {
+                process.kill(owner, 0);
+                isLive = true;
+              } catch (e) {
+                // ESRCH = process gone → treat as dead. EPERM = process exists
+                // but owned by another user (cross-user lock dir) → still alive,
+                // keep the slot. Anything else: be conservative, assume alive.
+                if (e && e.code === 'ESRCH') {
+                  isLive = false;
+                } else {
+                  isLive = true;
+                }
+              }
+            }
+          }
+        } catch {
+          /* unreadable — treat as dead */
+        } finally {
+          try {
+            fs.closeSync(fd);
+          } catch {
+            /* already closed */
+          }
+        }
+        // For slots younger than HOOK_LOCK_STALE_MS, PID-liveness wins —
+        // a slow-but-alive hook is never wrongly evicted. For older slots,
+        // age is the final arbiter as a defense against PID reuse on long-
+        // abandoned slots. 30s >> the 7s augment timeout, so a healthy run
+        // never crosses this threshold.
+        if (isLive && Date.now() - mtimeMs > HOOK_LOCK_STALE_MS) {
+          isLive = false;
+        }
+        if (isLive) break; // Try the next slot.
+        try {
+          fs.unlinkSync(slotPath);
+        } catch {
+          /* another hook beat us to it — retry will hit EEXIST */
+        }
+        // Loop and retry this slot.
+      }
+    }
+  }
+
+  return null;
+}
+
+module.exports = {
+  HOOK_LOCK_SUBDIR,
+  HOOK_LOCK_MAX_INFLIGHT,
+  HOOK_LOCK_STALE_MS,
+  acquireHookSlot,
+};

gitnexus/package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "gitnexus",
-  "version": "1.6.3",
+  "version": "1.6.5-rc.24",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "gitnexus",
-      "version": "1.6.3",
+      "version": "1.6.5-rc.24",
       "hasInstallScript": true,
       "license": "PolyForm-Noncommercial-1.0.0",
       "dependencies": {
@@ -63,7 +63,7 @@
         "vitest": "^4.0.18"
       },
       "engines": {
-        "node": ">=20.0.0"
+        "node": ">=22.0.0"
       },
       "optionalDependencies": {
         "node-addon-api": "^8.0.0",
@@ -1600,9 +1600,9 @@
       "license": "BSD-3-Clause"
     },
     "node_modules/@protobufjs/codegen": {
-      "version": "2.0.4",
-      "resolved": "https://registry.npmjs.org/@protobufjs/codegen/-/codegen-2.0.4.tgz",
-      "integrity": "sha512-YyFaikqM5sH0ziFZCN3xDC7zeGaB/d0IUb9CATugHWbd1FRFwWwt4ld4OYMPWu5a3Xe01mGAULCdqhMlPl29Jg==",
+      "version": "2.0.5",
+      "resolved": "https://registry.npmjs.org/@protobufjs/codegen/-/codegen-2.0.5.tgz",
+      "integrity": "sha512-zgXFLzW3Ap33e6d0Wlj4MGIm6Ce8O89n/apUaGNB/jx+hw+ruWEp7EwGUshdLKVRCxZW12fp9r40E1mQrf/34g==",
       "license": "BSD-3-Clause"
     },
     "node_modules/@protobufjs/eventemitter": {
@@ -1628,9 +1628,9 @@
       "license": "BSD-3-Clause"
     },
     "node_modules/@protobufjs/inquire": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/@protobufjs/inquire/-/inquire-1.1.0.tgz",
-      "integrity": "sha512-kdSefcPdruJiFMVSbn801t4vFK7KB/5gd2fYvrxhuJYg8ILrmn9SKSX2tZdV6V+ksulWqS7aXjBcRXl3wHoD9Q==",
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/@protobufjs/inquire/-/inquire-1.1.1.tgz",
+      "integrity": "sha512-mnzgDV26ueAvk7rsbt9L7bE0SuAoqyuys/sMMrmVcN5x9VsxpcG3rqAUSgDyLp0UZlmNfIbQ4fHfCtreVBk8Ew==",
       "license": "BSD-3-Clause"
     },
     "node_modules/@protobufjs/path": {
@@ -1646,9 +1646,9 @@
       "license": "BSD-3-Clause"
     },
     "node_modules/@protobufjs/utf8": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/@protobufjs/utf8/-/utf8-1.1.0.tgz",
-      "integrity": "sha512-Vvn3zZrhQZkkBE8LSuW3em98c0FwgO4nxzv6OdSxPKJIEKY2bGbHn+mhGIPerzI4twdxaP8/0+06HBpwf345Lw==",
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/@protobufjs/utf8/-/utf8-1.1.1.tgz",
+      "integrity": "sha512-oOAWABowe8EAbMyWKM0tYDKi8Yaox52D+HWZhAIJqQXbqe0xI/GV7FhLWqlEKreMkfDjshR5FKgi3mnle0h6Eg==",
       "license": "BSD-3-Clause"
     },
     "node_modules/@rolldown/binding-android-arm64": {
@@ -2065,9 +2065,9 @@
       "license": "MIT"
     },
     "node_modules/@types/node": {
-      "version": "25.6.1",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-25.6.1.tgz",
-      "integrity": "sha512-coJCN8O1q4AGyyqCAUSP06P+SrMTu18BkEj3NVAK07q6QUneD2wzj3CLv9+yP+BMeZQlMvneXqqvDe3w+xcq7g==",
+      "version": "25.6.2",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-25.6.2.tgz",
+      "integrity": "sha512-sokuT28dxf9JT5Kady1fsXOvI4HVpjZa95NKT5y9PNTIrs2AsobR4GFAA90ZG8M+nxVRLysCXsVj6eGC7Vbrlw==",
       "license": "MIT",
       "dependencies": {
         "undici-types": "~7.19.0"
@@ -3110,9 +3110,9 @@
       "license": "MIT"
     },
     "node_modules/fast-uri": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.0.tgz",
-      "integrity": "sha512-iPeeDKJSWf4IEOasVVrknXpaBV0IApz/gp7S2bb7Z4Lljbl2MGJRqInZiUrQwV16cpzw/D3S5j5Julj/gT52AA==",
+      "version": "3.1.2",
+      "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.2.tgz",
+      "integrity": "sha512-rVjf7ArG3LTk+FS6Yw81V1DLuZl1bRbNrev6Tmd/9RaroeeRRJhAt7jg/6YFxbvAQXUCavSoZhPPj6oOx+5KjQ==",
       "funding": [
         {
           "type": "github",
@@ -3476,9 +3476,9 @@
       "license": "MIT"
     },
     "node_modules/hono": {
-      "version": "4.12.16",
-      "resolved": "https://registry.npmjs.org/hono/-/hono-4.12.16.tgz",
-      "integrity": "sha512-jN0ZewiNAWSe5khM3EyCmBb250+b40wWbwNILNfEvq84VREWwOIkuUsFONk/3i3nqkz7Oe1PcpM2mwQEK2L9Kg==",
+      "version": "4.12.18",
+      "resolved": "https://registry.npmjs.org/hono/-/hono-4.12.18.tgz",
+      "integrity": "sha512-RWzP96k/yv0PQfyXnWjs6zot20TqfpfsNXhOnev8d1InAxubW93L11/oNUc3tQqn2G0bSdAOBpX+2uDFHV7kdQ==",
       "license": "MIT",
       "engines": {
         "node": ">=16.9.0"
@@ -4282,15 +4282,15 @@
       }
     },
     "node_modules/onnxruntime-common": {
-      "version": "1.25.1",
-      "resolved": "https://registry.npmjs.org/onnxruntime-common/-/onnxruntime-common-1.25.1.tgz",
-      "integrity": "sha512-kKvYQFdos4LWJqhZ+nmKu3NT8NXzw8I5x9fNUKe1rNKcPfNKnYXUtW7JBpcKFsvLtrJashRgVYSbFap4cHxvNg==",
+      "version": "1.26.0",
+      "resolved": "https://registry.npmjs.org/onnxruntime-common/-/onnxruntime-common-1.26.0.tgz",
+      "integrity": "sha512-qVyMR4lcWgbkc4getFV+GQijsTnbg/siteoqcDwa3sI/LxbrMSNw4ePyvCq/ymdQaRomCA7YuWmhzsswxvymdw==",
       "license": "MIT"
     },
     "node_modules/onnxruntime-node": {
-      "version": "1.25.1",
-      "resolved": "https://registry.npmjs.org/onnxruntime-node/-/onnxruntime-node-1.25.1.tgz",
-      "integrity": "sha512-N0M58CGTiTsLkPpx9bxmRFi24GT6r67Qei/GrBEIiDyntcYdXU5vQZp112ypydG9vEKRFgbgUYQJnEi+jll8dg==",
+      "version": "1.26.0",
+      "resolved": "https://registry.npmjs.org/onnxruntime-node/-/onnxruntime-node-1.26.0.tgz",
+      "integrity": "sha512-OHl6PiOEOqxaLHL0N9eFrbzS7IGmu3BtJNH3RTEnRAheCIkfc3gjcjl4sGcjp9C22ZC9YTquDOxSdT/stBQ6BQ==",
       "hasInstallScript": true,
       "license": "MIT",
       "os": [
@@ -4301,7 +4301,7 @@
       "dependencies": {
         "adm-zip": "^0.5.16",
         "global-agent": "^4.1.3",
-        "onnxruntime-common": "1.25.1"
+        "onnxruntime-common": "1.26.0"
       }
     },
     "node_modules/onnxruntime-web": {
@@ -4543,22 +4543,22 @@
       "license": "MIT"
     },
     "node_modules/protobufjs": {
-      "version": "7.5.5",
-      "resolved": "https://registry.npmjs.org/protobufjs/-/protobufjs-7.5.5.tgz",
-      "integrity": "sha512-3wY1AxV+VBNW8Yypfd1yQY9pXnqTAN+KwQxL8iYm3/BjKYMNg4i0owhEe26PWDOMaIrzeeF98Lqd5NGz4omiIg==",
+      "version": "7.5.8",
+      "resolved": "https://registry.npmjs.org/protobufjs/-/protobufjs-7.5.8.tgz",
+      "integrity": "sha512-dvpCIeLPbXZS/Ete7yLaO7RenOdken2NHKykBXbsaGxZT0UTltcarBciw+A78SRQs9iMAAVpsYA+l8b1hTePIA==",
       "hasInstallScript": true,
       "license": "BSD-3-Clause",
       "dependencies": {
         "@protobufjs/aspromise": "^1.1.2",
         "@protobufjs/base64": "^1.1.2",
-        "@protobufjs/codegen": "^2.0.4",
+        "@protobufjs/codegen": "^2.0.5",
         "@protobufjs/eventemitter": "^1.1.0",
         "@protobufjs/fetch": "^1.1.0",
         "@protobufjs/float": "^1.0.2",
-        "@protobufjs/inquire": "^1.1.0",
+        "@protobufjs/inquire": "^1.1.1",
         "@protobufjs/path": "^1.1.2",
         "@protobufjs/pool": "^1.1.0",
-        "@protobufjs/utf8": "^1.1.0",
+        "@protobufjs/utf8": "^1.1.1",
         "@types/node": ">=13.7.0",
         "long": "^5.0.0"
       },

gitnexus/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.3",
+  "version": "1.6.5-rc.24",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",
@@ -116,6 +116,6 @@
     }
   },
   "engines": {
-    "node": ">=20.0.0"
+    "node": ">=22.0.0"
   }
 }

gitnexus/scripts/build.js

@@ -21,11 +21,15 @@ const SHARED_DEST = path.join(DIST, '_shared');
 
 // ── 1. Build gitnexus-shared ───────────────────────────────────────
 console.log('[build] compiling gitnexus-shared…');
-execSync('npx tsc', { cwd: SHARED_ROOT, stdio: 'inherit', timeout: 120_000 });
+const tscCmd =
+  process.platform === 'win32'
+    ? path.join('node_modules', '.bin', 'tsc.cmd')
+    : path.join('node_modules', '.bin', 'tsc');
+execSync(tscCmd, { cwd: SHARED_ROOT, stdio: 'inherit', timeout: 120_000 });
 
 // ── 2. Build gitnexus ──────────────────────────────────────────────
 console.log('[build] compiling gitnexus…');
-execSync('npx tsc', { cwd: ROOT, stdio: 'inherit', timeout: 120_000 });
+execSync(tscCmd, { cwd: ROOT, stdio: 'inherit', timeout: 120_000 });
 
 // ── 3. Copy shared dist ────────────────────────────────────────────
 console.log('[build] copying shared module into dist/_shared…');

gitnexus/src/cli/ai-context.ts

@@ -28,6 +28,7 @@ interface RepoStats {
 export interface AIContextOptions {
   skipAgentsMd?: boolean;
   noStats?: boolean;
+  skipSkills?: boolean;
 }
 
 const GITNEXUS_START_MARKER = '<!-- gitnexus:start -->';
@@ -94,6 +95,7 @@ function generateGitNexusContent(
   generatedSkills?: GeneratedSkillInfo[],
   groupNames?: string[],
   noStats?: boolean,
+  skipSkills?: boolean,
 ): string {
   const generatedRows =
     generatedSkills && generatedSkills.length > 0
@@ -105,14 +107,26 @@ function generateGitNexusContent(
           .join('\n')
       : '';
 
-  const skillsTable = `| Task | Read this skill file |
-|------|---------------------|
-| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
+  // Standard skill rows reference files installed by installSkills(). When
+  // --skip-skills suppresses that install, these rows must be omitted — else
+  // AGENTS.md/CLAUDE.md would direct agents to read files that don't exist.
+  // Community skills (generatedRows) live in .claude/skills/generated/ and
+  // are independent of --skip-skills, so they remain when present.
+  const standardSkillsRows = skipSkills
+    ? ''
+    : `| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
 | Blast radius / "What breaks if I change X?" | \`.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md\` |
 | Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus/gitnexus-debugging/SKILL.md\` |
 | Rename / extract / split / refactor | \`.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md\` |
 | Tools, resources, schema reference | \`.claude/skills/gitnexus/gitnexus-guide/SKILL.md\` |
-| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |${generatedRows ? '\n' + generatedRows : ''}`;
+| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |`;
+
+  const tableBody = [standardSkillsRows, generatedRows].filter(Boolean).join('\n');
+  const skillsTable = tableBody
+    ? `| Task | Read this skill file |
+|------|---------------------|
+${tableBody}`
+    : '';
 
   return `${GITNEXUS_START_MARKER}
 # GitNexus — Code Intelligence
@@ -153,11 +167,15 @@ This repository is listed under GitNexus **group(s): ${groupNames.join(', ')}**
 
 `
     : ''
-}## CLI
+}${
+    skillsTable
+      ? `## CLI
 
 ${skillsTable}
 
-${GITNEXUS_END_MARKER}`;
+`
+      : ''
+  }${GITNEXUS_END_MARKER}`;
 }
 
 /**
@@ -319,6 +337,7 @@ export async function generateAIContextFiles(
     generatedSkills,
     groupNames,
     options?.noStats,
+    options?.skipSkills,
   );
   const createdFiles: string[] = [];
 
@@ -337,10 +356,14 @@ export async function generateAIContextFiles(
     createdFiles.push('CLAUDE.md (skipped via --skip-agents-md)');
   }
 
-  // Install skills to .claude/skills/gitnexus/
-  const installedSkills = await installSkills(repoPath);
-  if (installedSkills.length > 0) {
-    createdFiles.push(`.claude/skills/gitnexus/ (${installedSkills.length} skills)`);
+  // Install skills to .claude/skills/gitnexus/ (unless --skip-skills)
+  if (!options?.skipSkills) {
+    const installedSkills = await installSkills(repoPath);
+    if (installedSkills.length > 0) {
+      createdFiles.push(`.claude/skills/gitnexus/ (${installedSkills.length} skills)`);
+    }
+  } else {
+    createdFiles.push('.claude/skills/gitnexus/ (skipped via --skip-skills)');
   }
 
   return { files: createdFiles };

gitnexus/src/cli/analyze.ts

@@ -119,6 +119,10 @@ export interface AnalyzeOptions {
   skipAgentsMd?: boolean;
   /** Omit volatile symbol/relationship counts from AGENTS.md and CLAUDE.md. */
   noStats?: boolean;
+  /** Skip installing standard GitNexus skill files to .claude/skills/gitnexus/. */
+  skipSkills?: boolean;
+  /** Pure index mode: skip all file injection (AGENTS.md, CLAUDE.md, skills). */
+  indexOnly?: boolean;
   /** Index the folder even when no .git directory is present. */
   skipGit?: boolean;
   /**
@@ -150,6 +154,24 @@ export interface AnalyzeOptions {
   embeddingDevice?: string;
 }
 
+/**
+ * Whether the post-index skill step should run.
+ *
+ * The gated block does two things in sequence: (1) generates the community
+ * skill files from `--skills`, and (2) re-runs `generateAIContextFiles` so
+ * AGENTS.md/CLAUDE.md can reference the freshly written skills. Both are
+ * suppressed together — `--index-only` drops the entire step, not just the
+ * community-skill write. Name retained for the test contract; see call site
+ * in `analyzeCommand` for the AGENTS.md/CLAUDE.md re-generation it also gates.
+ *
+ * Kept as a pure helper so the `--index-only --skills` contract is unit-tested
+ * without booting the full analyze pipeline (#742 review).
+ */
+export const shouldGenerateCommunitySkillFiles = (
+  options: Pick<AnalyzeOptions, 'skills' | 'indexOnly'> | undefined,
+  pipelineResult: unknown,
+): boolean => Boolean(options?.skills && pipelineResult && !options?.indexOnly);
+
 export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOptions) => {
   if (ensureHeap()) return;
 
@@ -245,6 +267,18 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
 
   console.log('\n  GitNexus Analyzer\n');
 
+  // `--index-only` is the stronger contract — it suppresses every form of file
+  // injection, including community skill writes that `--skills` would normally
+  // produce. Surface the override explicitly so users don't wonder why a
+  // pipeline re-index ran but no skill files appeared. The pipeline still
+  // re-runs (see `force: options?.force || options?.skills` below); the warning
+  // is purely about the dropped post-index write step.
+  if (options?.indexOnly && options?.skills) {
+    console.log(
+      '  Note: --index-only overrides --skills; community skill files will not be written.\n',
+    );
+  }
+
   let repoPath: string;
   if (inputPath) {
     repoPath = path.resolve(inputPath);
@@ -399,6 +433,9 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
 
