Merge branch 'main' into feat/Desktop-app

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

@@ -32,6 +32,7 @@ import pathlib
 import re
 import sys
 import urllib.error
+import urllib.parse
 import urllib.request
 
 REPO_ROOT = pathlib.Path(__file__).resolve().parents[2]
@@ -190,7 +191,17 @@ def fetch_text(url: str, timeout: int = 8) -> str | None:
     set (raises the rate limit from 60 to 5 000 requests/hour).
     """
     headers: dict[str, str] = {}
-    if _GITHUB_TOKEN and ("github.com" in url or "githubusercontent.com" in url):
+    # Parse the URL and check the hostname rather than substring-matching
+    # on the full URL string (CodeQL py/incomplete-url-substring-sanitization).
+    # `https://evil.com/?u=github.com` would have passed the substring check.
+    try:
+        parsed_host = urllib.parse.urlparse(url).hostname or ""
+    except ValueError:
+        parsed_host = ""
+    is_github_host = parsed_host == "github.com" or parsed_host.endswith(
+        (".github.com", ".githubusercontent.com")
+    ) or parsed_host == "githubusercontent.com"
+    if _GITHUB_TOKEN and is_github_host:
         headers["Authorization"] = f"Bearer {_GITHUB_TOKEN}"
     try:
         req = urllib.request.Request(url, headers=headers)

.github/workflows/ci-quality.yml

@@ -11,7 +11,7 @@ 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 +24,7 @@ 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/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@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # 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/publish.yml

@@ -35,7 +35,7 @@ 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

@@ -149,7 +149,7 @@ 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 +294,11 @@ 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 +356,11 @@ 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

@@ -1,13 +1,19 @@
 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:
@@ -61,7 +67,7 @@ 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:
@@ -17,6 +20,27 @@ concurrency:
   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,

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
 
@@ -47,7 +59,7 @@ 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
 

README.md

@@ -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):

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/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",
@@ -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"
@@ -1396,25 +1396,25 @@
       }
     },
     "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",

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",

gitnexus-web/src/core/llm/agent.ts

@@ -277,8 +277,10 @@ const extractInstanceName = (endpoint: string): string => {
   try {
     const url = new URL(endpoint);
     const hostname = url.hostname;
-    // Extract the first part before .openai.azure.com
-    const match = hostname.match(/^([^.]+)\.openai\.azure\.com/);
+    // Extract the first part before .openai.azure.com. The trailing `$`
+    // anchor is required (CodeQL js/regex/missing-regexp-anchor): without
+    // it `evil.openai.azure.com.attacker.tld` would match.
+    const match = hostname.match(/^([^.]+)\.openai\.azure\.com$/);
     if (match) {
       return match[1];
     }

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/core/llm/tools.ts

@@ -278,8 +278,11 @@ export const createGraphRAGTools = (backend: GraphRAGBackend) => {
                 const val = row[col];
                 if (val === null || val === undefined) return '';
                 if (typeof val === 'object') return JSON.stringify(val);
-                // Truncate long values and escape pipe characters
-                const str = String(val).replace(/\|/g, '\\|');
+                // Truncate long values and escape pipe characters. Escape
+                // backslashes FIRST so the subsequent pipe escape isn't
+                // unescaped by a trailing backslash (CodeQL
+                // js/incomplete-sanitization).
+                const str = String(val).replace(/\\/g, '\\\\').replace(/\|/g, '\\|');
                 return str.length > 60 ? str.slice(0, 57) + '...' : str;
               });
               return `| ${values.join(' | ')} |`;

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/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/package-lock.json

@@ -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": {

gitnexus/package.json

@@ -116,6 +116,6 @@
     }
   },
   "engines": {
-    "node": ">=20.0.0"
+    "node": ">=22.0.0"
   }
 }

gitnexus/src/cli/analyze.ts

@@ -27,6 +27,7 @@ import { warnMissingOptionalGrammars } from './optional-grammars.js';
 import { glob } from 'glob';
 import fs from 'fs/promises';
 import { cliError } from './cli-message.js';
+import { isHfDownloadFailure } from '../core/embeddings/hf-env.js';
 
 // Capture stderr.write at module load BEFORE anything (LadybugDB native
 // init, progress bar, console redirection) can monkey-patch it. The
@@ -576,6 +577,26 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
       return;
     }
 