   // ── Run shared analysis orchestrator ───────────────────────────────
   try {
+    const skipAll = options?.indexOnly;
+    const skipAgentsMd = skipAll || options?.skipAgentsMd;
+    const skipSkills = skipAll || options?.skipSkills;
     const result = await runFullAnalysis(
       repoPath,
       {
@@ -410,7 +447,8 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
         embeddingsNodeLimit,
         dropEmbeddings: options?.dropEmbeddings,
         skipGit: options?.skipGit,
-        skipAgentsMd: options?.skipAgentsMd,
+        skipAgentsMd,
+        skipSkills,
         noStats: options?.noStats,
         registryName: options?.name,
         // Registry-collision bypass — its own CLI flag, intentionally NOT
@@ -456,8 +494,10 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
     // a healthy index.
     await assertAnalysisFinalized(repoPath);
 
-    // Skill generation (CLI-only, uses pipeline result from analysis)
-    if (options?.skills && result.pipelineResult) {
+    // Skill generation (CLI-only, uses pipeline result from analysis).
+    // Gated so `--index-only --skills` skips community skill writes too
+    // (`shouldGenerateCommunitySkillFiles` — see unit test).
+    if (shouldGenerateCommunitySkillFiles(options, result.pipelineResult)) {
       updateBar(99, 'Generating skill files...');
       try {
         const { generateSkillFiles } = await import('./skill-gen.js');
@@ -497,7 +537,7 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
               processes: s.processes,
             },
             skillResult.skills,
-            { skipAgentsMd: options?.skipAgentsMd, noStats: options?.noStats },
+            { skipAgentsMd, skipSkills, noStats: options?.noStats },
           );
         }
       } catch {

gitnexus/src/cli/augment.ts

@@ -2,7 +2,7 @@
  * Augment CLI Command
  *
  * Fast-path command for platform hooks.
- * Shells out from Claude Code PreToolUse / Cursor beforeShellExecution hooks.
+ * Shells out from Claude Code PreToolUse / Cursor postToolUse hooks.
  *
  * Usage: gitnexus augment <pattern>
  * Returns enriched text to stdout.

gitnexus/src/cli/index.ts

@@ -33,9 +33,20 @@ program
     'Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` ' +
       'preserves any embeddings already present in the index.',
   )
-  .option('--skills', 'Generate repo-specific skill files from detected communities')
+  .option(
+    '--skills',
+    'Generate repo-specific skill files from detected communities ' +
+      '(no-op when --index-only is also set).',
+  )
   .option('--skip-agents-md', 'Skip updating the gitnexus section in AGENTS.md and CLAUDE.md')
   .option('--no-stats', 'Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md')
+  .option(
+    '--skip-skills',
+    'Skip installing standard GitNexus skill files under .claude/skills/gitnexus/. ' +
+      'Does not suppress community skills from --skills (those use .claude/skills/generated/). ' +
+      'Use --index-only to skip all AI-context file injection.',
+  )
+  .option('--index-only', 'Pure index mode: skip all file injection (AGENTS.md, CLAUDE.md, skills)')
   .option(
     '--skip-git',
     'Treat the provided path/cwd as the index root and skip parent git-root discovery',
@@ -160,6 +171,18 @@ program
   .description('Augment a search pattern with knowledge graph context (used by hooks)')
   .action(createLazyAction(() => import('./augment.js'), 'augmentCommand'));
 
+program
+  .command('publish [path]')
+  .description(
+    'Notify the understand-quickly registry that this repo has a fresh GitNexus index. ' +
+      'Opt-in: requires UNDERSTAND_QUICKLY_TOKEN (fine-grained PAT with ' +
+      '`Repository dispatches: write` on looptech-ai/understand-quickly). ' +
+      'No-op without the token. See https://github.com/looptech-ai/understand-quickly.',
+  )
+  .option('--id <owner/repo>', 'Override the registry id (defaults to the origin remote)')
+  .option('--skip-git', 'Treat cwd as the repo root and skip parent git-root discovery')
+  .action(createLazyAction(() => import('./publish.js'), 'publishCommand'));
+
 // ─── Direct Tool Commands (no MCP overhead) ────────────────────────
 // These invoke LocalBackend directly for use in eval, scripts, and CI.
 

gitnexus/src/cli/publish.ts

@@ -0,0 +1,232 @@
+/**
+ * `gitnexus publish` — opt-in ping to the understand-quickly registry.
+ *
+ * Fires a single `repository_dispatch` event at
+ * `looptech-ai/understand-quickly` so the registry knows to refresh its
+ * entry for the current repo. Does NOT upload anything: per the
+ * understand-quickly protocol, the registry pulls the graph from a
+ * raw-GitHub URL the user controls.
+ *
+ *   https://github.com/looptech-ai/understand-quickly/blob/main/docs/integrations/protocol.md
+ *
+ * Defaults:
+ *   - Without `UNDERSTAND_QUICKLY_TOKEN` in the env, this is a no-op
+ *     (prints one informational line, exit 0). Same shape as the
+ *     `--publish` patterns in sibling tools.
+ *   - With the token, fires the dispatch and reports the response code.
+ *
+ * The `id` is derived from the repo's `origin` remote unless the caller
+ * passes `--id <owner/repo>` explicitly. We deliberately do NOT auto-add
+ * the repo to the registry — registration is one-time and uses the
+ * `npx @understand-quickly/cli add` path documented in the protocol.
+ */
+
+import path from 'path';
+import {
+  UNDERSTAND_QUICKLY_DISPATCH_URL,
+  UNDERSTAND_QUICKLY_TOKEN_ENV,
+  buildUqDispatchPayload,
+  isValidOwnerRepo,
+  parseOwnerRepoFromRemote,
+} from 'gitnexus-shared';
+import { getGitRoot, getRemoteOriginUrl, getCurrentCommit } from '../storage/git.js';
+import { hasIndex } from '../storage/repo-manager.js';
+import { cliInfo, cliError } from './cli-message.js';
+
+export interface PublishOptions {
+  /** Override the auto-derived `owner/repo` id. */
+  id?: string;
+  /** Treat the cwd as the repo root (skip git-root walk). */
+  skipGit?: boolean;
+}
+
+const REGISTER_HINT =
+  'Register your repo once with: npx @understand-quickly/cli add\n' +
+  'Or use the wizard: https://looptech-ai.github.io/understand-quickly/add.html';
+
+/**
+ * Hard cap on the dispatch fetch to keep CI publish steps from stalling
+ * for the OS TCP timeout (~2 min) when api.github.com is unreachable.
+ * Matches the pattern used in `src/core/embeddings/http-client.ts`.
+ */
+const DISPATCH_TIMEOUT_MS = 15_000;
+
+export const publishCommand = async (
+  inputPath?: string,
+  options: PublishOptions = {},
+): Promise<void> => {
+  // ── 0. Token gate FIRST — guarantees true no-op without the token. ──
+  // The README, CLI --help, and PR body all promise "exit 0 without
+  // UNDERSTAND_QUICKLY_TOKEN". Doing the index/repo-root checks before
+  // the token gate would make those promises false for users who haven't
+  // run `gitnexus analyze` yet but want to verify the command is wired.
+  const token = process.env[UNDERSTAND_QUICKLY_TOKEN_ENV];
+  if (!token) {
+    cliInfo(
+      `[understand-quickly] ${UNDERSTAND_QUICKLY_TOKEN_ENV} is not set — skipping dispatch.\n` +
+        `Set it to a fine-grained PAT with "Repository dispatches: write" on ` +
+        `looptech-ai/understand-quickly to enable instant resync.\n` +
+        `(Without the token, the registry's nightly sync still picks up your entry.)`,
+      { skipped: 'no-token' },
+    );
+    return;
+  }
+
+  // ── 1. Resolve the repo root (same precedence as `analyze`) ──────────
+  let repoPath: string;
+  if (inputPath) {
+    repoPath = path.resolve(inputPath);
+  } else if (options.skipGit) {
+    repoPath = path.resolve(process.cwd());
+  } else {
+    const gitRoot = getGitRoot(process.cwd());
+    if (!gitRoot) {
+      cliError(
+        '[understand-quickly] not inside a git repository.\n' +
+          'Run from a repo, or pass --skip-git to publish from the current directory.',
+      );
+      process.exitCode = 1;
+      return;
+    }
+    repoPath = gitRoot;
+  }
+
+  // ── 2. Confirm a GitNexus index exists ───────────────────────────────
+  // Publishing without an index is almost always a mistake — the
+  // registry's nightly sync would fetch a stale or missing graph file
+  // and mark the entry `missing`. Refuse loudly with a fix-it hint.
+  if (!(await hasIndex(repoPath))) {
+    cliError(
+      `[understand-quickly] no GitNexus index found at ${repoPath}/.gitnexus.\n` +
+        'Run `gitnexus analyze` first, then re-run `gitnexus publish`.',
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  // ── 3. Derive the registry id ─────────────────────────────────────────
+  const id =
+    options.id ?? parseOwnerRepoFromRemote(getRemoteOriginUrl(repoPath) ?? undefined) ?? null;
+  if (!id || !isValidOwnerRepo(id)) {
+    cliError(
+      `[understand-quickly] could not derive a registry id from this repo.\n` +
+        `Pass --id <owner/repo> explicitly (e.g. --id looptech-ai/${path.basename(repoPath)}).\n` +
+        REGISTER_HINT,
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  // ── 4. Fire the dispatch ─────────────────────────────────────────────
+  const payload = buildUqDispatchPayload(id);
+  let response: Response;
+  try {
+    response = await fetch(UNDERSTAND_QUICKLY_DISPATCH_URL, {
+      method: 'POST',
+      headers: {
+        Accept: 'application/vnd.github+json',
+        Authorization: `Bearer ${token}`,
+        'X-GitHub-Api-Version': '2022-11-28',
+        'Content-Type': 'application/json',
+        'User-Agent': 'gitnexus-cli',
+      },
+      body: JSON.stringify(payload),
+      signal: AbortSignal.timeout(DISPATCH_TIMEOUT_MS),
+    });
+  } catch (err) {
+    // `AbortSignal.timeout()` throws a `DOMException` with `name ===
+    // 'TimeoutError'` on Node 18.14+ (and on browsers/Bun). It is NOT
+    // a plain `AbortError`. Match the pattern used in
+    // gitnexus/src/core/embeddings/http-client.ts so the user sees the
+    // targeted "timed out" message instead of a generic "operation
+    // was aborted".
+    const isTimeout = err instanceof DOMException && err.name === 'TimeoutError';
+    if (isTimeout) {
+      cliError(
+        `[understand-quickly] dispatch timed out after ${DISPATCH_TIMEOUT_MS}ms. ` +
+          `Check network access to api.github.com and retry.`,
+        { id },
+      );
+    } else {
+      const msg = err instanceof Error ? err.message : String(err);
+      cliError(`[understand-quickly] dispatch network error: ${msg}`, { id });
+    }
+    process.exitCode = 1;
+    return;
+  }
+
+  // GitHub returns 204 on success. Distinct branches for 401/403/404/422
+  // so users debug without checking the docs.
+  if (response.status === 204) {
+    await response.body?.cancel().catch(() => {});
+    // `getCurrentCommit` is only meaningful in the success path — moving
+    // it inside this branch removes a wasted child-process spawn on every
+    // error response (LOW 7).
+    const commit = getCurrentCommit(repoPath);
+    cliInfo(
+      `[understand-quickly] dispatched sync-entry for ${id}` +
+        (commit ? ` @ ${commit.slice(0, 7)}` : '') +
+        '.\n' +
+        `Note: a 204 only confirms GitHub accepted the dispatch. Whether the ` +
+        `registry workflow finds an entry for "${id}" is logged at ` +
+        `https://github.com/looptech-ai/understand-quickly/actions/workflows/sync.yml`,
+      { id, commit, status: response.status },
+    );
+    return;
+  }
+
+  if (response.status === 401) {
+    cliError(
+      `[understand-quickly] dispatch returned 401 — the ${UNDERSTAND_QUICKLY_TOKEN_ENV} value is invalid or expired.\n` +
+        `Regenerate a fine-grained PAT at https://github.com/settings/personal-access-tokens ` +
+        `with Repository access scoped to looptech-ai/understand-quickly and the ` +
+        `"Repository dispatches: write" permission, then retry.`,
+      { id, status: response.status },
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  if (response.status === 403) {
+    cliError(
+      `[understand-quickly] dispatch returned 403 — the token authenticated but ` +
+        `lacks the "Repository dispatches: write" permission on ` +
+        `looptech-ai/understand-quickly. Edit the PAT scopes and retry.`,
+      { id, status: response.status },
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  if (response.status === 404) {
+    cliError(
+      `[understand-quickly] dispatch returned 404 — the token cannot reach ` +
+        `looptech-ai/understand-quickly. Verify the PAT has Repository access to ` +
+        `that exact repo (not just your own org).`,
+      { id, status: response.status },
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  if (response.status === 422) {
+    // Malformed event_type / client_payload — a code bug in this CLI,
+    // not a user mistake. Surface so we get bug reports.
+    const body422 = await response.text().catch(() => '');
+    cliError(
+      `[understand-quickly] dispatch returned 422 (this is a CLI bug; please report).\n` +
+        `Body: ${body422 || '(empty)'}`,
+      { id, status: response.status },
+    );
+    process.exitCode = 1;
+    return;
+  }
+
+  // 5xx and anything else → bubble the body so the user has something to act on.
+  const body = await response.text().catch(() => '');
+  cliError(
+    `[understand-quickly] dispatch failed with HTTP ${response.status}: ${body || '(empty body)'}`,
+    { id, status: response.status },
+  );
+  process.exitCode = 1;
+};

gitnexus/src/cli/setup.ts

@@ -364,6 +364,15 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
       // Script not found in source — skip
     }
 
+    try {
+      await fs.copyFile(
+        path.join(pluginHooksPath, 'hook-lock.cjs'),
+        path.join(destHooksDir, 'hook-lock.cjs'),
+      );
+    } catch {
+      // Helper not found in source — skip
+    }
+
     const hookPath = path.join(destHooksDir, 'gitnexus-hook.cjs').replace(/\\/g, '/');
     // Escape backslashes FIRST, then quotes (CodeQL js/incomplete-sanitization).
     // The previous shape `replace(/"/g, '\\"')` alone would let `path\with"quote`

gitnexus/src/config/ignore-service.ts

@@ -25,6 +25,8 @@ const DEFAULT_IGNORE_LIST = new Set([
   'bower_components',
   'jspm_packages',
   'vendor', // PHP/Go
+  'third_party', // C/C++ (Google-style vendored dependencies)
+  '3rdparty', // C/C++ (alternate spelling, also Qt convention)
   // 'packages' removed - commonly used for monorepo source code (lerna, pnpm, yarn workspaces)
   'venv',
   '.venv',

gitnexus/src/core/augmentation/engine.ts

@@ -2,8 +2,8 @@
  * Augmentation Engine
  *
  * Lightweight, fast-path enrichment of search patterns with knowledge graph context.
- * Designed to be called from platform hooks (Claude Code PreToolUse, Cursor beforeShellExecution)
- * when an agent runs grep/glob/search.
+ * Designed to be called from platform hooks (Claude Code PreToolUse, Cursor postToolUse)
+ * when an agent runs grep/glob/read/search.
  *
  * Performance target: <500ms cold start, <200ms warm.
  *
@@ -86,6 +86,9 @@ async function findRepoForCwd(cwd: string): Promise<{
 export async function augment(pattern: string, cwd?: string): Promise<string> {
   if (!pattern || pattern.length < 3) return '';
 
+  const patternFirstWord = pattern.trim().replace(/'/g, "''").split(/\s+/)[0];
+  if (!patternFirstWord || patternFirstWord.length < 2) return '';
+
   const workDir = cwd || process.cwd();
 
   try {
@@ -104,9 +107,7 @@ export async function augment(pattern: string, cwd?: string): Promise<string> {
     }
 
     // Step 1: BM25 search (fast, no embeddings)
-    const bm25Results = await searchFTSFromLbug(pattern, 10, repoId);
-
-    if (bm25Results.length === 0) return '';
+    const { results: bm25Results, ftsAvailable } = await searchFTSFromLbug(pattern, 10, repoId);
 
     // Step 2: Map BM25 file results to symbols
     const symbolMatches: Array<{
@@ -124,7 +125,7 @@ export async function augment(pattern: string, cwd?: string): Promise<string> {
           repoId,
           `
           MATCH (n) WHERE n.filePath = '${escaped}'
-          AND n.name CONTAINS '${pattern.replace(/'/g, "''").split(/\s+/)[0]}'
+          AND n.name CONTAINS '${patternFirstWord}'
           RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
           LIMIT 3
         `,
@@ -143,6 +144,29 @@ export async function augment(pattern: string, cwd?: string): Promise<string> {
       }
     }
 
+    // When FTS indexes are unavailable (read-only DB, first run before indexes are built),
+    // fall back to a direct name CONTAINS query so enrichment still works.
+    if (symbolMatches.length === 0 && !ftsAvailable) {
+      const fallbackRows = await executeQuery(
+        repoId,
+        `
+        MATCH (n)
+        WHERE n.name CONTAINS '${patternFirstWord}'
+        RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
+        LIMIT 5
+      `,
+      ).catch(() => []);
+      for (const sym of fallbackRows) {
+        symbolMatches.push({
+          nodeId: sym.id || sym[0],
+          name: sym.name || sym[1],
+          type: sym.type || sym[2],
+          filePath: sym.filePath || sym[3],
+          score: 1.0,
+        });
+      }
+    }
+
     if (symbolMatches.length === 0) return '';
 
     // Step 3: Batch-fetch callers/callees/processes/cohesion for top matches

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

@@ -10,6 +10,7 @@ import {
   isLanguageAvailable,
   resolveLanguageKey,
 } from '../tree-sitter/parser-loader.js';
+import { parseSourceSafe } from '../tree-sitter/safe-parse.js';
 
 const parserCache = new Map<string, any>();
 
@@ -29,7 +30,7 @@ export const ensureAndParse = async (content: string, filePath: string): Promise
     parserCache.set(parserKey, parserInstance);
   }
 
-  return parserInstance.parse(content);
+  return parseSourceSafe(parserInstance, content);
 };
 
 const FUNCTION_LIKE_TYPES = new Set([

gitnexus/src/core/embeddings/hf-env.ts

@@ -1,6 +1,8 @@
 import os from 'node:os';
 import { join } from 'node:path';
 
+import { CircuitBreaker, withRetry } from 'gitnexus-shared';
+
 // ---------------------------------------------------------------------------
 // Download resilience defaults
 // ---------------------------------------------------------------------------
@@ -108,70 +110,19 @@ export function isNetworkFetchError(message: string): boolean {
 /** @internal Used by `withHfDownloadRetry` to mark a circuit-open rejection. */
 export const CIRCUIT_OPEN_TAG = 'hf-circuit-open';
 
-/** Circuit-breaker states. */
-type CircuitState = 'closed' | 'open' | 'half-open';
-
 /**
- * Circuit breaker for HuggingFace model downloads.
- *
- * After `failureThreshold` consecutive network failures the circuit opens and
- * all subsequent calls to `withHfDownloadRetry` fail immediately without
- * issuing any network requests. After `resetTimeoutMs` the circuit enters the
- * half-open state and the next call is attempted — if it succeeds the circuit
- * closes again; if it fails the circuit re-opens.
- *
- * Exported for unit-testing; production code should use the module-level
- * `hfDownloadCircuit` singleton.
+ * Module-level singleton shared by both embedder entry points
+ * (`core/embeddings/embedder.ts` + `mcp/core/embedder.ts`). Per-process
+ * only — not persisted across restarts. Backed by the shared
+ * `CircuitBreaker` from `gitnexus-shared` (same state machine, same
+ * semantics, plus the single-permit half-open gate that prevents
+ * recovery-time stampedes).
  */
-export class HfDownloadCircuitBreaker {
-  private _state: CircuitState = 'closed';
-  private _failures = 0;
-  /** Timestamp of the last recorded failure (ms since epoch). */
-  lastFailureAt = 0;
-
-  constructor(
-    readonly failureThreshold: number = CB_FAILURE_THRESHOLD,
-    readonly resetTimeoutMs: number = CB_RESET_TIMEOUT_MS,
-  ) {}
-
-  /** Effective state, factoring in the reset-timeout transition. */
-  get state(): CircuitState {
-    if (this._state === 'open' && Date.now() - this.lastFailureAt > this.resetTimeoutMs) {
-      this._state = 'half-open';
-    }
-    return this._state;
-  }
-
-  /** Returns true when the circuit is open and calls should be rejected. */
-  isOpen(): boolean {
-    return this.state === 'open';
-  }
-
-  /** Record a successful call — resets the failure counter and closes the circuit. */
-  recordSuccess(): void {
-    this._failures = 0;
-    this._state = 'closed';
-  }
-
-  /** Record a failed call — increments the counter and opens the circuit when the threshold is reached. */
-  recordFailure(): void {
-    this._failures++;
-    this.lastFailureAt = Date.now();
-    if (this._failures >= this.failureThreshold) {
-      this._state = 'open';
-    }
-  }
-
-  /** @internal Reset to initial state (used in tests). */
-  reset(): void {
-    this._failures = 0;
-    this._state = 'closed';
-    this.lastFailureAt = 0;
-  }
-}
-
-/** Module-level singleton shared by both embedder entry points. */
-export const hfDownloadCircuit = new HfDownloadCircuitBreaker();
+export const hfDownloadCircuit = new CircuitBreaker({
+  failureThreshold: CB_FAILURE_THRESHOLD,
+  cooldownMs: CB_RESET_TIMEOUT_MS,
+  key: 'hf-download',
+});
 
 // ---------------------------------------------------------------------------
 // Retry + timeout wrapper
@@ -219,11 +170,6 @@ export function withDownloadTimeout<T>(fn: () => Promise<T>, timeoutMs: number):
   });
 }
 
-/** @internal Async sleep (exposed for testing). */
-export function sleep(ms: number): Promise<void> {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
 export interface HfRetryOptions {
   /** Maximum total attempts including the initial one (default: `HF_MAX_ATTEMPTS`). */
   maxAttempts?: number;
@@ -235,7 +181,7 @@ export interface HfRetryOptions {
    * Circuit-breaker instance to use. Defaults to the module-level
    * `hfDownloadCircuit` singleton. Pass a fresh instance in tests.
    */
-  circuit?: HfDownloadCircuitBreaker;
+  circuit?: CircuitBreaker;
   /**
    * Optional callback invoked before each retry (not the initial attempt).
    * @param attempt - 1-based retry number
@@ -295,49 +241,74 @@ export async function withHfDownloadRetry<T>(
     circuit = hfDownloadCircuit,
     onRetry,
   } = options;
-  if (circuit.isOpen()) {
-    const secsUntilReset = Math.ceil(
-      (circuit.resetTimeoutMs - (Date.now() - circuit.lastFailureAt)) / 1000,
-    );
+  if (circuit.getState() === 'open') {
+    // Compute remaining cooldown without consuming a probe permit.
+    const openedAt = circuit.getOpenedAt();
+    const secsUntilReset =
+      openedAt !== null ? Math.ceil((circuit.getCooldownMs() - (Date.now() - openedAt)) / 1000) : 0;
     throw new Error(
       `${CIRCUIT_OPEN_TAG}: HuggingFace download circuit is open after repeated network failures` +
         (secsUntilReset > 0 ? ` — will reset in ~${secsUntilReset}s` : ''),
     );
   }
 
-  let lastError: Error = new Error('unknown error');
+  // Retry budget delegated to `withRetry` from gitnexus-shared. The
+  // HF-specific bits — per-attempt timeout, network-vs-non-network
+  // classification, circuit-breaker recording, onRetry callback — wire
+  // through the `isRetryable` callback. `circuitTripped` is the
+  // sentinel that lets us replace the final thrown error with a
+  // CIRCUIT_OPEN_TAG message when the breaker tripped mid-loop.
+  let circuitTripped = false;
 
-  for (let attempt = 0; attempt < maxAttempts; attempt++) {
-    try {
-      const result = await withDownloadTimeout(fn, timeoutMs);
-      circuit.recordSuccess();
-      return result;
-    } catch (err) {
-      lastError = err instanceof Error ? err : new Error(String(err));
-
-      if (!isNetworkFetchError(lastError.message)) {
-        // Non-network error (e.g. CUDA unavailable) — propagate without retry
-        throw lastError;
-      }
-
-      circuit.recordFailure();
-
-      if (circuit.isOpen()) {
-        // Circuit just tripped — fail fast, no more retries
-        throw new Error(
-          `${CIRCUIT_OPEN_TAG}: HuggingFace download circuit opened after ${circuit.failureThreshold} consecutive failures`,
-        );
-      }
-
-      if (attempt < maxAttempts - 1) {
-        const delay = baseDelayMs * Math.pow(2, attempt);
-        onRetry?.(attempt + 1, maxAttempts, lastError);
-        await sleep(delay);
-      }
+  try {
+    return await withRetry(
+      async () => {
+        const result = await withDownloadTimeout(fn, timeoutMs);
+        circuit.recordSuccess();
+        return result;
+      },
+      {
+        maxAttempts,
+        baseDelayMs,
+        // Disable the cap to match the bespoke pure-exponential
+        // progression. With the default `HF_MAX_ATTEMPTS_CAP = 10` and
+        // `baseDelayMs = 2000`, the largest possible delay is
+        // `2000 * 2^9 = ~17 minutes` — bounded enough not to need a cap.
+        capDelayMs: Number.MAX_SAFE_INTEGER,
+        isRetryable: (err, attempt) => {
+          const error = err instanceof Error ? err : new Error(String(err));
+          if (!isNetworkFetchError(error.message)) {
+            // Non-network error (e.g. CUDA unavailable) — propagate
+            // without retry. Use recordNeutral so the breaker's existing
+            // failure-count progress isn't reset by a non-network failure
+            // that says nothing about the CDN's health.
+            circuit.recordNeutral();
+            return { retry: false };
+          }
+          circuit.recordFailure();
+          if (circuit.getState() === 'open') {
+            // Circuit just tripped — fail fast, no more retries.
+            circuitTripped = true;
+            return { retry: false };
+          }
+          // Mirror the bespoke onRetry contract: fire only when there's
+          // actually a next attempt.
+          if (attempt + 1 < maxAttempts) {
+            onRetry?.(attempt + 1, maxAttempts, error);
+          }
+          return { retry: true };
+        },
+      },
+    );
+  } catch (err) {
+    if (circuitTripped) {
+      throw new Error(
+        `${CIRCUIT_OPEN_TAG}: HuggingFace download circuit opened after ${CB_FAILURE_THRESHOLD} consecutive failures`,
+      );
     }
+    // All retries exhausted — rethrow the last network error so
+    // isNetworkFetchError patterns in the calling code still match and
+    // surface HF_ENDPOINT guidance.
+    throw err;
   }
-
-  // All retries exhausted — throw the last network error so isNetworkFetchError
-  // patterns in the calling code still match and surface HF_ENDPOINT guidance.
-  throw lastError;
 }

gitnexus/src/core/embeddings/http-client.ts

@@ -3,13 +3,22 @@
  *
  * Shared fetch+retry logic for OpenAI-compatible /v1/embeddings endpoints.
  * Imported by both the core embedder (batch) and MCP embedder (query).
+ *
+ * Network resilience is delegated to `resilientFetch` from
+ * `gitnexus-shared` — bounded retries with exponential-backoff jitter,
+ * `Retry-After` honored on 429, and an in-process circuit breaker that
+ * fails fast on a flapping endpoint. Per-attempt timeout is enforced
+ * via `AbortSignal.timeout` on the underlying fetch.
  */
 
+import { CircuitOpenError, ResilientFetchExhaustedError, resilientFetch } from 'gitnexus-shared';
+
 const HTTP_TIMEOUT_MS = 30_000;
 const HTTP_MAX_RETRIES = 2;
 const HTTP_RETRY_BACKOFF_MS = 1_000;
 const HTTP_BATCH_SIZE = 64;
 const DEFAULT_DIMS = 384;
+const HTTP_BREAKER_KEY = 'embeddings-http';
 
 interface HttpConfig {
   baseUrl: string;
@@ -31,8 +40,11 @@ const readConfig = (): HttpConfig | null => {
   const rawDims = process.env.GITNEXUS_EMBEDDING_DIMS;
   let dimensions: number | undefined;
   if (rawDims !== undefined) {
+    if (!/^\d+$/.test(rawDims)) {
+      throw new Error(`GITNEXUS_EMBEDDING_DIMS must be a positive integer, got "${rawDims}"`);
+    }
     const parsed = parseInt(rawDims, 10);
-    if (Number.isNaN(parsed) || parsed <= 0) {
+    if (parsed <= 0) {
       throw new Error(`GITNEXUS_EMBEDDING_DIMS must be a positive integer, got "${rawDims}"`);
     }
     dimensions = parsed;
@@ -82,7 +94,13 @@ interface EmbeddingItem {
  * @param model - Model name for the request body
  * @param apiKey - Bearer token (only used in Authorization header)
  * @param batchIndex - Logical batch number (for error context)
- * @param attempt - Current retry attempt (internal)
+ * @param dimensions - Optional output-vector size. When provided, sent as
+ *   the `dimensions` field in the request body. Endpoints that implement
+ *   Matryoshka truncation (OpenAI text-embedding-3-*, Cohere embed-v3,
+ *   Voyage) return a truncated vector at that size; endpoints that do not
+ *   recognise the field may ignore it or return 400. Leave
+ *   `GITNEXUS_EMBEDDING_DIMS` unset for strict backends that reject
+ *   unknown fields.
  */
 const httpEmbedBatch = async (
   url: string,
@@ -90,46 +108,60 @@ const httpEmbedBatch = async (
   model: string,
   apiKey: string,
   batchIndex = 0,
-  attempt = 0,
+  dimensions?: number,
 ): Promise<EmbeddingItem[]> => {
+  const requestBody: { input: string[]; model: string; dimensions?: number } = {
+    input: batch,
+    model,
+  };
+  if (dimensions !== undefined) {
+    requestBody.dimensions = dimensions;
+  }
+
   let resp: Response;
   try {
-    resp = await fetch(url, {
-      method: 'POST',
-      signal: AbortSignal.timeout(HTTP_TIMEOUT_MS),
-      headers: {
-        'Content-Type': 'application/json',
-        Authorization: `Bearer ${apiKey}`,
+    resp = await resilientFetch(
+      url,
+      {
+        method: 'POST',
+        signal: AbortSignal.timeout(HTTP_TIMEOUT_MS),
+        headers: {
+          'Content-Type': 'application/json',
+          Authorization: `Bearer ${apiKey}`,
+        },
+        body: JSON.stringify(requestBody),
       },
-      body: JSON.stringify({ input: batch, model }),
-    });
+      {
+        breakerKey: HTTP_BREAKER_KEY,
+        retry: { maxAttempts: HTTP_MAX_RETRIES + 1, baseDelayMs: HTTP_RETRY_BACKOFF_MS },
+      },
+    );
   } catch (err) {
-    // Timeouts should not be retried — the server is unresponsive.
-    // AbortSignal.timeout() throws DOMException with name 'TimeoutError'.
-    const isTimeout = err instanceof DOMException && err.name === 'TimeoutError';
-    if (isTimeout) {
+    if (err instanceof CircuitOpenError) {
+      throw new Error(
+        `Embedding endpoint circuit open (${safeUrl(url)}, batch ${batchIndex}): retry in ${Math.ceil(err.retryAfterMs / 1000)}s`,
+      );
+    }
+    if (err instanceof DOMException && err.name === 'TimeoutError') {
       throw new Error(
         `Embedding request timed out after ${HTTP_TIMEOUT_MS}ms (${safeUrl(url)}, batch ${batchIndex})`,
       );
     }
-    // DNS, connection errors — retry with backoff
-    if (attempt < HTTP_MAX_RETRIES) {
-      const delay = HTTP_RETRY_BACKOFF_MS * (attempt + 1);
-      await new Promise((r) => setTimeout(r, delay));
-      return httpEmbedBatch(url, batch, model, apiKey, batchIndex, attempt + 1);
+    if (err instanceof ResilientFetchExhaustedError) {
+      throw new Error(
+        `Embedding endpoint returned ${err.response.status} (${safeUrl(url)}, batch ${batchIndex})`,
+      );
     }
     const reason = err instanceof Error ? err.message : String(err);
     throw new Error(`Embedding request failed (${safeUrl(url)}, batch ${batchIndex}): ${reason}`);
   }
 
   if (!resp.ok) {
-    const status = resp.status;
-    if ((status === 429 || status >= 500) && attempt < HTTP_MAX_RETRIES) {
-      const delay = HTTP_RETRY_BACKOFF_MS * (attempt + 1);
-      await new Promise((r) => setTimeout(r, delay));
-      return httpEmbedBatch(url, batch, model, apiKey, batchIndex, attempt + 1);
-    }
-    throw new Error(`Embedding endpoint returned ${status} (${safeUrl(url)}, batch ${batchIndex})`);
+    // resilientFetch already retried 5xx/429; any non-OK response here is
+    // a terminal client error (4xx other than 429).
+    throw new Error(
+      `Embedding endpoint returned ${resp.status} (${safeUrl(url)}, batch ${batchIndex})`,
+    );
   }
 
   const data = (await resp.json()) as { data: EmbeddingItem[] };
@@ -155,7 +187,14 @@ export const httpEmbed = async (texts: string[]): Promise<Float32Array[]> => {
   for (let i = 0; i < texts.length; i += HTTP_BATCH_SIZE) {
     const batch = texts.slice(i, i + HTTP_BATCH_SIZE);
     const batchIndex = Math.floor(i / HTTP_BATCH_SIZE);
-    const items = await httpEmbedBatch(url, batch, config.model, config.apiKey, batchIndex);
+    const items = await httpEmbedBatch(
+      url,
+      batch,
+      config.model,
+      config.apiKey,
+      batchIndex,
+      config.dimensions,
+    );
 
     if (items.length !== batch.length) {
       throw new Error(
@@ -198,7 +237,14 @@ export const httpEmbedQuery = async (text: string): Promise<number[]> => {
   if (!config) throw new Error('HTTP embedding not configured');
 
   const url = `${config.baseUrl}/embeddings`;
-  const items = await httpEmbedBatch(url, [text], config.model, config.apiKey);
+  const items = await httpEmbedBatch(
+    url,
+    [text],
+    config.model,
+    config.apiKey,
+    0,
+    config.dimensions,
+  );
   if (!items.length) {
     throw new Error(`Embedding endpoint returned empty response (${safeUrl(url)})`);
   }

gitnexus/src/core/group/bridge-db.ts

@@ -722,13 +722,15 @@ export async function openBridgeDbReadOnly(groupDir: string): Promise<BridgeHand
       await new Promise((r) => setTimeout(r, delay));
     }
   }
-  // Pino's NDJSON serialization is structurally injection-resistant
-  // (CodeQL js/log-injection): groupDir and err.message are JSON-escaped
-  // by the serializer, so no manual CRLF / U+2028 / ANSI sanitization is
-  // needed. Demoted to debug — only fires when the bridge truly gave up
-  // after retries, and operators only need it at debug verbosity.
+  // Strip CRLF from user-controlled strings before logging to close
+  // CodeQL js/log-injection. Pino's NDJSON serialization already
+  // JSON-escapes all values, but we sanitize here as a defence-in-depth
+  // measure so CodeQL can see the taint flow is broken.
+  const safeGroupDir = String(groupDir).replace(/[\r\n]/g, ' ');
+  const safeErrMsg =
+    lastErr instanceof Error ? String(lastErr.message).replace(/[\r\n]/g, ' ') : undefined;
   bridgeLogger.debug(
-    { groupDir, err: lastErr, attempts: LBUG_OPEN_RETRY_ATTEMPTS },
+    { groupDir: safeGroupDir, errMsg: safeErrMsg, attempts: LBUG_OPEN_RETRY_ATTEMPTS },
     'openBridgeDbReadOnly gave up',
   );
   return null;

gitnexus/src/core/group/config-parser.ts

@@ -4,9 +4,26 @@ import type { GroupConfig, GroupManifestLink, ContractType, ContractRole } from
 const _require = createRequire(import.meta.url);
 const yaml = _require('js-yaml') as typeof import('js-yaml');
 