+    // HF download failure — show clean guidance without the raw stack trace.
+    // Checked before writeFatalToStderr so the user sees one focused message
+    // rather than a stack-trace dump followed by a second remediation block.
+    if (isHfDownloadFailure(msg) || msg.includes('Failed to download embedding model')) {
+      cliError(
+        `  The embedding model could not be downloaded.\n` +
+          `  huggingface.co may be unreachable from your network\n` +
+          `  (e.g. behind a corporate proxy or a regional firewall).\n` +
+          `  Suggestions:\n` +
+          `    1. Set HF_ENDPOINT to a mirror and retry:\n` +
+          `         HF_ENDPOINT=https://hf-mirror.com npx gitnexus analyze --embeddings\n` +
+          `         (Windows: set HF_ENDPOINT=https://hf-mirror.com && npx gitnexus analyze --embeddings)\n` +
+          `    2. Check your proxy / VPN settings.\n` +
+          `    3. Once downloaded the model is cached — future runs work offline.\n`,
+        { recoveryHint: 'hf-endpoint-unreachable' },
+      );
+      process.exitCode = 1;
+      return;
+    }
+
     // Bypass the redirected console.error and write the full stack to
     // the real stderr captured at module load. The redirected
     // console.error wraps every line with `\\x1b[2K\\r` (ANSI clear-line)

gitnexus/src/cli/index.ts

@@ -160,6 +160,18 @@ 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

@@ -365,7 +365,12 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
     }
 
     const hookPath = path.join(destHooksDir, 'gitnexus-hook.cjs').replace(/\\/g, '/');
-    const hookCmd = `node "${hookPath.replace(/"/g, '\\"')}"`;
+    // Escape backslashes FIRST, then quotes (CodeQL js/incomplete-sanitization).
+    // The previous shape `replace(/"/g, '\\"')` alone would let `path\with"quote`
+    // become `path\with\"quote`, where the trailing `\` before `"` could
+    // unescape the quote inside the surrounding double-quoted shell context.
+    const escapedHookPath = hookPath.replace(/\\/g, '\\\\').replace(/"/g, '\\"');
+    const hookCmd = `node "${escapedHookPath}"`;
 
     // Check which hook events need entries (idempotent: skip if already registered)
     const parsed = await (async () => {

gitnexus/src/cli/wiki.ts

@@ -602,6 +602,38 @@ function hasGhCLI(): boolean {
   }
 }
 
+/**
+ * Strict Gist URL predicate. Rejects:
+ *   - any URL that does not parse (URL constructor throws)
+ *   - schemes other than https (drops `http:`, `file:`, `gist:`-style spoofs)
+ *   - hostnames that are not exactly `gist.github.com` (drops substring spoofs
+ *     like `https://evil.com/?u=gist.github.com` and userinfo-prefixed shapes
+ *     like `https://[email protected]/...` — note that URL.hostname
+ *     strips userinfo, so the equality check rejects the userinfo-prefixed
+ *     spoof if the actual host differs from gist.github.com)
+ *   - any URL containing userinfo (`username[:password]@`), which the URL
+ *     parser exposes via `.username` / `.password`. Defense-in-depth: even
+ *     when hostname matches, a credential-bearing URL is suspect and not
+ *     produced by `gh gist create`.
+ *
+ * Closes the substring-bypass class CodeQL `js/incomplete-url-substring-
+ * sanitization` flags.
+ */
+function isGistUrl(line: string): boolean {
+  const trimmed = line.trim();
+  try {
+    const u = new URL(trimmed);
+    return (
+      u.protocol === 'https:' &&
+      u.hostname === 'gist.github.com' &&
+      u.username === '' &&
+      u.password === ''
+    );
+  } catch {
+    return false;
+  }
+}
+
 function publishGist(htmlPath: string): { url: string; rawUrl: string } | null {
   try {
     const output = execFileSync(
@@ -610,13 +642,14 @@ function publishGist(htmlPath: string): { url: string; rawUrl: string } | null {
       { encoding: 'utf-8', stdio: ['pipe', 'pipe', 'pipe'] },
     ).trim();
 