-const VALID_CONTRACT_TYPES: ContractType[] = ['http', 'grpc', 'thrift', 'topic', 'lib', 'custom'];
+const VALID_CONTRACT_TYPES: ContractType[] = [
+  'http',
+  'grpc',
+  'thrift',
+  'topic',
+  'lib',
+  'custom',
+  'include',
+];
 const VALID_ROLES: ContractRole[] = ['provider', 'consumer'];
 
+// Defaults matter for backward compatibility: any group.yaml that omits a
+// `detect.<type>` key inherits its value from this constant. Adding a new
+// extractor that defaults to `true` silently changes the behavior of every
+// existing group on the next sync. New extractors must default to `false`
+// (opt-in) so operators consciously enable them via group.yaml.
+//
+// `includes`: opt-in. The C/C++ IncludeExtractor (PR #1156) ships disabled by
+// default; enable with `detect.includes: true` for groups containing C/C++
+// repos that need cross-repo header tracking.
 const DEFAULT_DETECT = {
   http: true,
   grpc: true,
@@ -14,6 +31,7 @@ const DEFAULT_DETECT = {
   topics: true,
   shared_libs: true,
   embedding_fallback: true,
+  includes: false,
   workspace_deps: false,
 };
 

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

@@ -5,6 +5,7 @@ import { createIgnoreFilter } from '../../../config/ignore-service.js';
 import type { ContractExtractor, CypherExecutor } from '../contract-extractor.js';
 import type { ExtractedContract, RepoHandle } from '../types.js';
 import { readSafe } from './fs-utils.js';
+import { parseSourceSafe } from '../../tree-sitter/safe-parse.js';
 import { logger } from '../../logger.js';
 import {
   GRPC_SCAN_GLOB,
@@ -428,7 +429,7 @@ export class GrpcExtractor implements ContractExtractor {
       let detections: GrpcDetection[] = [];
       try {
         parser.setLanguage(plugin.language);
-        const tree = parser.parse(content);
+        const tree = parseSourceSafe(parser, content);
         detections = plugin.scan(tree);
       } catch {
         continue;

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

@@ -1,3 +1,4 @@
+import type Parser from 'tree-sitter';
 import Python from 'tree-sitter-python';
 import {
   compilePatterns,
@@ -12,6 +13,7 @@ import type { HttpDetection, HttpLanguagePlugin } from './types.js';
  *   - FastAPI `@app.get("/path")` provider decorators
  *   - `requests.get/post/...("url")` consumer calls
  *   - Generic `requests.request("METHOD", "url")` consumer calls
+ *   - `httpx.AsyncClient` instances calling `.get/.post/...("url")`
  */
 
 const FASTAPI_VERBS: Record<string, string> = {
@@ -77,11 +79,161 @@ const REQUESTS_GENERIC_PATTERNS = compilePatterns({
   ],
 } satisfies LanguagePatterns<Record<string, never>>);
 
+// ─── Consumer: httpx.AsyncClient assignments ────────────────────────
+// NOTE: This targeted detector only tracks explicit `httpx.AsyncClient(...)`
+// construction. Direct imports (`from httpx import AsyncClient`) and module
+// aliases (`import httpx as hx`) and annotated assignments (`client: httpx.AsyncClient = ...`)
+// are intentionally left for a follow-up. Module-scope clients are only matched
+// at module scope; calls inside functions require a function/class-local tracked
+// client to avoid false positives from same-name local variables.
+const HTTPX_ASYNC_CLIENT_ASSIGN_PATTERNS = compilePatterns({
+  name: 'python-httpx-async-client-assign',
+  language: Python,
+  patterns: [
+    {
+      meta: {},
+      query: `
+        (assignment
+          left: (_) @client
+          right: (call
+            function: (attribute
+              object: (identifier) @module (#eq? @module "httpx")
+              attribute: (identifier) @client_class (#eq? @client_class "AsyncClient"))))
+      `,
+    },
+  ],
+} satisfies LanguagePatterns<Record<string, never>>);
+
+// ─── Consumer: async with httpx.AsyncClient() as client ──────────────
+const HTTPX_ASYNC_CLIENT_WITH_ALIAS_PATTERNS = compilePatterns({
+  name: 'python-httpx-async-client-with-alias',
+  language: Python,
+  patterns: [
+    {
+      meta: {},
+      query: `
+        (as_pattern
+          (call
+            function: (attribute
+              object: (identifier) @module (#eq? @module "httpx")
+              attribute: (identifier) @client_class (#eq? @client_class "AsyncClient")))
+          (as_pattern_target (identifier) @client))
+      `,
+    },
+  ],
+} satisfies LanguagePatterns<Record<string, never>>);
+
+function getScopeKey(node: Parser.SyntaxNode | null, preferClass = false): string {
+  if (preferClass) {
+    let current: Parser.SyntaxNode | null = node;
+    while (current) {
+      if (current.type === 'class_definition') {
+        return `class:${current.startIndex}:${current.endIndex}`;
+      }
+      current = current.parent;
+    }
+  }
+
+  let current: Parser.SyntaxNode | null = node;
+  while (current) {
+    if (current.type === 'function_definition') {
+      return `function:${current.startIndex}:${current.endIndex}`;
+    }
+    current = current.parent;
+  }
+
+  return 'module';
+}
+
+function trackedClientScopeKey(clientNode: Parser.SyntaxNode): string {
+  return getScopeKey(clientNode.parent, clientNode.text.includes('.'));
+}
+
+function callScopeKeys(clientNode: Parser.SyntaxNode): string[] {
+  const keys = new Set<string>();
+  const preferClass = clientNode.text.includes('.');
+  const nearestScope = getScopeKey(clientNode.parent, preferClass);
+
+  keys.add(nearestScope);
+
+  return [...keys];
+}
+
+function collectHttpxAsyncClients(tree: Parser.Tree): Map<string, Set<string>> {
+  const clients = new Map<string, Set<string>>();
+
+  const addClient = (clientNode: Parser.SyntaxNode | undefined) => {
+    if (!clientNode) return;
+    const scopeKey = trackedClientScopeKey(clientNode);
+    const clientText = clientNode.text;
+    const scopes = clients.get(clientText) ?? new Set<string>();
+    scopes.add(scopeKey);
+    clients.set(clientText, scopes);
+  };
+
+  for (const match of runCompiledPatterns(HTTPX_ASYNC_CLIENT_ASSIGN_PATTERNS, tree)) {
+    addClient(match.captures.client);
+  }
+
+  for (const match of runCompiledPatterns(HTTPX_ASYNC_CLIENT_WITH_ALIAS_PATTERNS, tree)) {
+    addClient(match.captures.client);
+  }
+
+  return clients;
+}
+
+function hasTrackedHttpxAsyncClient(
+  clients: Map<string, Set<string>>,
+  clientNode: Parser.SyntaxNode,
+): boolean {
+  const scopes = clients.get(clientNode.text);
+  if (!scopes) return false;
+
+  return callScopeKeys(clientNode).some((scopeKey) => scopes.has(scopeKey));
+}
+
+// ─── Consumer: httpx AsyncClient .get/.post/...("url") ──────────────
+const HTTPX_ASYNC_CLIENT_VERB_PATTERNS = compilePatterns({
+  name: 'python-httpx-async-client-verb',
+  language: Python,
+  patterns: [
+    {
+      meta: {},
+      query: `
+        (call
+          function: (attribute
+            object: (_) @client
+            attribute: (identifier) @method (#match? @method "^(get|post|put|delete|patch)$"))
+          arguments: (argument_list . (string) @path))
+      `,
+    },
+  ],
+} satisfies LanguagePatterns<Record<string, never>>);
+
+// ─── Consumer: httpx AsyncClient .request("METHOD", "url") ─────────
+const HTTPX_ASYNC_CLIENT_GENERIC_PATTERNS = compilePatterns({
+  name: 'python-httpx-async-client-generic',
+  language: Python,
+  patterns: [
+    {
+      meta: {},
+      query: `
+        (call
+          function: (attribute
+            object: (_) @client
+            attribute: (identifier) @method (#eq? @method "request"))
+          arguments: (argument_list . (string) @http_method (string) @path))
+      `,
+    },
+  ],
+} satisfies LanguagePatterns<Record<string, never>>);
+
 export const PYTHON_HTTP_PLUGIN: HttpLanguagePlugin = {
   name: 'python-http',
   language: Python,
   scan(tree) {
     const out: HttpDetection[] = [];
+    const httpxAsyncClients = collectHttpxAsyncClients(tree);
 
     // Providers: FastAPI
     for (const match of runCompiledPatterns(FASTAPI_PATTERNS, tree)) {
@@ -137,6 +289,45 @@ export const PYTHON_HTTP_PLUGIN: HttpLanguagePlugin = {
       });
     }
 
+    // Consumers: httpx.AsyncClient.<verb>("url")
+    for (const match of runCompiledPatterns(HTTPX_ASYNC_CLIENT_VERB_PATTERNS, tree)) {
+      const clientNode = match.captures.client;
+      const methodNode = match.captures.method;
+      const pathNode = match.captures.path;
+      if (!clientNode || !methodNode || !pathNode) continue;
+      if (!hasTrackedHttpxAsyncClient(httpxAsyncClients, clientNode)) continue;
+      const path = unquoteLiteral(pathNode.text);
+      if (path === null) continue;
+      out.push({
+        role: 'consumer',
+        framework: 'python-httpx',
+        method: methodNode.text.toUpperCase(),
+        path,
+        name: null,
+        confidence: 0.7,
+      });
+    }
+
+    // Consumers: httpx.AsyncClient.request("METHOD", "url")
+    for (const match of runCompiledPatterns(HTTPX_ASYNC_CLIENT_GENERIC_PATTERNS, tree)) {
+      const clientNode = match.captures.client;
+      const methodNode = match.captures.http_method;
+      const pathNode = match.captures.path;
+      if (!clientNode || !methodNode || !pathNode) continue;
+      if (!hasTrackedHttpxAsyncClient(httpxAsyncClients, clientNode)) continue;
+      const methodRaw = unquoteLiteral(methodNode.text);
+      const path = unquoteLiteral(pathNode.text);
+      if (methodRaw === null || path === null) continue;
+      out.push({
+        role: 'consumer',
+        framework: 'python-httpx',
+        method: methodRaw.toUpperCase(),
+        path,
+        name: null,
+        confidence: 0.7,
+      });
+    }
+
     return out;
   },
 };

gitnexus/src/core/group/extractors/http-route-extractor.ts

@@ -5,6 +5,7 @@ import { createIgnoreFilter } from '../../../config/ignore-service.js';
 import type { ContractExtractor, CypherExecutor } from '../contract-extractor.js';
 import type { ExtractedContract, RepoHandle } from '../types.js';
 import { readSafe } from './fs-utils.js';
+import { parseSourceSafe } from '../../tree-sitter/safe-parse.js';
 import { getPluginForFile, HTTP_SCAN_GLOB, type HttpDetection } from './http-patterns/index.js';
 
 /**
@@ -172,7 +173,7 @@ export class HttpRouteExtractor implements ContractExtractor {
       }
       try {
         parser.setLanguage(plugin.language);
-        const tree = parser.parse(content);
+        const tree = parseSourceSafe(parser, content);
         const detections = plugin.scan(tree);
         cachedDetections.set(rel, detections);
         return detections;

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

@@ -0,0 +1,611 @@
+import * as path from 'node:path';
+import * as fs from 'node:fs/promises';
+import { glob } from 'glob';
+import Parser from 'tree-sitter';
+import C from 'tree-sitter-c';
+import Cpp from 'tree-sitter-cpp';
+import type { ContractExtractor, CypherExecutor } from '../contract-extractor.js';
+import type { ExtractedContract, RepoHandle } from '../types.js';
+import { readSafe } from './fs-utils.js';
+import { buildSuffixIndex, type SuffixIndex } from '../../ingestion/import-resolvers/utils.js';
+import { createIgnoreFilter } from '../../../config/ignore-service.js';
+import { getMaxFileSizeBytes } from '../../ingestion/utils/max-file-size.js';
+import { parseSourceSafe } from '../../tree-sitter/safe-parse.js';
+import { logger } from '../../logger.js';
+
+/**
+ * Cross-repo C/C++ `#include` dependency extractor.
+ *
+ * **Provider side:** registers every `.h/.hpp/.hxx/.hh` file in the repo
+ * as a provider contract with `include::<relative-path>`.
+ *
+ * **Consumer side:** parses all C/C++ source/header files for `#include "…"`
+ * directives, attempts suffix-based resolution against the repo's own file
+ * list (reusing the same algorithm as the single-repo ingestion pipeline),
+ * and emits unresolved include paths as consumer contracts.
+ *
+ * Matching: a consumer's `include::map/base/dice_map_view.h` in repo A
+ * matches a provider's `include::map/base/dice_map_view.h` in repo B via
+ * exact contract-id equality in `runExactMatch`.
+ */
+
+// ---------- constants ----------
+
+const HEADER_EXTENSIONS = new Set(['.h', '.hpp', '.hxx', '.hh']);
+
+// Source = headers (provider-eligible) ∪ implementation files (.c/.cpp/.cc/.cxx).
+// Spread keeps the subset relationship explicit so a future contributor adding
+// a new header extension to HEADER_EXTENSIONS does not have to remember to
+// also add it here.
+const SOURCE_EXTENSIONS = new Set<string>([...HEADER_EXTENSIONS, '.c', '.cpp', '.cc', '.cxx']);
+
+const INCLUDE_QUERY_SRC = '(preproc_include path: (_) @import.source) @import';
+
+/**
+ * Well-known C/C++ standard library headers that can appear in `#include "…"`
+ * form (some projects use quotes for system headers).
+ */
+const SYSTEM_HEADERS = new Set([
+  // C standard
+  'assert.h',
+  'complex.h',
+  'ctype.h',
+  'errno.h',
+  'fenv.h',
+  'float.h',
+  'inttypes.h',
+  'iso646.h',
+  'limits.h',
+  'locale.h',
+  'math.h',
+  'setjmp.h',
+  'signal.h',
+  'stdalign.h',
+  'stdarg.h',
+  'stdatomic.h',
+  'stdbool.h',
+  'stddef.h',
+  'stdint.h',
+  'stdio.h',
+  'stdlib.h',
+  'stdnoreturn.h',
+  'string.h',
+  'tgmath.h',
+  'threads.h',
+  'time.h',
+  'uchar.h',
+  'wchar.h',
+  'wctype.h',
+  // C++ standard (extensionless)
+  'algorithm',
+  'any',
+  'array',
+  'atomic',
+  'barrier',
+  'bit',
+  'bitset',
+  'cassert',
+  'cctype',
+  'cerrno',
+  'cfenv',
+  'cfloat',
+  'charconv',
+  'chrono',
+  'cinttypes',
+  'climits',
+  'clocale',
+  'cmath',
+  'codecvt',
+  'compare',
+  'complex',
+  'concepts',
+  'condition_variable',
+  'coroutine',
+  'csetjmp',
+  'csignal',
+  'cstdarg',
+  'cstddef',
+  'cstdint',
+  'cstdio',
+  'cstdlib',
+  'cstring',
+  'ctime',
+  'cuchar',
+  'cwchar',
+  'cwctype',
+  'deque',
+  'exception',
+  'execution',
+  'expected',
+  'filesystem',
+  'format',
+  'forward_list',
+  'fstream',
+  'functional',
+  'future',
+  'generator',
+  'initializer_list',
+  'iomanip',
+  'ios',
+  'iosfwd',
+  'iostream',
+  'istream',
+  'iterator',
+  'latch',
+  'limits',
+  'list',
+  'locale',
+  'map',
+  'mdspan',
+  'memory',
+  'memory_resource',
+  'mutex',
+  'new',
+  'numbers',
+  'numeric',
+  'optional',
+  'ostream',
+  'print',
+  'queue',
+  'random',
+  'ranges',
+  'ratio',
+  'regex',
+  'scoped_allocator',
+  'semaphore',
+  'set',
+  'shared_mutex',
+  'source_location',
+  'span',
+  'spanstream',
+  'sstream',
+  'stack',
+  'stacktrace',
+  'stdexcept',
+  'stdfloat',
+  'stop_token',
+  'streambuf',
+  'string',
+  'string_view',
+  'strstream',
+  'syncstream',
+  'system_error',
+  'thread',
+  'tuple',
+  'type_traits',
+  'typeindex',
+  'typeinfo',
+  'unordered_map',
+  'unordered_set',
+  'utility',
+  'valarray',
+  'variant',
+  'vector',
+  'version',
+]);
+
+/** Path prefixes that indicate system/kernel headers. */
+const SYSTEM_PATH_PREFIXES = [
+  'sys/',
+  'net/',
+  'netinet/',
+  'arpa/',
+  'linux/',
+  'asm/',
+  'bits/',
+  'gnu/',
+  'mach/',
+  'machine/',
+  'xlocale/',
+];
+
+/** Regex fallback for files that exceed tree-sitter's 32 KB parse limit. */
+const INCLUDE_REGEX = /^[ \t]*#\s*include\s*"([^"]+)"/gm;
+
+// ---------- helpers ----------
+
+/**
+ * Normalize an include path to a canonical lowercase forward-slash form.
+ *
+ * IMPORTANT — case-folding caveat (PR #1156 review finding #3):
+ *   Header paths are lowercased so consumer `#include "Foo/Bar.h"` and
+ *   provider file `Foo/Bar.h` normalize to the same contract-id. This is
+ *   the right trade-off on case-insensitive filesystems (macOS, Windows)
+ *   but on case-sensitive Linux filesystems two distinct headers `Foo.h`
+ *   and `foo.h` in the same repo will collide onto the same provider
+ *   contract-id; only one survives `dedupe()`. The gain (reliable
+ *   cross-platform matching) outweighs the cost (extremely rare header
+ *   casing collisions inside a single repo).
+ */
+function normalizeIncludePath(raw: string): string {
+  return raw.replace(/\\/g, '/').replace(/^\.\//, '').replace(/\/+/g, '/').toLowerCase();
+}
+
+/**
+ * Strip C/C++ block comments from a source blob. Used only by the
+ * regex-fallback path to avoid emitting consumer contracts for
+ * commented-out #include directives. Line comments (`// …`) cannot hide
+ * #include directives because the regex anchors on start-of-line.
+ * See PR #1156 review finding #5.
+ */
+function stripBlockComments(src: string): string {
+  return src.replace(/\/\*[\s\S]*?\*\//g, '');
+}
+
+function isAngleBracketInclude(rawNodeText: string): boolean {
+  const trimmed = rawNodeText.trim();
+  return trimmed.startsWith('<') && trimmed.endsWith('>');
+}
+
+function isSystemHeader(cleanedPath: string): boolean {
+  // Check well-known standard headers
+  if (SYSTEM_HEADERS.has(cleanedPath)) return true;
+  // Check system path prefixes
+  const lower = cleanedPath.toLowerCase();
+  return SYSTEM_PATH_PREFIXES.some((prefix) => lower.startsWith(prefix));
+}
+
+function isHeaderFile(filePath: string): boolean {
+  return HEADER_EXTENSIONS.has(path.extname(filePath).toLowerCase());
+}
+
+function getLanguageForFile(filePath: string): unknown | null {
+  const ext = path.extname(filePath).toLowerCase();
+  switch (ext) {
+    case '.c':
+    case '.h':
+      return C;
+    case '.cpp':
+    case '.cc':
+    case '.cxx':
+    case '.hpp':
+    case '.hxx':
+    case '.hh':
+      return Cpp;
+    default:
+      return null;
+  }
+}
+
+/**
+ * Check whether an include path resolves to a file inside the local repo.
+ *
+ * Uses *exact full-path* matching on the suffix index — we never accept a
+ * truncated suffix match. For `#include "foo/bar.h"` this checks:
+ *   (a) a file whose path ends with the full `foo/bar.h`
+ *   (b) if the include omitted the extension, a file whose path ends with
+ *       the include + one of the C/C++ header extensions
+ *
+ * Returns `true` when a local file matches — caller should suppress the
+ * cross-repo consumer contract.
+ *
+ * See PR #1156 review finding #4 (suffixResolve ambiguity).
+ */
+function isLocalInclude(cleaned: string, suffixIndex: SuffixIndex): boolean {
+  const candidates = [cleaned];
+  if (!/\.[a-zA-Z0-9]+$/.test(cleaned)) {
+    for (const ext of ['.h', '.hpp', '.hxx', '.hh']) candidates.push(cleaned + ext);
+  }
+  for (const c of candidates) {
+    if (suffixIndex.get(c) || suffixIndex.getInsensitive(c)) return true;
+  }
+  return false;
+}
+
+// ---------- main class ----------
+
+export class IncludeExtractor implements ContractExtractor {
+  type = 'include' as const;
+
+  /**
+   * Always returns `true`. NOT called by `sync.ts`, which gates extraction via
+   * `config.detect.includes` instead (see `sync.ts:174`). Kept solely to satisfy
+   * the `ContractExtractor` interface so the type stays uniform across extractors.
+   */
+  async canExtract(_repo: RepoHandle): Promise<boolean> {
+    return true;
+  }
+
+  async extract(
+    dbExecutor: CypherExecutor | null,
+    repoPath: string,
+    _repo: RepoHandle,
+  ): Promise<ExtractedContract[]> {
+    // 1. Build the local file list using the same discovery as ingestion
+    //    (createIgnoreFilter + getMaxFileSizeBytes). This guarantees the
+    //    universe of provider/consumer paths matches the universe of File
+    //    nodes in the LadybugDB graph — so no cross-link points at a UID
+    //    that group impact cannot fan out to.
+    //    (PR #1156 Codex follow-up: discovery aligned with ingestion.)
+    const allFiles = await this.discoverIndexableFiles(repoPath);
+    const normalizedFiles = allFiles.map((f) => f.replace(/\\/g, '/'));
+    const suffixIndex = buildSuffixIndex(normalizedFiles, allFiles);
+
+    // 2. Provider: register all header files
+    const providers = await this.extractProviders(dbExecutor, repoPath, allFiles);
+
+    // 3. Consumer: filter the shared discovery list for source extensions
+    //    and parse #include directives in those files.
+    const sourceFiles = allFiles.filter((f) =>
+      SOURCE_EXTENSIONS.has(path.extname(f).toLowerCase()),
+    );
+    const consumers = await this.extractConsumers(repoPath, sourceFiles, suffixIndex);
+
+    return this.dedupe([...providers, ...consumers]);
+  }
+
+  /**
+   * Discover repo-relative file paths using exactly the same rules the
+   * ingestion pipeline uses (`walkRepositoryPaths` in
+   * `gitnexus/src/core/ingestion/filesystem-walker.ts`):
+   *   - `createIgnoreFilter` honors `.gitignore`, `.gitnexusignore`, the
+   *     hardcoded ignore list, and `.gitnexusignore` last-match-wins
+   *     negation.
+   *   - `getMaxFileSizeBytes()` drops files larger than the cap so we
+   *     never emit `File:<rel>` UIDs for files ingestion would skip.
+   *
+   * Uses sequential stat — there is no `READ_CONCURRENCY` batching here
+   * because group sync runs at startup-time, not the ingestion hot path,
+   * and parallelism gains are not worth the import-graph weight.
+   *
+   * MAINTENANCE: if `walkRepositoryPaths` changes its glob options, ignore
+   * filter shape, or size-cap logic, mirror those changes here. The two
+   * implementations exist because the consumers need different return
+   * shapes (string[] vs ScannedFile[]) and different concurrency, but
+   * they MUST agree on which files are reachable — that is what makes
+   * `File:<rel>` UIDs in cross-links correspond to graph File nodes.
+   */
+  private async discoverIndexableFiles(repoPath: string): Promise<string[]> {
+    const ignoreFilter = await createIgnoreFilter(repoPath);
+    const maxFileSizeBytes = getMaxFileSizeBytes();
+
+    const candidates = await glob('**/*', {
+      cwd: repoPath,
+      nodir: true,
+      dot: false,
+      ignore: ignoreFilter,
+    });
+
+    const survivors: string[] = [];
+    for (const rel of candidates) {
+      try {
+        const stat = await fs.stat(path.join(repoPath, rel));
+        if (stat.size > maxFileSizeBytes) continue;
+        survivors.push(rel);
+      } catch (err) {
+        // ENOENT is the documented benign race (glob enumerated a file
+        // that was deleted before we stat'd it — same race
+        // walkRepositoryPaths absorbs via Promise.allSettled). Anything
+        // else (EACCES, EMFILE, EIO) deserves a warning so an operator
+        // can spot a permission/resource problem instead of silently
+        // shipping fewer contracts than expected.
+        const code = (err as NodeJS.ErrnoException | undefined)?.code;
+        if (code !== 'ENOENT') {
+          logger.warn(
+            { err: (err as Error).message, file: rel, repoPath },
+            '⚠️ IncludeExtractor: stat failed during discovery; skipping file',
+          );
+        }
+      }
+    }
+    return survivors;
+  }
+
+  // ---------- provider extraction ----------
+
+  private async extractProviders(
+    dbExecutor: CypherExecutor | null,
+    repoPath: string,
+    allFiles: string[],
+  ): Promise<ExtractedContract[]> {
+    // Strategy A: graph-assisted
+    if (dbExecutor) {
+      const graphProviders = await this.extractProvidersGraph(dbExecutor, repoPath);
+      if (graphProviders.length > 0) return graphProviders;
+    }
+    // Strategy B: filesystem fallback
+    return this.extractProvidersFallback(repoPath, allFiles);
+  }
+
+  private async extractProvidersGraph(
+    db: CypherExecutor,
+    repoPath: string,
+  ): Promise<ExtractedContract[]> {
+    try {
+      const rows = await db(
+        `MATCH (f:File)
+         WHERE f.filePath =~ '.*\\\\.(h|hpp|hxx|hh)$'
+         RETURN f.filePath AS filePath, f.id AS fileId`,
+      );
+      // gitnexus analyze stores absolute paths in the File.filePath column.
+      // Provider contract IDs MUST be repo-relative — otherwise the consumer
+      // emits `include::map/base/view.h` and the provider emits
+      // `include::/abs/path/to/repo/map/base/view.h`, which never match
+      // through runExactMatch and the cross-link silently disappears.
+      // (PR #1156 follow-up review: graph provider absolute-path bug.)
+      const normalizedRepoPath = path.resolve(repoPath);
+      const out: ExtractedContract[] = [];
+      for (const r of rows) {
+        if (typeof r.filePath !== 'string' || !r.filePath) continue;
+        const absolute = r.filePath as string;
+        const rel = path.relative(normalizedRepoPath, absolute);
+        // Skip rows that resolve outside the repo (e.g., system headers
+        // somehow indexed, or stale absolute paths from a different machine).
+        // path.relative returns a `..`-prefixed path or an absolute path
+        // when the target is outside the base — both are wrong for our IDs.
+        if (!rel || rel.startsWith('..') || path.isAbsolute(rel)) continue;
+        const normalizedRel = rel.replace(/\\/g, '/');
+        out.push({
+          contractId: `include::${normalizeIncludePath(normalizedRel)}`,
+          type: 'include' as const,
+          role: 'provider' as const,
+          symbolUid: String(r.fileId ?? ''),
+          symbolRef: { filePath: normalizedRel, name: path.basename(normalizedRel) },
+          symbolName: path.basename(normalizedRel),
+          confidence: 1.0,
+          meta: { source: 'graph' },
+        });
+      }
+      return out;
+    } catch {
+      return [];
+    }
+  }
+
+  private extractProvidersFallback(_repoPath: string, allFiles: string[]): ExtractedContract[] {
+    return allFiles
+      .filter((f) => isHeaderFile(f))
+      .map((f) => {
+        const filePath = f.replace(/\\/g, '/');
+        return {
+          contractId: `include::${normalizeIncludePath(filePath)}`,
+          type: 'include' as const,
+          role: 'provider' as const,
+          symbolUid: `File:${filePath}`,
+          symbolRef: { filePath, name: path.basename(filePath) },
+          symbolName: path.basename(filePath),
+          confidence: 0.95,
+          meta: { source: 'filesystem' },
+        };
+      });
+  }
+
+  // ---------- consumer extraction ----------
+
+  private async extractConsumers(
+    repoPath: string,
+    sourceFiles: string[],
+    suffixIndex: SuffixIndex,
+  ): Promise<ExtractedContract[]> {
+    const parser = new Parser();
+    const out: ExtractedContract[] = [];
+    // Compile the include query once per grammar to avoid re-compilation per file
+    const queryCache = new Map<unknown, Parser.Query>();
+
+    for (const rel of sourceFiles) {
+      const lang = getLanguageForFile(rel);
+      if (!lang) continue;
+
+      const content = readSafe(repoPath, rel);
+      if (!content) continue;
+
+      let query = queryCache.get(lang);
+      if (!query) {
+        try {
+          query = new Parser.Query(lang, INCLUDE_QUERY_SRC);
+          queryCache.set(lang, query);
+        } catch {
+          continue;
+        }
+      }
+
+      // Collect raw include paths: tree-sitter first, regex fallback for large files.
+      // `extractionSource` is stamped on each emitted consumer contract so
+      // regex-fallback contracts stay auditable post-hoc (PR #1156 review finding #6).
+      let rawIncludes: string[];
+      let extractionSource: 'tree_sitter' | 'regex_fallback';
+      try {
+        parser.setLanguage(lang);
+        const tree = parseSourceSafe(parser, content);
+        let matches: Parser.QueryMatch[];
+        try {
+          matches = query.matches(tree.rootNode);
+        } catch {
+          matches = [];
+        }
+        rawIncludes = [];
+        extractionSource = 'tree_sitter';
+        for (const match of matches) {
+          const sourceNode = match.captures.find((c) => c.name === 'import.source');
+          if (!sourceNode) continue;
+          const rawText = sourceNode.node.text;
+          if (isAngleBracketInclude(rawText)) continue;
+          const cleaned = rawText.replace(/['"<>]/g, '');
+          if (cleaned && cleaned.length <= 2048) rawIncludes.push(cleaned);
+        }
+      } catch {
+        // tree-sitter failed (e.g. file > 32 KB) — fall back to regex.
+        // Strip block comments first so we don't emit a consumer contract
+        // for a commented-out #include (PR #1156 review finding #5).
+        rawIncludes = [];
+        extractionSource = 'regex_fallback';
+        const scanTarget = stripBlockComments(content);
+        INCLUDE_REGEX.lastIndex = 0;
+        let m: RegExpExecArray | null;
+        while ((m = INCLUDE_REGEX.exec(scanTarget)) !== null) {
+          if (m[1] && m[1].length <= 2048) rawIncludes.push(m[1]);
+        }
+      }
+
+      for (const cleaned of rawIncludes) {
+        // Filter: skip known system headers and system path prefixes
+        if (isSystemHeader(cleaned)) continue;
+
+        // Skip relative-up includes: `#include "../include/foo.h"` is
+        // almost always an intra-repo reference. The suffix index is built
+        // from repo-relative paths, so isLocalInclude can never match
+        // `../foo.h`, and emitting it as a consumer contract just pollutes
+        // the registry with an entry no provider can ever satisfy.
+        // (PR #1156 follow-up review: `../` relative includes produce
+        // spurious consumer contracts.)
+        if (cleaned.startsWith('../') || cleaned.startsWith('..\\')) continue;
+
+        // Skip macro-style includes: `#include PLATFORM_HEADER` parses as an
+        // identifier under tree-sitter's `(_) @import.source` wildcard. The
+        // identifier text passes the strip/clean step unchanged, so without
+        // this guard we would emit `include::platform_header` as a consumer
+        // contract — and no provider in any repo will ever expose a contract
+        // for a macro identifier (no file is named `PLATFORM_HEADER`). The
+        // contract would sit permanently orphaned in the registry. Real
+        // header references always contain a path separator (`/`, `\`) or an
+        // extension dot (`foo.h`), so an absent both is a reliable signal we
+        // are looking at a macro identifier. (PR #1156 follow-up review:
+        // macro includes emit orphaned consumer contracts.)
+        if (!/[./\\]/.test(cleaned)) continue;
+
+        // Local resolution (PR #1156 review finding #4): only accept an
+        // exact-suffix match on the *full* include path. The generic
+        // suffixResolve() iterates all truncated suffixes, which would
+        // silently suppress a cross-repo `#include "map/base/view.h"`
+        // when the local repo has any `internal/view.h` — a realistic
+        // false-negative in large C++ codebases. Here we only resolve
+        // locally if a file path ends with the complete include string
+        // (optionally re-appending one of the C/C++ header extensions
+        // when the include already omits it).
+        if (isLocalInclude(cleaned, suffixIndex)) continue;
+
+        // Unresolved: emit as consumer contract
+        const normalizedRel = rel.replace(/\\/g, '/');
+        out.push({
+          contractId: `include::${normalizeIncludePath(cleaned)}`,
+          type: 'include' as const,
+          role: 'consumer' as const,
+          symbolUid: `File:${normalizedRel}`,
+          symbolRef: { filePath: normalizedRel, name: cleaned },
+          symbolName: cleaned,
+          confidence: 0.85,
+          meta: {
+            source: extractionSource,
+            includePath: cleaned,
+          },
+        });
+      }
+    }
+
+    return out;
+  }
+
+  // ---------- deduplication ----------
+
+  private dedupe(items: ExtractedContract[]): ExtractedContract[] {
+    const seen = new Set<string>();
+    const out: ExtractedContract[] = [];
+    for (const c of items) {
+      const k = `${c.contractId}|${c.role}|${c.symbolRef.filePath}`;
+      if (seen.has(k)) continue;
+      seen.add(k);
+      out.push(c);
+    }
+    return out;
+  }
+}

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

@@ -274,6 +274,14 @@ export class ManifestExtractor {
            LIMIT 1`,
           { contract: link.contract },
         );
+      } else if (link.type === 'include') {
+        rows = await executor(
+          `MATCH (f:File) WHERE f.filePath = $contract
+           RETURN f.id AS uid, f.name AS name, f.filePath AS filePath
+           ORDER BY f.filePath ASC
+           LIMIT 1`,
+          { contract: link.contract },
+        );
       } else if (link.type === 'custom') {
         // Workspace extractors produce qualified contracts like "mathlex::Expression".
         // Graph nodes store the unqualified symbol name ("Expression"), so strip
@@ -358,6 +366,8 @@ export class ManifestExtractor {
         return `lib::${contract}`;
       case 'custom':
         return `custom::${contract}`;
+      case 'include':
+        return `include::${contract}`;
       default: {
         const _exhaustive: never = type;
         throw new Error(`Unhandled ContractType: ${String(_exhaustive)}`);

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

@@ -3,6 +3,7 @@ import Parser from 'tree-sitter';
 import type { ContractExtractor, CypherExecutor } from '../contract-extractor.js';
 import type { ExtractedContract, RepoHandle } from '../types.js';
 import { readSafe } from './fs-utils.js';
+import { parseSourceSafe } from '../../tree-sitter/safe-parse.js';
 import {
   getPluginForFile,
   THRIFT_SCAN_GLOB,
@@ -217,6 +218,10 @@ export async function buildThriftContext(repoPath: string): Promise<ThriftContex
     cwd: repoPath,
     absolute: false,
     nodir: true,
+    // TODO(#1156-followup): replace this hand-rolled list with createIgnoreFilter
+    // (the canonical ingestion ignore filter, like include-extractor.ts now uses).
+    // New entries to DEFAULT_IGNORE_LIST in src/config/ignore-service.ts (e.g.
+    // third_party, 3rdparty added in commit a9936a9b) silently do not apply here.
     ignore: ['**/node_modules/**', '**/.git/**', '**/vendor/**', '**/dist/**', '**/build/**'],
   });
   const namespacesByThrift = new Map<string, string>();
@@ -290,6 +295,10 @@ export class ThriftExtractor implements ContractExtractor {
       cwd: repoPath,
       absolute: false,
       nodir: true,
+      // TODO(#1156-followup): replace this hand-rolled list with createIgnoreFilter
+      // (the canonical ingestion ignore filter, like include-extractor.ts now uses).
+      // New entries to DEFAULT_IGNORE_LIST in src/config/ignore-service.ts (e.g.
+      // third_party, 3rdparty added in commit a9936a9b) silently do not apply here.
       ignore: ['**/node_modules/**', '**/.git/**', '**/vendor/**', '**/dist/**', '**/build/**'],
     });
 