-    // gh gist create prints the gist URL as the last line
-    const lines = output.split('\n');
-    const gistUrl = lines.find((l) => l.includes('gist.github.com')) || lines[lines.length - 1];
+    // `gh gist create` prints the gist URL as a line in the output. Find the
+    // first parseable Gist URL — if no line is a valid Gist URL, fail closed
+    // (do NOT fall back to lines[last]: a non-Gist last line would propagate
+    // through the regex below and produce a malformed `rawUrl`).
+    const gistUrl = output.split('\n').find(isGistUrl);
+    if (!gistUrl) return null;
 
-    if (!gistUrl || !gistUrl.includes('gist.github.com')) return null;
-
-    // Build a raw viewer URL via gist.githack.com
+    // Build a raw viewer URL via gist.githack.com.
     // gist URL format: https://gist.github.com/{user}/{id}
     const match = gistUrl.match(/gist\.github\.com\/([^/]+)\/([a-f0-9]+)/);
     let rawUrl = gistUrl;

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

@@ -104,7 +104,7 @@ export async function augment(pattern: string, cwd?: string): Promise<string> {
     }
 
     // Step 1: BM25 search (fast, no embeddings)
-    const bm25Results = await searchFTSFromLbug(pattern, 10, repoId);
+    const { results: bm25Results } = await searchFTSFromLbug(pattern, 10, repoId);
 
     if (bm25Results.length === 0) return '';
 

gitnexus/src/core/embeddings/embedder.ts

@@ -14,7 +14,12 @@ if (!process.env.ORT_LOG_LEVEL) {
   process.env.ORT_LOG_LEVEL = '3';
 }
 
-import { pipeline, env, type FeatureExtractionPipeline } from '@huggingface/transformers';
+import {
+  pipeline,
+  env,
+  type FeatureExtractionPipeline,
+  type ProgressInfo,
+} from '@huggingface/transformers';
 import { existsSync } from 'fs';
 import { execFileSync } from 'child_process';
 import { join, dirname } from 'path';
@@ -22,7 +27,7 @@ import { createRequire } from 'module';
 import { DEFAULT_EMBEDDING_CONFIG, type EmbeddingConfig, type ModelProgress } from './types.js';
 import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
-import { applyHfEnvOverrides } from './hf-env.js';
+import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry } from './hf-env.js';
 import { logger } from '../logger.js';
 
 /**
@@ -171,13 +176,18 @@ export const initEmbedder = async (
       }
 
       const progressCallback = onProgress
-        ? (data: any) => {
+        ? (data: ProgressInfo) => {
             const progress: ModelProgress = {
-              status: data.status || 'progress',
-              file: data.file,
-              progress: data.progress,
-              loaded: data.loaded,
-              total: data.total,
+              // Map the `progress_total` aggregate event (not in ModelProgress.status)
+              // back to 'progress' so callers don't need to handle it separately.
+              status:
+                data.status === 'progress_total'
+                  ? 'progress'
+                  : ((data.status as ModelProgress['status']) ?? 'progress'),
+              file: 'file' in data ? data.file : undefined,
+              progress: 'progress' in data ? data.progress : undefined,
+              loaded: 'loaded' in data ? data.loaded : undefined,
+              total: 'total' in data ? data.total : undefined,
             };
             onProgress(progress);
           }
@@ -202,17 +212,29 @@ export const initEmbedder = async (
             logger.info('🔧 Using WASM backend (slower)...');
           }
 
-          embedderInstance = await (pipeline as any)('feature-extraction', finalConfig.modelId, {
-            device: device,
-            dtype: 'fp32',
-            progress_callback: progressCallback,
-            session_options: {
-              logSeverityLevel: 3,
-              intraOpNumThreads: finalConfig.threads,
-              interOpNumThreads: 1,
-              executionMode: 'sequential',
+          embedderInstance = await withHfDownloadRetry(
+            () =>
+              pipeline('feature-extraction', finalConfig.modelId, {
+                device: device,
+                dtype: 'fp32',
+                progress_callback: progressCallback,
+                session_options: {
+                  logSeverityLevel: 3,
+                  intraOpNumThreads: finalConfig.threads,
+                  interOpNumThreads: 1,
+                  executionMode: 'sequential',
+                },
+              }),
+            {
+              onRetry: isDev
+                ? (attempt, max, err) =>
+                    logger.warn(
+                      { attempt, max, err: err.message },
+                      `⚠️  Model download network error (attempt ${attempt}/${max}), retrying…`,
+                    )
+                : undefined,
             },
-          });
+          );
           currentDevice = device;
 