@@ -303,7 +312,7 @@ export class ThriftExtractor implements ContractExtractor {
       let detections: ThriftDetection[] = [];
       try {
         parser.setLanguage(plugin.language);
-        const tree = parser.parse(content);
+        const tree = parseSourceSafe(parser, content);
         detections = plugin.scan(tree);
       } catch {
         continue;

gitnexus/src/core/group/extractors/tree-sitter-scanner.ts

@@ -1,4 +1,5 @@
 import Parser from 'tree-sitter';
+import { parseSourceSafe } from '../../tree-sitter/safe-parse.js';
 
 /**
  * Shared, language-agnostic tree-sitter scanning utilities used by group
@@ -155,7 +156,7 @@ export function scanFile<TMeta>(
   let tree: Parser.Tree;
   try {
     parser.setLanguage(plugin.language);
-    tree = parser.parse(content);
+    tree = parseSourceSafe(parser, content);
   } catch {
     return [];
   }

gitnexus/src/core/group/matching.ts

@@ -107,6 +107,8 @@ export function normalizeContractId(id: string): string {
       return `topic::${rest.trim().toLowerCase()}`;
     case 'lib':
       return `lib::${rest.toLowerCase()}`;
+    case 'include':
+      return `include::${rest.replace(/\\/g, '/').replace(/^\.\//, '').replace(/\/+/g, '/').toLowerCase()}`;
     default:
       return id;
   }

gitnexus/src/core/group/storage.ts

@@ -4,6 +4,7 @@ import * as path from 'node:path';
 import * as os from 'node:os';
 import { randomBytes } from 'node:crypto';
 import type { ContractRegistry } from './types.js';
+import { retryRename } from './bridge-db.js';
 
 /**
  * Build an unpredictable suffix for atomic-write tmp files. Replaces the
@@ -59,7 +60,13 @@ export async function writeContractRegistry(
   } finally {
     await handle.close();
   }
-  await fsp.rename(tmpPath, targetPath);
+  // retryRename absorbs the documented Windows EPERM/EBUSY/EACCES race that
+  // fires when AV scanners or another concurrent rename briefly hold the
+  // destination handle between rename calls. Same helper bridge-db.ts uses
+  // (lines 304, 583, 587, 595, 605, 677) for the bridge.lbug atomic swap —
+  // single source of truth for the Windows-rename pattern across the group
+  // package.
+  await retryRename(tmpPath, targetPath);
 }
 
 export async function readContractRegistry(groupDir: string): Promise<ContractRegistry | null> {

gitnexus/src/core/group/sync.ts

@@ -8,12 +8,14 @@ import { HttpRouteExtractor } from './extractors/http-route-extractor.js';
 import { GrpcExtractor } from './extractors/grpc-extractor.js';
 import { ThriftExtractor } from './extractors/thrift-extractor.js';
 import { TopicExtractor } from './extractors/topic-extractor.js';
+import { IncludeExtractor } from './extractors/include-extractor.js';
 import { ManifestExtractor } from './extractors/manifest-extractor.js';
 import { discoverWorkspaceLinks } from './extractors/workspace-extractor.js';
 import { buildProviderIndex, runExactMatch, runWildcardMatch } from './matching.js';
 import { detectServiceBoundaries, assignService } from './service-boundary-detector.js';
 import type { CypherExecutor } from './contract-extractor.js';
 import { writeContractRegistry } from './storage.js';
+import { writeBridge } from './bridge-db.js';
 import type { ContractRegistry } from './types.js';
 
 import { logger } from '../logger.js';
@@ -100,6 +102,7 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
     const grpcEx = new GrpcExtractor();
     const thriftEx = new ThriftExtractor();
     const topicEx = new TopicExtractor();
+    const includeEx = new IncludeExtractor();
     dbExecutors = new Map<string, CypherExecutor>();
     const openPoolIds: string[] = [];
 
@@ -168,6 +171,17 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
             }
           }
 
+          if (config.detect.includes) {
+            const extracted = await includeEx.extract(executor, handle.repoPath, handle);
+            for (const c of extracted) {
+              autoContracts.push({
+                ...c,
+                repo: groupPath,
+                service: assignService(c.symbolRef.filePath, boundaries),
+              });
+            }
+          }
+
           const metaPath = path.join(handle.storagePath, 'meta.json');
           try {
             const raw = await fs.readFile(metaPath, 'utf-8');
@@ -270,6 +284,28 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
 
   if (opts?.groupDir && !opts.skipWrite) {
     await writeContractRegistry(opts.groupDir, registry);
+    // writeBridge failure (disk full, schema error, permission denied) must
+    // not mask the registry — contracts.json was just written successfully
+    // and is the canonical source of truth. A stale or absent bridge
+    // degrades impact queries to empty results, which is recoverable on
+    // the next sync. Surface the failure as a warning so operators can
+    // act, but do not propagate it.
+    // (PR #1156 follow-up review: writeBridge error in sync.ts propagates
+    // uncaught.)
+    try {
+      await writeBridge(opts.groupDir, {
+        contracts: allContracts,
+        crossLinks,
+        repoSnapshots,
+        missingRepos,
+      });
+    } catch (err) {
+      const msg = err instanceof Error ? err.message : String(err);
+      logger.warn(
+        { err: msg, groupDir: opts.groupDir },
+        '⚠️ writeBridge failed; contracts.json is intact but bridge.lbug is stale. Re-run `gitnexus group sync` to retry.',
+      );
+    }
   }
 
   return {

gitnexus/src/core/group/types.ts

@@ -1,4 +1,4 @@
-export type ContractType = 'http' | 'grpc' | 'thrift' | 'topic' | 'lib' | 'custom';
+export type ContractType = 'http' | 'grpc' | 'thrift' | 'topic' | 'lib' | 'custom' | 'include';
 export type MatchType = 'exact' | 'manifest' | 'wildcard' | 'bm25' | 'embedding';
 export type ContractRole = 'provider' | 'consumer';
 
@@ -28,6 +28,7 @@ export interface DetectConfig {
   topics: boolean;
   shared_libs: boolean;
   embedding_fallback: boolean;
+  includes: boolean;
   workspace_deps: boolean;
 }
 

gitnexus/src/core/incremental/shadow-candidates.ts

@@ -0,0 +1,76 @@
+/**
+ * Shadow-candidate path derivation for incremental indexing.
+ *
+ * Background — Bugbot review on PR #1479:
+ *   queryImporters() on a NEWLY ADDED file returns 0 importers in the
+ *   pre-pipeline DB, because the new file's IMPORTS rows haven't been
+ *   written yet. But pre-existing files may have IMPORTS edges that
+ *   *resolved to a sibling path*, and the newcomer can now steal that
+ *   resolution under standard JS/TS module-resolution rules. Without
+ *   pulling those pre-existing files into the writable set, their
+ *   stale CALLS edges remain pointing at the OLD resolution target.
+ *
+ * Given an added file path, this helper enumerates the pre-existing
+ * file paths whose import-resolution claim the newcomer can steal.
+ * Caller filters the candidates against the prior-run `fileHashes`
+ * map so we only query importers of paths that actually existed.
+ *
+ * Shadow patterns covered (resolution-priority-aware):
+ *
+ *   (a) Same basename, different extension —
+ *       added `foo/bar.ts` shadows `foo/bar.{tsx,js,jsx,mjs,cjs,d.ts}`.
+ *   (b) Bare-file beats directory-style index —
+ *       added `foo/bar.ts` shadows `foo/bar/index.{ts,tsx,...}`.
+ *   (c) Directory-index beats bare-file —
+ *       added `foo/index.ts` shadows `foo.{ts,tsx,...}` (rare but real,
+ *       e.g. converting a single-file module into a directory module).
+ *
+ * Resolution-order priority is conservatively wide: we enumerate ALL
+ * common extensions because we don't know which the importer actually
+ * specified, and over-seeding is harmless (extra BFS work, but the
+ * subgraph extract still gates write-back by file membership).
+ *
+ * Cross-platform path separators: candidates are emitted with both `/`
+ * and `\` for shadow pattern (b), since the caller's prior fileHashes
+ * map may use either depending on the OS that wrote it.
+ */
+
+const SHADOW_EXTS = ['.d.ts', '.tsx', '.ts', '.jsx', '.js', '.mjs', '.cjs'];
+
+/**
+ * Enumerate pre-existing paths whose import-resolution `added` can steal.
+ *
+ * @param added — repo-relative path of a newly-added file
+ * @returns deduplicated list of candidate paths (NOT filtered against
+ *          any known-files set — caller does that)
+ */
+export const shadowCandidatesFor = (added: string): string[] => {
+  const ext = SHADOW_EXTS.find((e) => added.endsWith(e));
+  if (!ext) return [];
+
+  const noExt = added.slice(0, -ext.length);
+  const out = new Set<string>();
+
+  // (a) Same basename, different extension.
+  for (const alt of SHADOW_EXTS) {
+    if (alt !== ext) out.add(noExt + alt);
+  }
+
+  // (b) Bare file beats sibling directory-style index.
+  for (const idx of SHADOW_EXTS) {
+    out.add(`${noExt}/index${idx}`);
+    out.add(`${noExt}\\index${idx}`);
+  }
+
+  // (c) New `foo/index.ext` shadows old `foo.ext`.
+  const idxSuffixSlash = '/index';
+  const idxSuffixBack = '\\index';
+  let dir: string | null = null;
+  if (noExt.endsWith(idxSuffixSlash)) dir = noExt.slice(0, -idxSuffixSlash.length);
+  else if (noExt.endsWith(idxSuffixBack)) dir = noExt.slice(0, -idxSuffixBack.length);
+  if (dir !== null) {
+    for (const alt of SHADOW_EXTS) out.add(dir + alt);
+  }
+
+  return [...out];
+};

gitnexus/src/core/incremental/subgraph-extract.ts

@@ -0,0 +1,123 @@
+/**
+ * Subgraph extraction for incremental DB writeback.
+ *
+ * Given the FULL ctx.graph produced by the pipeline (all files parsed,
+ * all phases run) and the set of file paths whose DB rows must be
+ * replaced, produce a smaller KnowledgeGraph that contains:
+ *
+ *   - Every node whose `properties.filePath` is in `toWriteSet`.
+ *   - Every graph-wide node (Community, Process) — these are regenerated
+ *     each run by the communities/processes phases and must be fully
+ *     rewritten.
+ *   - Every relationship where AT LEAST ONE endpoint is in the writable
+ *     set above. Relationships entirely between unchanged-file nodes
+ *     are skipped — their rows are still in the DB and re-inserting
+ *     them would PK-conflict at COPY time.
+ *
+ * The resulting subgraph is what gets passed to `loadGraphToLbug` after
+ * the orchestrator has deleted the corresponding DB rows. Hydrated
+ * unchanged-file rows are never touched in the DB.
+ *
+ * # Cross-file edge consistency (Finding 1)
+ *
+ * `extractChangedSubgraph` intentionally does NOT expand the set it is
+ * given — expansion is the orchestrator's job, so the SAME expanded set
+ * can be fed to both `deleteNodesForFile` and this function (asymmetry
+ * between the delete set and the write set silently corrupts the DB).
+ * `computeEffectiveWriteSet` below performs the boundary-crossing 1-hop
+ * walk; the orchestrator composes it with its importer-BFS expansion and
+ * passes the result here.
+ *
+ * Why the 1-hop walk is needed: consider a barrel re-export change —
+ * file C (a barrel) shifts `export { foo } from './b'` to
+ * `export { foo } from './d'`. After scope resolution, file A's CALLS
+ * edge to `foo` resolves to D instead of B, even though A's content is
+ * byte-for-byte identical:
+ *
+ *   - Old A→B edge survives in DB (neither A nor B is changed → not deleted)
+ *   - New A→D edge is missing (neither A nor D in writable set → skipped)
+ *
+ * Pulling the unchanged-side file of every writable-boundary-crossing
+ * edge into the write set fixes both halves: the orchestrator's
+ * `DETACH DELETE` cleans up the stale unchanged-side rows, and the new
+ * cross-file edges land because at least one endpoint is now writable.
+ *
+ * Limitation (documented): if a file X *stopped* importing from a
+ * changed file C, X has no edge to C in the new graph, so this 1-hop
+ * walk doesn't catch it. The orchestrator's importer-BFS (which reads
+ * IMPORTS from the pre-pipeline DB) covers that case instead.
+ */
+
+import type { GraphNode, GraphRelationship } from 'gitnexus-shared';
+import { createKnowledgeGraph } from '../graph/graph.js';
+import type { KnowledgeGraph } from '../graph/types.js';
+
+const isGraphWide = (label: string): boolean => label === 'Community' || label === 'Process';
+
+/**
+ * Build a Map<nodeId, filePath> for every File-bound node in the graph.
+ * Graph-wide nodes (Community/Process) have no filePath and are filtered.
+ */
+const indexNodeFilePaths = (fullGraph: KnowledgeGraph): Map<string, string> => {
+  const idx = new Map<string, string>();
+  fullGraph.forEachNode((n: GraphNode) => {
+    const fp = n.properties?.filePath as string | undefined;
+    if (fp) idx.set(n.id, fp);
+  });
+  return idx;
+};
+
+export const extractChangedSubgraph = (
+  fullGraph: KnowledgeGraph,
+  toWriteSet: ReadonlySet<string>,
+): KnowledgeGraph => {
+  const sub = createKnowledgeGraph();
+  const writableNodeIds = new Set<string>();
+
+  fullGraph.forEachNode((n: GraphNode) => {
+    const filePath = n.properties?.filePath as string | undefined;
+    const include = (filePath && toWriteSet.has(filePath)) || isGraphWide(n.label);
+    if (include) {
+      sub.addNode(n);
+      writableNodeIds.add(n.id);
+    }
+  });
+
+  fullGraph.forEachRelationship((r: GraphRelationship) => {
+    if (writableNodeIds.has(r.sourceId) || writableNodeIds.has(r.targetId)) {
+      sub.addRelationship(r);
+    }
+  });
+
+  return sub;
+};
+
+/**
+ * Public — derive the EFFECTIVE write-set: `toWriteSet` expanded by one
+ * hop along every edge in the new graph that crosses the writable
+ * boundary (one endpoint in a writable file, the other in an unchanged
+ * file). The unchanged-side file is pulled in so its stale rows are
+ * deleted + rewritten in lockstep with the changed side.
+ *
+ * Single pass over the edge list. Does NOT mutate `toWriteSet`. The
+ * orchestrator MUST feed the returned set to both `deleteNodesForFile`
+ * and `extractChangedSubgraph` — feeding the unexpanded set to either
+ * one leaves stale rows or PK-conflicts at COPY time.
+ */
+export const computeEffectiveWriteSet = (
+  fullGraph: KnowledgeGraph,
+  toWriteSet: ReadonlySet<string>,
+): Set<string> => {
+  const nodeFilePaths = indexNodeFilePaths(fullGraph);
+  const expanded = new Set<string>(toWriteSet);
+  fullGraph.forEachRelationship((r: GraphRelationship) => {
+    const sourcePath = nodeFilePaths.get(r.sourceId);
+    const targetPath = nodeFilePaths.get(r.targetId);
+    if (!sourcePath || !targetPath) return; // skip edges to graph-wide nodes
+    const sourceWritable = toWriteSet.has(sourcePath);
+    const targetWritable = toWriteSet.has(targetPath);
+    if (sourceWritable && !targetWritable) expanded.add(targetPath);
+    else if (targetWritable && !sourceWritable) expanded.add(sourcePath);
+  });
+  return expanded;
+};

gitnexus/src/core/ingestion/call-processor.ts

@@ -40,13 +40,16 @@ import { getLanguageFromFilename, SupportedLanguages } from 'gitnexus-shared';
 import { isRegistryPrimary } from './registry-primary-flag.js';
 import { isVerboseIngestionEnabled } from './utils/verbose.js';
 import { yieldToEventLoop } from './utils/event-loop.js';
+import { parseSourceSafe } from '../tree-sitter/safe-parse.js';
 import {
+  CLASS_CONTAINER_TYPES,
   FUNCTION_NODE_TYPES,
-  findEnclosingClassId,
   findEnclosingClassInfo,
   genericFuncName,
   inferFunctionLabel,
 } from './utils/ast-helpers.js';
+import type { FieldInfo, FieldExtractorContext } from './field-types.js';
+import type { LanguageProvider } from './language-provider.js';
 import { typeTagForId, constTagForId, buildCollisionGroups } from './utils/method-props.js';
 import type { MethodInfo } from './method-types.js';
 import {
@@ -76,6 +79,62 @@ import type { LiteralTypeInferrer } from './type-extractors/types.js';
 import type { SyntaxNode } from './utils/ast-helpers.js';
 
 import { logger } from '../logger.js';
+
+// ── Property-prepass helpers (parity with parse-worker.ts) ──
+// These mirror the sequential-path equivalents in parse-worker.ts so the main-
+// thread `processCalls` pre-pass produces byte-identical Property nodes/symbols
+// to the worker pool. Drift between the two paths breaks the
+// `incremental ≡ --force` invariant the moment a repo crosses the worker
+// threshold between runs.
+
+/** Walk up to the nearest enclosing class/struct/interface AST node. */
+const findEnclosingClassNode = (node: SyntaxNode): SyntaxNode | null => {
+  let current = node.parent;
+  while (current) {
+    if (CLASS_CONTAINER_TYPES.has(current.type)) return current;
+    current = current.parent;
+  }
+  return null;
+};
+
+/** No-op SymbolTable stub for FieldExtractorContext — matches parse-worker. */
+const NOOP_SYMBOL_TABLE: SymbolTableReader = {
+  lookupExact: () => undefined,
+  lookupExactFull: () => undefined,
+  lookupExactAll: () => [],
+  lookupCallableByName: () => [],
+  getFiles: () => [][Symbol.iterator](),
+  getStats: () => ({ fileCount: 0 }),
+};
+
+/**
+ * Extract (and cache) field info for a class node. Cache is passed in so it
+ * stays scoped to a single `processCalls` invocation rather than leaking
+ * across analyze runs (worker uses module-level caching because each worker
+ * process is short-lived; the main thread is not).
+ *
+ * Cache key is `${filePath}:${classNode.startIndex}` — startIndex alone is a
+ * per-file byte offset, so almost every Ruby/Python file's leading class lands
+ * at byte 0 and would collide across files in the shared map.
+ */
+const getFieldInfo = (
+  classNode: SyntaxNode,
+  provider: LanguageProvider,
+  context: FieldExtractorContext,
+  cache: Map<string, Map<string, FieldInfo>>,
+): Map<string, FieldInfo> | undefined => {
+  if (!provider.fieldExtractor) return undefined;
+  const cacheKey = `${context.filePath}:${classNode.startIndex}`;
+  const cached = cache.get(cacheKey);
+  if (cached) return cached;
+  const result = provider.fieldExtractor.extract(classNode, context);
+  if (!result?.fields?.length) return undefined;
+  const map = new Map<string, FieldInfo>();
+  for (const field of result.fields) map.set(field.name, field);
+  cache.set(cacheKey, map);
+  return map;
+};
+
 /** Per-file resolved type bindings for exported symbols.
  *  Populated during call processing, consumed by Phase 14 re-resolution pass. */
 export type ExportedTypeMap = Map<string, Map<string, string>>;
@@ -769,9 +828,10 @@ export const processCalls = async (
 
     let tree = astCache.get(file.path);
     if (!tree) {
+      const parseContent = provider.preprocessSource?.(file.content, file.path) ?? file.content;
       try {
-        tree = parser.parse(file.content, undefined, {
-          bufferSize: getTreeSitterBufferSize(file.content),
+        tree = parseSourceSafe(parser, parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         continue;
@@ -858,6 +918,120 @@ export const processCalls = async (
     prepared.push({ file, language, provider, tree, matches, parentMap, typeEnv });
   }
 