           if (isDev) {
@@ -228,6 +250,20 @@ export const initEmbedder = async (
 
           return embedderInstance!;
         } catch (deviceError) {
+          // Network errors and circuit-open errors are not device-specific —
+          // they will fail the same way on every device. Rethrow immediately
+          // with actionable HF_ENDPOINT guidance rather than silently falling
+          // back to the next device.
+          const errMsg = deviceError instanceof Error ? deviceError.message : String(deviceError);
+          if (isHfDownloadFailure(errMsg)) {
+            const endpointHint = process.env.HF_ENDPOINT
+              ? `The configured endpoint (${process.env.HF_ENDPOINT}) may be unreachable.`
+              : `huggingface.co may be unreachable from your network.\n` +
+                `  Set HF_ENDPOINT to a mirror and retry:\n` +
+                `    HF_ENDPOINT=https://hf-mirror.com npx gitnexus analyze --embeddings\n` +
+                `    (Windows: set HF_ENDPOINT=https://hf-mirror.com && npx gitnexus analyze --embeddings)`;
+            throw new Error(`Failed to download embedding model: ${errMsg}\n  ${endpointHint}`);
+          }
           if (isDev && (device === 'cuda' || device === 'dml')) {
             const gpuType = device === 'dml' ? 'DirectML' : 'CUDA';
             logger.info(`⚠️  ${gpuType} not available, falling back to CPU...`);

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

@@ -1,6 +1,27 @@
 import os from 'node:os';
 import { join } from 'node:path';
 
+import { CircuitBreaker, withRetry } from 'gitnexus-shared';
+
+// ---------------------------------------------------------------------------
+// Download resilience defaults
+// ---------------------------------------------------------------------------
+
+/** Per-attempt timeout for the full model download (5 minutes). */
+export const HF_DOWNLOAD_TIMEOUT_MS = 5 * 60 * 1_000;
+/** Maximum total download attempts (1 initial + N-1 retries). */
+export const HF_MAX_ATTEMPTS = 3;
+/** Initial delay between retry attempts; doubles on each subsequent retry. */
+export const HF_BASE_DELAY_MS = 2_000;
+/** Number of consecutive failures required to open the circuit. */
+export const CB_FAILURE_THRESHOLD = 3;
+/** How long the circuit stays open before transitioning to half-open. */
+export const CB_RESET_TIMEOUT_MS = 60_000;
+/** Upper bound clamped on the env-override per-attempt timeout (30 minutes). */
+export const HF_MAX_TIMEOUT_MS = 30 * 60 * 1_000;
+/** Upper bound clamped on the env-override attempt count. */
+export const HF_MAX_ATTEMPTS_CAP = 10;
+
 /**
  * @internal Exported only for unit tests and the two embedder entry points
  * (`core/embeddings/embedder.ts` + `mcp/core/embedder.ts`). Not part of the
@@ -60,3 +81,234 @@ export function applyHfEnvOverrides(env: HfEnvSubset): void {
     env.remoteHost = endpoint.endsWith('/') ? endpoint : endpoint + '/';
   }
 }
+
+/**
+ * @internal Exported for unit tests and the two embedder entry points.
+ *
+ * Returns true when an error message indicates a network-level fetch failure
+ * during HuggingFace model download (e.g. `TypeError: fetch failed`,
+ * `ECONNREFUSED`, `ENOTFOUND`, `ETIMEDOUT`, `ECONNRESET`).
+ *
+ * These errors are not device-specific and cannot be fixed by falling back to
+ * a different ONNX device — the caller should rethrow immediately with
+ * guidance about `HF_ENDPOINT`.
+ */
+export function isNetworkFetchError(message: string): boolean {
+  return (
+    message.includes('fetch failed') ||
+    message.includes('ECONNREFUSED') ||
+    message.includes('ENOTFOUND') ||
+    message.includes('ETIMEDOUT') ||
+    message.includes('ECONNRESET')
+  );
+}
+
+// ---------------------------------------------------------------------------
+// Circuit breaker
+// ---------------------------------------------------------------------------
+
+/** @internal Used by `withHfDownloadRetry` to mark a circuit-open rejection. */
+export const CIRCUIT_OPEN_TAG = 'hf-circuit-open';
+
+/**
+ * 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 const hfDownloadCircuit = new CircuitBreaker({
+  failureThreshold: CB_FAILURE_THRESHOLD,
+  cooldownMs: CB_RESET_TIMEOUT_MS,
+  key: 'hf-download',
+});
+
+// ---------------------------------------------------------------------------
+// Retry + timeout wrapper
+// ---------------------------------------------------------------------------
+
+/** @internal Returns true for errors that should abort without retry (circuit-open). */
+export function isHfCircuitOpenError(message: string): boolean {
+  return message.includes(CIRCUIT_OPEN_TAG);
+}
+
+/**
+ * Returns true for any HuggingFace download failure that warrants showing the
+ * `HF_ENDPOINT` remediation hint: either a raw network error or a
+ * circuit-open rejection (which itself was caused by repeated network errors).
+ */
+export function isHfDownloadFailure(message: string): boolean {
+  return isNetworkFetchError(message) || isHfCircuitOpenError(message);
+}
+
+/** @internal Wraps `fn` in a hard time-limit. The timeout error contains
+ *  `ETIMEDOUT` so that `isNetworkFetchError` classifies it correctly.
+ */
+export function withDownloadTimeout<T>(fn: () => Promise<T>, timeoutMs: number): Promise<T> {
+  return new Promise<T>((resolve, reject) => {
+    const timer = setTimeout(
+      () =>
+        reject(
+          new Error(
+            `ETIMEDOUT: model download timed out after ${Math.round(timeoutMs / 1000)}s — ` +
+              `check your network speed or set HF_ENDPOINT to a faster mirror`,
+          ),
+        ),
+      timeoutMs,
+    );
+    fn().then(
+      (v) => {
+        clearTimeout(timer);
+        resolve(v);
+      },
+      (e) => {
+        clearTimeout(timer);
+        reject(e);
+      },
+    );
+  });
+}
+
+export interface HfRetryOptions {
+  /** Maximum total attempts including the initial one (default: `HF_MAX_ATTEMPTS`). */
+  maxAttempts?: number;
+  /** Delay before the first retry; doubles on each subsequent attempt (default: `HF_BASE_DELAY_MS`). */
+  baseDelayMs?: number;
+  /** Per-attempt wall-clock timeout in ms (default: `HF_DOWNLOAD_TIMEOUT_MS`). */
+  timeoutMs?: number;
+  /**
+   * Circuit-breaker instance to use. Defaults to the module-level
+   * `hfDownloadCircuit` singleton. Pass a fresh instance in tests.
+   */
+  circuit?: CircuitBreaker;
+  /**
+   * Optional callback invoked before each retry (not the initial attempt).
+   * @param attempt - 1-based retry number
+   * @param max - total allowed attempts
+   * @param error - the error that triggered the retry
+   */
+  onRetry?: (attempt: number, max: number, error: Error) => void;
+}
+
+/**
+ * Retry wrapper for HuggingFace model downloads with per-attempt timeout and
+ * circuit-breaker protection.
+ *
+ * Behaviour:
+ * - If the circuit is **open**, fails immediately with a `CIRCUIT_OPEN_TAG`
+ *   message (so `isHfDownloadFailure` still returns true and the caller can
+ *   show `HF_ENDPOINT` guidance).
+ * - Each attempt is wrapped in `withDownloadTimeout`.
+ * - On a network-level error (`isNetworkFetchError`) the attempt is retried
+ *   with exponential back-off; non-network errors (e.g. ONNX device failure)
+ *   are rethrown immediately without retry.
+ * - Every network failure is recorded on the circuit breaker; a success resets
+ *   it.
+ * - After all attempts are exhausted, the last network error is rethrown
+ *   so the existing `isNetworkFetchError` / `isHfDownloadFailure` guards in
+ *   the calling code still fire.
+ */
+export async function withHfDownloadRetry<T>(
+  fn: () => Promise<T>,
+  options: HfRetryOptions = {},
+): Promise<T> {
+  // Resolve effective values — explicit options take precedence over env vars,
+  // which take precedence over built-in defaults. This lets users lower the
+  // per-attempt timeout without rebuilding (e.g.
+  //   HF_DOWNLOAD_TIMEOUT_MS=60000 npx gitnexus analyze --embeddings
+  // reduces the worst-case wait from 15 minutes to ~3 minutes).
+  //
+  // Upper bounds are clamped to prevent accidental runaway configuration:
+  //   - timeoutMs is capped at HF_MAX_TIMEOUT_MS (30 min)
+  //   - maxAttempts is floored (fractional values → integer) and capped at
+  //     HF_MAX_ATTEMPTS_CAP (10).  Values ≤ 0, NaN, or Infinity fall back to
+  //     the built-in defaults.
+  const envTimeout = Number(process.env.HF_DOWNLOAD_TIMEOUT_MS);
+  const envMaxAttempts = Number(process.env.HF_MAX_ATTEMPTS);
+  const resolvedTimeout =
+    Number.isFinite(envTimeout) && envTimeout > 0
+      ? Math.min(envTimeout, HF_MAX_TIMEOUT_MS)
+      : HF_DOWNLOAD_TIMEOUT_MS;
+  const resolvedMaxAttempts =
+    Number.isFinite(envMaxAttempts) && envMaxAttempts > 0
+      ? Math.min(Math.floor(envMaxAttempts), HF_MAX_ATTEMPTS_CAP)
+      : HF_MAX_ATTEMPTS;
+  const {
+    maxAttempts = resolvedMaxAttempts,
+    baseDelayMs = HF_BASE_DELAY_MS,
+    timeoutMs = resolvedTimeout,
+    circuit = hfDownloadCircuit,
+    onRetry,
+  } = options;
+  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` : ''),
+    );
+  }
+
+  // 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;
+
+  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;
+  }
+}