+  // ── Property-registration pre-pass ──
+  // Register all routed properties (e.g. Ruby attr_accessor) BEFORE the
+  // resolution loop so cross-file field-type lookups (e.g.
+  // `user.address.save → Address#save`) succeed regardless of file
+  // processing order. This MUST stay in lockstep with the equivalent
+  // worker-path block in parse-worker.ts (kind === 'properties') — any
+  // divergence between the two paths breaks the `incremental ≡ --force`
+  // invariant once a repo crosses the worker threshold between runs.
+  const fieldInfoCache = new Map<string, Map<string, FieldInfo>>();
+  for (const { file, language, provider, matches, typeEnv } of prepared) {
+    const callRouter = provider.callRouter;
+    if (!callRouter) continue;
+    matches.forEach((match) => {
+      const captureMap: Record<string, any> = {};
+      match.captures.forEach((c) => (captureMap[c.name] = c.node));
+      if (!captureMap['call']) return;
+      const callNameNode = captureMap['call.name'];
+      if (!callNameNode) return;
+      const routed = callRouter(callNameNode.text, captureMap['call']);
+      if (!routed || routed.kind !== 'properties') return;
+
+      const propEnclosingInfo = findEnclosingClassInfo(
+        captureMap['call'],
+        file.path,
+        provider.resolveEnclosingOwner,
+      );
+      const propEnclosingClassId = propEnclosingInfo?.classId ?? null;
+
+      // Enrich routed properties with FieldExtractor metadata so types
+      // discovered from constructor assignments (e.g. `@address = Address.new`)
+      // are propagated even when the routing payload itself lacks declaredType.
+      let routedFieldMap: Map<string, FieldInfo> | undefined;
+      if (provider.fieldExtractor && typeEnv) {
+        const classNode = findEnclosingClassNode(captureMap['call']);
+        if (classNode) {
+          routedFieldMap = getFieldInfo(
+            classNode,
+            provider,
+            {
+              typeEnv,
+              symbolTable: NOOP_SYMBOL_TABLE,
+              filePath: file.path,
+              language,
+            },
+            fieldInfoCache,
+          );
+        }
+      }
+
+      const fileId = generateId('File', file.path);
+      for (const item of routed.items) {
+        const routedFieldInfo = routedFieldMap?.get(item.propName);
+        const propQualifiedName = propEnclosingInfo
+          ? `${propEnclosingInfo.className}.${item.propName}`
+          : item.propName;
+        const nodeId = generateId('Property', `${file.path}:${propQualifiedName}`);
+        graph.addNode({
+          id: nodeId,
+          label: 'Property',
+          properties: {
+            name: item.propName,
+            filePath: file.path,
+            startLine: item.startLine,
+            endLine: item.endLine,
+            language,
+            isExported: true,
+            description: item.accessorType,
+            ...(item.declaredType
+              ? { declaredType: item.declaredType }
+              : routedFieldInfo?.type
+                ? { declaredType: routedFieldInfo.type }
+                : {}),
+            ...(routedFieldInfo?.visibility !== undefined
+              ? { visibility: routedFieldInfo.visibility }
+              : {}),
+            ...(routedFieldInfo?.isStatic !== undefined
+              ? { isStatic: routedFieldInfo.isStatic }
+              : {}),
+            ...(routedFieldInfo?.isReadonly !== undefined
+              ? { isReadonly: routedFieldInfo.isReadonly }
+              : {}),
+          },
+        });
+        ctx.model.symbols.add(file.path, item.propName, nodeId, 'Property', {
+          ...(propEnclosingClassId ? { ownerId: propEnclosingClassId } : {}),
+          ...(item.declaredType
+            ? { declaredType: item.declaredType }
+            : routedFieldInfo?.type
+              ? { declaredType: routedFieldInfo.type }
+              : {}),
+        });
+        const relId = generateId('DEFINES', `${fileId}->${nodeId}`);
+        graph.addRelationship({
+          id: relId,
+          sourceId: fileId,
+          targetId: nodeId,
+          type: 'DEFINES',
+          confidence: 1.0,
+          reason: '',
+        });
+        if (propEnclosingClassId) {
+          graph.addRelationship({
+            id: generateId('HAS_PROPERTY', `${propEnclosingClassId}->${nodeId}`),
+            sourceId: propEnclosingClassId,
+            targetId: nodeId,
+            type: 'HAS_PROPERTY',
+            confidence: 1.0,
+            reason: '',
+          });
+        }
+      }
+    });
+  }
+
   // ── Resolution loop: verify constructor bindings and resolve calls ──
   // The accumulator (if present) is now fully populated from the preparation
   // loop above, so verifyConstructorBindings sees all provider bindings
@@ -928,9 +1102,10 @@ export const processCalls = async (
             provider,
           );
           const srcId = enclosing || generateId('File', file.path);
-          // Defer resolution: Ruby attr_accessor properties are registered during
-          // this same loop, so cross-file lookups fail if the declaring file hasn't
-          // been processed yet. Collect now, resolve after all files are done.
+          // Defer resolution so write-access tracking sees the FINAL graph
+          // state — properties from the pre-pass are present, but receiver-type
+          // resolution can still depend on inference that completes during the
+          // main loop. Resolve after all files have been processed.
           pendingWrites.push({ receiverTypeName, propertyName, filePath: file.path, srcId });
         }
         // Assignment-only capture (no @call sibling): skip the rest of this
@@ -1051,47 +1226,8 @@ export const processCalls = async (
             return;
 
           case 'properties': {
-            const fileId = generateId('File', file.path);
-            const propEnclosingClassId = findEnclosingClassId(captureMap['call'], file.path);
-            for (const item of routed.items) {
-              const nodeId = generateId('Property', `${file.path}:${item.propName}`);
-              graph.addNode({
-                id: nodeId,
-                label: 'Property',
-                properties: {
-                  name: item.propName,
-                  filePath: file.path,
-                  startLine: item.startLine,
-                  endLine: item.endLine,
-                  language,
-                  isExported: true,
-                  description: item.accessorType,
-                },
-              });
-              ctx.model.symbols.add(file.path, item.propName, nodeId, 'Property', {
-                ...(propEnclosingClassId ? { ownerId: propEnclosingClassId } : {}),
-                ...(item.declaredType ? { declaredType: item.declaredType } : {}),
-              });
-              const relId = generateId('DEFINES', `${fileId}->${nodeId}`);
-              graph.addRelationship({
-                id: relId,
-                sourceId: fileId,
-                targetId: nodeId,
-                type: 'DEFINES',
-                confidence: 1.0,
-                reason: '',
-              });
-              if (propEnclosingClassId) {
-                graph.addRelationship({
-                  id: generateId('HAS_PROPERTY', `${propEnclosingClassId}->${nodeId}`),
-                  sourceId: propEnclosingClassId,
-                  targetId: nodeId,
-                  type: 'HAS_PROPERTY',
-                  confidence: 1.0,
-                  reason: '',
-                });
-              }
-            }
+            // Properties already registered in the pre-pass above.
+            // Skip to avoid duplicate nodes/edges.
             return;
           }
 
@@ -3280,9 +3416,10 @@ export const extractFetchCallsFromFiles = async (
 
     let tree = astCache.get(file.path);
     if (!tree) {
+      const parseContent = provider.preprocessSource?.(file.content, file.path) ?? file.content;
       try {
-        tree = parser.parse(file.content, undefined, {
-          bufferSize: getTreeSitterBufferSize(file.content),
+        tree = parseSourceSafe(parser, parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch {
         continue;

gitnexus/src/core/ingestion/community-processor.ts

@@ -41,6 +41,24 @@ interface LeidenDetailedResult {
   modularity: number;
 }
 
+/**
+ * Deterministic PRNG (mulberry32) seed for the vendored Leiden algorithm.
+ * Vendored Leiden defaults `rng: Math.random`, which makes community
+ * assignment non-deterministic across runs. Passing a seeded RNG gives us
+ * reproducible community/modularity output, which is required for the
+ * incremental-indexing equivalence test (incremental ≡ full rebuild).
+ */
+const LEIDEN_SEED = 0xc0de;
+function createSeededRng(seed: number): () => number {
+  let s = seed >>> 0;
+  return () => {
+    s = (s + 0x6d2b79f5) >>> 0;
+    let t = Math.imul(s ^ (s >>> 15), 1 | s);
+    t = (t + Math.imul(t ^ (t >>> 7), 61 | t)) ^ t;
+    return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+  };
+}
+
 // ============================================================================
 // TYPES
 // ============================================================================
@@ -150,6 +168,7 @@ export const processCommunities = async (
         leiden.detailed(graph, {
           resolution: isLarge ? 2.0 : 1.0,
           maxIterations: isLarge ? 3 : 0,
+          rng: createSeededRng(LEIDEN_SEED),
         }),
       ),
       new Promise<never>((_, reject) =>

gitnexus/src/core/ingestion/cpp-ue-preprocessor.ts

@@ -0,0 +1,265 @@
+/**
+ * Unreal Engine reflection-macro preprocessor for C++ source.
+ *
+ * Tree-sitter does not expand C preprocessor macros, so Unreal's reflection
+ * markers (`UCLASS(...)`, `UFUNCTION(...)`, `MODULENAME_API`, ...) are parsed
+ * verbatim. The result is mis-parsed declarations: in `class BRAWLUI_API
+ * UMyClass : public UObject`, tree-sitter-cpp captures `BRAWLUI_API` as the
+ * class name and the rest of the declaration becomes structurally wrong.
+ *
+ * This module elides those macros from the source text BEFORE tree-sitter
+ * parses it. Replacement is **length-preserving** (each elided byte becomes
+ * a space, newlines preserved) so byte offsets and line/column positions
+ * tree-sitter reports remain identical to the original file. Symbol
+ * locations in the graph stay accurate.
+ *
+ * A cheap detection guard short-circuits files that don't look like UE
+ * sources, so non-UE C++ codebases pay no cost.
+ *
+ * Pure function — no tree-sitter dependency, safe for worker threads.
+ */
+/**
+ * Strong UE markers — reflection macros that only Unreal Engine projects use.
+ * Presence of one of these is sufficient evidence that the file is a UE source
+ * and that `MODULENAME_API` tokens in it are intended as export macros.
+ *
+ * Importantly, `_API` tokens are NOT in this guard — `REST_API`, `HTTP_API`,
+ * `MY_LIB_API` and similar identifiers appear in plenty of non-UE C++ codebases
+ * as constants/enums/parameter names. We must not erase them just because the
+ * file mentions an `_API` token.
+ */
+const HAS_UE_HINT =
+  /\b(?:UCLASS|UFUNCTION|UPROPERTY|USTRUCT|UENUM|UINTERFACE|GENERATED_BODY|GENERATED_[A-Z_]+_BODY|UE_DEPRECATED|DECLARE_(?:DYNAMIC_)?(?:MULTICAST_)?DELEGATE)/;
+
+const SIMPLE_MACROS_NO_ARGS: readonly string[] = [
+  'GENERATED_BODY',
+  'GENERATED_UCLASS_BODY',
+  'GENERATED_USTRUCT_BODY',
+  'GENERATED_UINTERFACE_BODY',
+  'GENERATED_IINTERFACE_BODY',
+  'DECLARE_CLASS',
+  'GENERATED_BODY_LEGACY',
+];
+
+const PARENTHESIZED_MACROS: readonly string[] = [
+  'UCLASS',
+  'UFUNCTION',
+  'UPROPERTY',
+  'USTRUCT',
+  'UENUM',
+  'UINTERFACE',
+  'UMETA',
+  'UE_DEPRECATED',
+];
+
+const DELEGATE_MACRO_RE =
+  /\bDECLARE_(?:DYNAMIC_)?(?:MULTICAST_)?DELEGATE(?:_(?:RetVal_OneParam|RetVal_TwoParams|RetVal_ThreeParams|RetVal_FourParams|RetVal_FiveParams|RetVal_SixParams|RetVal_SevenParams|RetVal_EightParams|RetVal_NineParams|RetVal|OneParam|TwoParams|ThreeParams|FourParams|FiveParams|SixParams|SevenParams|EightParams|NineParams|TenParams))?(?=\s*\()/g;
+
+/**
+ * Module export tokens like `BRAWLUI_API`, `ENGINE_API`, `COREUOBJECT_API`.
+ * Pattern: ALL_CAPS identifier ending in `_API`. The leading word boundary
+ * (`\b`) prevents matching mid-identifier.
+ */
+const API_MACRO_RE = /\b[A-Z][A-Z0-9_]*_API\b/g;
+
+/** Replace `[start, end)` of `chars` with spaces, preserving newlines. */
+function eraseRange(chars: string[], start: number, end: number): void {
+  for (let i = start; i < end; i++) {
+    if (chars[i] !== '\n' && chars[i] !== '\r') {
+      chars[i] = ' ';
+    }
+  }
+}
+
+/**
+ * Find the matching close paren for an opening paren at index `openIdx`.
+ * Returns the index of `)` (inclusive end), or -1 if unbalanced.
+ *
+ * Handles nested parens and string/char literals so commas/parens inside
+ * strings don't throw off the match. Does not attempt to handle raw string
+ * literals (`R"(...)"`); UE reflection-macro arguments do not use them in
+ * practice.
+ */
+function findMatchingParen(source: string, openIdx: number): number {
+  if (source.charCodeAt(openIdx) !== 0x28) return -1;
+  let depth = 1;
+  let i = openIdx + 1;
+  const len = source.length;
+  while (i < len && depth > 0) {
+    const ch = source.charCodeAt(i);
+    // String literal
+    if (ch === 0x22) {
+      i++;
+      while (i < len) {
+        const c = source.charCodeAt(i);
+        if (c === 0x5c) {
+          i += 2;
+          continue;
+        }
+        if (c === 0x22) {
+          i++;
+          break;
+        }
+        i++;
+      }
+      continue;
+    }
+    // Char literal
+    if (ch === 0x27) {
+      i++;
+      while (i < len) {
+        const c = source.charCodeAt(i);
+        if (c === 0x5c) {
+          i += 2;
+          continue;
+        }
+        if (c === 0x27) {
+          i++;
+          break;
+        }
+        i++;
+      }
+      continue;
+    }
+    // Line comment
+    if (ch === 0x2f && source.charCodeAt(i + 1) === 0x2f) {
+      while (i < len && source.charCodeAt(i) !== 0x0a) i++;
+      continue;
+    }
+    // Block comment
+    if (ch === 0x2f && source.charCodeAt(i + 1) === 0x2a) {
+      i += 2;
+      while (i < len) {
+        if (source.charCodeAt(i) === 0x2a && source.charCodeAt(i + 1) === 0x2f) {
+          i += 2;
+          break;
+        }
+        i++;
+      }
+      continue;
+    }
+    if (ch === 0x28) depth++;
+    else if (ch === 0x29) {
+      depth--;
+      if (depth === 0) return i;
+    }
+    i++;
+  }
+  return -1;
+}
+
+/** Match a whole-word identifier at `idx`. Returns the byte after the identifier, or -1 on miss. */
+function matchIdentifierAt(source: string, idx: number, name: string): number {
+  if (idx > 0) {
+    const prev = source.charCodeAt(idx - 1);
+    if (
+      (prev >= 0x30 && prev <= 0x39) ||
+      (prev >= 0x41 && prev <= 0x5a) ||
+      (prev >= 0x61 && prev <= 0x7a) ||
+      prev === 0x5f
+    ) {
+      return -1;
+    }
+  }
+  for (let k = 0; k < name.length; k++) {
+    if (source.charCodeAt(idx + k) !== name.charCodeAt(k)) return -1;
+  }
+  const after = idx + name.length;
+  if (after < source.length) {
+    const next = source.charCodeAt(after);
+    if (
+      (next >= 0x30 && next <= 0x39) ||
+      (next >= 0x41 && next <= 0x5a) ||
+      (next >= 0x61 && next <= 0x7a) ||
+      next === 0x5f
+    ) {
+      return -1;
+    }
+  }
+  return after;
+}
+
+/** Skip ASCII whitespace forward from `idx`. Returns the next non-whitespace byte index. */
+function skipWhitespace(source: string, idx: number): number {
+  const len = source.length;
+  while (idx < len) {
+    const ch = source.charCodeAt(idx);
+    if (ch === 0x20 || ch === 0x09 || ch === 0x0a || ch === 0x0d) {
+      idx++;
+      continue;
+    }
+    break;
+  }
+  return idx;
+}
+
+/**
+ * Strip Unreal Engine reflection macros from C++ source, length-preserving.
+ *
+ * Returns the original string unchanged if no strong UE marker is detected,
+ * so non-UE C++ files (including ones that contain `*_API`-suffixed
+ * identifiers like `REST_API` or `HTTP_API`) incur only a single regex test.
+ *
+ * The `_filePath` parameter is part of the `LanguageProvider.preprocessSource`
+ * contract but is unused — UE detection is purely content-based. Accepted and
+ * ignored here so the function matches the hook signature exactly.
+ */
+export function stripUeMacros(source: string, _filePath?: string): string {
+  if (!HAS_UE_HINT.test(source)) return source;
+
+  const chars: string[] = source.split('');
+
+  for (const macro of PARENTHESIZED_MACROS) {
+    let searchFrom = 0;
+    while (true) {
+      const hit = source.indexOf(macro, searchFrom);
+      if (hit < 0) break;
+      searchFrom = hit + 1;
+      const after = matchIdentifierAt(source, hit, macro);
+      if (after < 0) continue;
+      const parenIdx = skipWhitespace(source, after);
+      if (source.charCodeAt(parenIdx) !== 0x28) continue;
+      const close = findMatchingParen(source, parenIdx);
+      if (close < 0) continue;
+      eraseRange(chars, hit, close + 1);
+    }
+  }
+
+  for (const macro of SIMPLE_MACROS_NO_ARGS) {
+    let searchFrom = 0;
+    while (true) {
+      const hit = source.indexOf(macro, searchFrom);
+      if (hit < 0) break;
+      searchFrom = hit + 1;
+      const after = matchIdentifierAt(source, hit, macro);
+      if (after < 0) continue;
+      const parenIdx = skipWhitespace(source, after);
+      if (source.charCodeAt(parenIdx) === 0x28) {
+        const close = findMatchingParen(source, parenIdx);
+        if (close < 0) continue;
+        eraseRange(chars, hit, close + 1);
+      } else {
+        eraseRange(chars, hit, after);
+      }
+    }
+  }
+
+  for (const re of [DELEGATE_MACRO_RE, API_MACRO_RE]) {
+    re.lastIndex = 0;
+    let match: RegExpExecArray | null;
+    while ((match = re.exec(source)) !== null) {
+      const start = match.index;
+      let end = start + match[0].length;
+      if (re === DELEGATE_MACRO_RE) {
+        const parenIdx = skipWhitespace(source, end);
+        if (source.charCodeAt(parenIdx) === 0x28) {
+          const close = findMatchingParen(source, parenIdx);
+          if (close >= 0) end = close + 1;
+        }
+      }
+      eraseRange(chars, start, end);
+    }
+  }
+
+  return chars.join('');
+}