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;
@@ -90,46 +99,51 @@ const httpEmbedBatch = async (
   model: string,
   apiKey: string,
   batchIndex = 0,
-  attempt = 0,
 ): Promise<EmbeddingItem[]> => {
   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 ${apiKey}`,
+        },
+        body: JSON.stringify({ input: batch, model }),
       },
-      body: JSON.stringify({ input: batch, model }),
-    });
+      {
+        breakerKey: HTTP_BREAKER_KEY,
+        retry: { maxAttempts: HTTP_MAX_RETRIES + 1, baseDelayMs: HTTP_RETRY_BACKOFF_MS },
+      },
+    );
   } catch (err) {
-    // Timeouts should not be retried — the server is unresponsive.
-    // AbortSignal.timeout() throws DOMException with name 'TimeoutError'.
-    const isTimeout = err instanceof DOMException && err.name === 'TimeoutError';
-    if (isTimeout) {
+    if (err instanceof CircuitOpenError) {
+      throw new Error(
+        `Embedding endpoint circuit open (${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[] };

gitnexus/src/core/git-staleness.ts

@@ -3,11 +3,14 @@
  * Lives in core/ so application code does not depend on the MCP package layer.
  */
 
-import { execFileSync } from 'node:child_process';
+import { execFile, execFileSync } from 'node:child_process';
+import { promisify } from 'node:util';
 import path from 'path';
 import { readRegistry, type RegistryEntry, type CwdMatch } from '../storage/repo-manager.js';
 import { findGitRootByDotGit, getCurrentCommit, getRemoteUrl } from '../storage/git.js';
 
+const execFileAsync = promisify(execFile);
+
 export interface StalenessInfo {
   isStale: boolean;
   commitsBehind: number;
@@ -41,6 +44,39 @@ export function checkStaleness(repoPath: string, lastCommit: string): StalenessI
   }
 }
 
+/**
+ * Async variant of {@link checkStaleness} — spawns git as a child process
+ * instead of blocking the event loop.  Used by `listRepos()` to check many
+ * repos in parallel (issue #1363: 200 repos × sync spawn ≈ 50 s).
+ */
+export async function checkStalenessAsync(
+  repoPath: string,
+  lastCommit: string,
+): Promise<StalenessInfo> {
+  try {
+    // Note: promisified execFile captures stdout/stderr by default (no stdio option needed,
+    // unlike the sync variant which requires explicit stdio: ['pipe','pipe','pipe']).
+    const { stdout } = await execFileAsync('git', ['rev-list', '--count', `${lastCommit}..HEAD`], {
+      cwd: repoPath,
+      encoding: 'utf-8',
+    });
+
+    const commitsBehind = parseInt(stdout.trim(), 10) || 0;
+
+    if (commitsBehind > 0) {
+      return {
+        isStale: true,
+        commitsBehind,
+        hint: `⚠️ Index is ${commitsBehind} commit${commitsBehind > 1 ? 's' : ''} behind HEAD. Run analyze tool to update.`,
+      };
+    }
+
+    return { isStale: false, commitsBehind: 0 };
+  } catch {
+    return { isStale: false, commitsBehind: 0 };
+  }
+}
+
 /**
  * Compare a sibling-clone HEAD against an indexed `lastCommit`. Returns
  * `undefined` when the indexed commit is not reachable from the sibling