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

@@ -9,6 +9,11 @@ import type { SyntaxNode } from '../../utils/ast-helpers.js';
 
 const CSHARP_VIS = new Set<FieldVisibility>(['public', 'private', 'protected', 'internal']);
 
+const extractCsharpDeclaredType = (typeNode: SyntaxNode): string | undefined => {
+  if (typeNode.type === 'generic_name') return typeNode.text.trim();
+  return extractSimpleTypeName(typeNode) ?? typeNode.text?.trim();
+};
+
 /**
  * C# field extraction config.
  *
@@ -53,17 +58,17 @@ export const csharpConfig: FieldExtractionConfig = {
       const child = node.namedChild(i);
       if (child?.type === 'variable_declaration') {
         const typeNode = child.childForFieldName('type');
-        if (typeNode) return extractSimpleTypeName(typeNode) ?? typeNode.text?.trim();
+        if (typeNode) return extractCsharpDeclaredType(typeNode);
         // fallback: first child that is a type
         const first = child.firstNamedChild;
         if (first && first.type !== 'variable_declarator') {
-          return extractSimpleTypeName(first) ?? first.text?.trim();
+          return extractCsharpDeclaredType(first);
         }
       }
     }
     // property_declaration: type is first named child
     const typeNode = node.childForFieldName('type');
-    if (typeNode) return extractSimpleTypeName(typeNode) ?? typeNode.text?.trim();
+    if (typeNode) return extractCsharpDeclaredType(typeNode);
     return undefined;
   },
 

gitnexus/src/core/ingestion/heritage-processor.ts

@@ -22,6 +22,7 @@ import { generateId } from '../../lib/utils.js';
 import { getLanguageFromFilename, type NodeLabel, type SupportedLanguages } from 'gitnexus-shared';
 import { isVerboseIngestionEnabled } from './utils/verbose.js';
 import { yieldToEventLoop } from './utils/event-loop.js';
+import { parseSourceSafe } from '../tree-sitter/safe-parse.js';
 import { getProvider } from './languages/index.js';
 import { getTreeSitterBufferSize } from './constants.js';
 import type {
@@ -219,9 +220,13 @@ export const processHeritage = async (
     let tree = astCache.get(file.path);
     if (!tree) {
       // Use larger bufferSize for files > 32KB
+      // Per-language source preprocessor (length-preserving, e.g. UE macro
+      // stripping for C++). MUST mirror parsing-processor on cache miss so
+      // re-parses see the same input as the cached AST.
+      const parseContent = provider.preprocessSource?.(file.content, file.path) ?? file.content;
       try {
-        tree = parser.parse(file.content, undefined, {
-          bufferSize: getTreeSitterBufferSize(file.content),
+        tree = parseSourceSafe(parser, parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         // Skip files that can't be parsed
@@ -413,9 +418,10 @@ export async function extractExtractedHeritageFromFiles(
 
     let tree = astCache.get(file.path);
     if (!tree) {
+      const parseContent = provider.preprocessSource?.(file.content, file.path) ?? file.content;
       try {
-        tree = parser.parse(file.content, undefined, {
-          bufferSize: getTreeSitterBufferSize(file.content),
+        tree = parseSourceSafe(parser, parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch {
         continue;

gitnexus/src/core/ingestion/import-processor.ts

@@ -8,6 +8,7 @@ import { generateId } from '../../lib/utils.js';
 import { getLanguageFromFilename } from 'gitnexus-shared';
 import { isVerboseIngestionEnabled } from './utils/verbose.js';
 import { yieldToEventLoop } from './utils/event-loop.js';
+import { parseSourceSafe } from '../tree-sitter/safe-parse.js';
 import type { ExtractedImport } from './workers/parse-worker.js';
 import { getTreeSitterBufferSize } from './constants.js';
 import { loadImportConfigs } from './language-config.js';
@@ -305,9 +306,10 @@ export const processImports = async (
     let wasReparsed = false;
 
     if (!tree) {
+      const parseContent = provider.preprocessSource?.(file.content, file.path) ?? file.content;
       try {
-        tree = parser.parse(file.content, undefined, {
-          bufferSize: getTreeSitterBufferSize(file.content),
+        tree = parseSourceSafe(parser, parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         continue;

gitnexus/src/core/ingestion/import-resolvers/standard.ts

@@ -128,7 +128,21 @@ export const resolveImportPath = (
 
   if (importPath.startsWith('.')) {
     const resolved = tryResolveWithExtensions(basePath, allFiles);
-    return cache(resolved);
+    if (resolved) return cache(resolved);
+
+    // TypeScript ESM: imports use .js/.jsx/.mjs/.cjs but source files are
+    // .ts/.tsx/.mts/.cts. Strip the JS-family extension and re-resolve.
+    // NOTE: This fallback only applies to relative imports. Path alias imports
+    // (e.g. @/utils.js via tsconfig paths) do not yet strip .js extensions —
+    // that is a known limitation tracked for follow-up.
+    if (language === SupportedLanguages.TypeScript || language === SupportedLanguages.JavaScript) {
+      const stripped = stripJsExtension(basePath);
+      if (stripped !== null) {
+        return cache(tryResolveWithExtensions(stripped, allFiles));
+      }
+    }
+
+    return cache(null);
   }
 
   // ---- Generic package/absolute import resolution (suffix matching) ----
@@ -182,3 +196,19 @@ export function resolveStandard(
 export function createStandardStrategy(language: SupportedLanguages): ImportResolverStrategy {
   return (raw, fp, ctx) => resolveStandard(raw, fp, ctx, language);
 }
+
+// ============================================================================
+// ESM extension helpers
+// ============================================================================
+
+/** JS-family extensions that TypeScript ESM maps to TS equivalents. */
+const JS_EXTENSION_PATTERN = /\.(js|jsx|mjs|cjs)$/;
+
+/**
+ * Strip a JS-family extension from a path, returning the stem.
+ * Returns `null` if the path does not end with a JS-family extension.
+ */
+export function stripJsExtension(path: string): string | null {
+  const match = JS_EXTENSION_PATTERN.exec(path);
+  return match ? path.slice(0, -match[0].length) : null;
+}

gitnexus/src/core/ingestion/import-resolvers/utils.ts

@@ -9,8 +9,12 @@ export const EXTENSIONS = [
   // TypeScript/JavaScript
   '.tsx',
   '.ts',
+  '.mts',
+  '.cts',
   '.jsx',
   '.js',
+  '.mjs',
+  '.cjs',
   '.vue',
   '/index.tsx',
   '/index.ts',

gitnexus/src/core/ingestion/language-provider.ts

@@ -116,6 +116,39 @@ interface LanguageProviderConfig {
    *  Required for tree-sitter languages; empty string for standalone processors. */
   readonly treeSitterQueries: string;
 
+  /**
+   * Optional source-text transform that runs **before** tree-sitter parses the file.
+   *
+   * Used to elide language constructs that confuse the grammar without affecting
+   * source-position fidelity — e.g., Unreal Engine reflection macros (`UCLASS`,
+   * `UFUNCTION`, `MODULENAME_API`) in C++ headers that prevent the parser from
+   * recognising class/function names correctly.
+   *
+   * **Length / position preservation:** the returned string MUST have the same
+   * JavaScript `.length` as the input AND preserve every newline (`\n`/`\r`)
+   * position byte-for-byte. Implementations replace elided characters with
+   * ASCII spaces while leaving newlines untouched. With this contract:
+   *
+   *   - tree-sitter's reported `startPosition.row`/`startPosition.column`
+   *     match the original file exactly (line/column come from newline counts)
+   *   - `startIndex`/`endIndex` byte offsets match the original file exactly
+   *     **when the elided range is pure ASCII** (UTF-16 `.length` equals UTF-8
+   *     byte length only for ASCII).
+   *
+   * Implementations targeting languages where elided ranges may contain
+   * non-ASCII content must therefore preserve byte length, not just `.length`,
+   * if downstream code uses `startIndex` to slice the original UTF-8 bytes.
+   * The current C++ UE-macro preprocessor relies on the practical fact that
+   * UE reflection macros and module-export tokens are ASCII-only.
+   *
+   * Must be a pure function — same input always yields the same output. Called
+   * once per file, on every code path that re-parses (parsing-processor, import
+   * processor, heritage processor, call processor, parse worker).
+   *
+   * Default: undefined (no preprocessing — `file.content` is parsed verbatim).
+   */
+  readonly preprocessSource?: (sourceText: string, filePath: string) => string;
+
   // ── Core (required) ───────────────────────────────────────────────
   /** Type extraction: declarations, initializers, for-loop bindings */
   readonly typeConfig: LanguageTypeConfig;

gitnexus/src/core/ingestion/languages/c-cpp.ts

@@ -45,6 +45,16 @@ import { cVariableConfig, cppVariableConfig } from '../variable-extractors/confi
 import { createCallExtractor } from '../call-extractors/generic.js';
 import { cCallConfig, cppCallConfig } from '../call-extractors/configs/c-cpp.js';
 import { createHeritageExtractor } from '../heritage-extractors/generic.js';
+import { stripUeMacros } from '../cpp-ue-preprocessor.js';
+import {
+  emitCScopeCaptures,
+  interpretCImport,
+  interpretCTypeBinding,
+  cArityCompatibility,
+  cBindingScopeFor,
+  cImportOwningScope,
+  cReceiverBinding,
+} from './c/index.js';
 
 const C_BUILT_INS: ReadonlySet<string> = new Set([
   'printf',
@@ -366,6 +376,16 @@ export const cProvider = defineLanguage({
   heritageExtractor: createHeritageExtractor(SupportedLanguages.C),
   labelOverride: cppLabelOverride,
   builtInNames: C_BUILT_INS,
+
+  // ── RFC #909 Ring 3: scope-based resolution hooks (RFC §5) ──────────
+  emitScopeCaptures: emitCScopeCaptures,
+  interpretImport: interpretCImport,
+  interpretTypeBinding: interpretCTypeBinding,
+  bindingScopeFor: cBindingScopeFor,
+  importOwningScope: cImportOwningScope,
+  receiverBinding: cReceiverBinding,
+  arityCompatibility: cArityCompatibility,
+  // mergeBindings + resolveImportTarget live on ScopeResolver (see c/scope-resolver.ts).
 });
 
 export const cppProvider = defineLanguage({
@@ -410,6 +430,7 @@ export const cppProvider = defineLanguage({
     },
   ] satisfies AstFrameworkPatternConfig[],
   treeSitterQueries: CPP_QUERIES,
+  preprocessSource: stripUeMacros,
   typeConfig: cCppConfig,
   exportChecker: cCppExportChecker,
   importResolver: createImportResolver(cppImportConfig),

gitnexus/src/core/ingestion/languages/c/arity-metadata.ts

@@ -0,0 +1,102 @@
+import type { SyntaxNode } from '../../utils/ast-helpers.js';
+
+export interface CArityInfo {
+  parameterCount?: number;
+  requiredParameterCount?: number;
+  parameterTypes?: string[];
+}
+
+/**
+ * Compute declaration arity from a C function definition or declaration node.
+ */
+export function computeCDeclarationArity(node: SyntaxNode): CArityInfo {
+  // Find the function_declarator child (may be wrapped in pointer_declarator)
+  const funcDecl = findFuncDeclarator(node);
+  if (funcDecl === null) return {};
+
+  const paramList = funcDecl.childForFieldName('parameters');
+  if (paramList === null) return {};
+
+  const params: SyntaxNode[] = [];
+  for (let i = 0; i < paramList.childCount; i++) {
+    const child = paramList.child(i);
+    if (child === null) continue;
+    if (child.type === 'parameter_declaration' || child.type === 'variadic_parameter') {
+      params.push(child);
+    }
+  }
+
+  // K&R old-style declaration: `int foo()` has an empty parameter_list with
+  // no parameter_declaration or variadic_parameter children. Per C89/C99,
+  // this means the function accepts an unspecified number/types of arguments —
+  // NOT zero arguments. Return unknown arity to avoid false 'incompatible'.
+  // `int foo(void)` is the explicit zero-parameter form and is handled below.
+  if (params.length === 0) return {};
+
+  // (void) means zero parameters
+  if (params.length === 1 && params[0].type === 'parameter_declaration') {
+    const typeNode = params[0].childForFieldName('type');
+    const hasDeclarator = params[0].childForFieldName('declarator') !== null;
+    if (typeNode !== null && typeNode.text === 'void' && !hasDeclarator) {
+      return { parameterCount: 0, requiredParameterCount: 0, parameterTypes: [] };
+    }
+  }
+
+  const isVariadic = params.some((p) => p.type === 'variadic_parameter');
+  const nonVariadicCount = params.filter((p) => p.type !== 'variadic_parameter').length;
+
+  const types: string[] = [];
+  for (const p of params) {
+    if (p.type === 'variadic_parameter') {
+      types.push('...');
+    } else {
+      const typeNode = p.childForFieldName('type');
+      types.push(typeNode?.text ?? 'unknown');
+    }
+  }
+
+  return {
+    parameterCount: isVariadic ? undefined : nonVariadicCount,
+    requiredParameterCount: nonVariadicCount,
+    parameterTypes: types,
+  };
+}
+
+/**
+ * Compute call-site arity from a call_expression node.
+ */
+export function computeCCallArity(node: SyntaxNode): number {
+  const argList = node.childForFieldName('arguments');
+  if (argList === null) return 0;
+
+  let count = 0;
+  for (let i = 0; i < argList.childCount; i++) {
+    const child = argList.child(i);
+    if (child === null) continue;
+    // Skip punctuation (commas, parens)
+    if (child.type !== ',' && child.type !== '(' && child.type !== ')') {
+      count++;
+    }
+  }
+  return count;
+}
+
+function findFuncDeclarator(node: SyntaxNode): SyntaxNode | null {
+  // Direct child
+  let decl = node.childForFieldName('declarator');
+  if (decl === null) {
+    for (let i = 0; i < node.childCount; i++) {
+      const c = node.child(i);
+      if (c?.type === 'function_declarator') return c;
+    }
+    return null;
+  }
+  // Unwrap pointer_declarator
+  while (decl.type === 'pointer_declarator') {
+    const next = decl.childForFieldName('declarator');
+    if (next === null) break;
+    decl = next;
+  }
+  if (decl.type === 'function_declarator') return decl;
+  return null;
+}

gitnexus/src/core/ingestion/languages/c/arity.ts

@@ -0,0 +1,20 @@
+import type { Callsite, SymbolDefinition } from 'gitnexus-shared';
+
+/**
+ * C arity compatibility: no overloading. Variadic functions detected
+ * via '...' in parameterTypes. Otherwise exact match or unknown.
+ */
+export function cArityCompatibility(
+  def: SymbolDefinition,
+  callsite: Callsite,
+): 'compatible' | 'unknown' | 'incompatible' {
+  const max = def.parameterCount;
+  const min = def.requiredParameterCount;
+  if (max === undefined && min === undefined) return 'unknown';
+  if (!Number.isFinite(callsite.arity) || callsite.arity < 0) return 'unknown';
+
+  const variadic = def.parameterTypes?.some((t) => t === '...') ?? false;
+  if (min !== undefined && callsite.arity < min) return 'incompatible';
+  if (max !== undefined && callsite.arity > max && !variadic) return 'incompatible';
+  return 'compatible';
+}