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

@@ -44,26 +44,6 @@ async function removeLbugFile(basePath: string): Promise<void> {
   }
 }
 
-/**
- * Remove all stale `bridge.lbug.tmp.*` files (and their sidecars) from a
- * group directory.  With randomBytes-based temp names, a crashed writeBridge
- * leaves behind a uniquely-named tmp file that no future run will target by
- * name — so we glob for the prefix and clean up everything matching.
- */
-async function cleanStaleBridgeTmpFiles(groupDir: string): Promise<void> {
-  try {
-    const entries = await fsp.readdir(groupDir);
-    const staleBases = entries.filter(
-      (e) => e.startsWith('bridge.lbug.tmp.') && !LBUG_SIDECAR_SUFFIXES.some((s) => e.endsWith(s)),
-    );
-    for (const name of staleBases) {
-      await removeLbugFile(path.join(groupDir, name));
-    }
-  } catch {
-    /* best-effort: directory may not exist yet */
-  }
-}
-
 export function contractNodeId(
   repo: string,
   contractId: string,
@@ -299,8 +279,24 @@ export async function retryRename(src: string, dst: string, attempts = 3): Promi
 
 export async function writeBridgeMeta(groupDir: string, meta: BridgeMeta): Promise<void> {
   const target = path.join(groupDir, 'meta.json');
+  // Unpredictable suffix + O_EXCL via `'wx'` flag closes the symlink/
+  // pre-create attack window. The third argument `0o600` is the
+  // user-only mode mask — CodeQL's `js/insecure-temporary-file` query
+  // sources its verdict from the `mode` argument, NOT from `flags`:
+  // its `isSecureMode(mode)` predicate requires the low 6 bits to be
+  // zero (no group/world bits). Without an explicit mode the file is
+  // created with the process umask (typically 0o644 = group/world
+  // readable), which the query treats as the actual vulnerability.
+  // Both `'wx'` (runtime O_EXCL) AND `0o600` (CodeQL-credited mode)
+  // are needed: one closes the symlink race, the other closes the
+  // permissions exposure.
   const tmp = `${target}.tmp.${randomBytes(8).toString('hex')}`;
-  await fsp.writeFile(tmp, JSON.stringify(meta, null, 2), 'utf-8');
+  const handle = await fsp.open(tmp, 'wx', 0o600);
+  try {
+    await handle.writeFile(JSON.stringify(meta, null, 2), 'utf-8');
+  } finally {
+    await handle.close();
+  }
   // Use retryRename for consistency with writeBridge's atomic swap — on
   // Windows a concurrent reader can cause EBUSY/EPERM even on a tiny
   // meta.json, and we don't want meta write to be less robust than the
@@ -369,7 +365,19 @@ export async function writeBridge(
   const crossLinks = dedupeCrossLinks(input.crossLinks);
 
   const finalPath = path.join(groupDir, 'bridge.lbug');
-  const tmpPath = path.join(groupDir, `bridge.lbug.tmp.${randomBytes(8).toString('hex')}`);
+  // Stage the temp database inside a unique mkdtemp directory rather than
+  // a fixed `bridge.lbug.tmp` name. The previous shape was flagged by
+  // CodeQL js/insecure-temporary-file as a predictable path: a co-located
+  // attacker (or a parallel writeBridge call into the same group) could
+  // pre-create or symlink that path before this writer opens it. mkdtemp
+  // returns a directory whose suffix is filled with cryptographically
+  // random bytes, so the staging path is unguessable AND collision-free
+  // across parallel callers. We anchor the staging directory inside
+  // `groupDir` so the subsequent rename of `bridge.lbug` (and its
+  // `.wal` / `.shadow` sidecars) into place stays on the same filesystem
+  // and remains atomic — moving across `os.tmpdir()` could trip EXDEV.
+  const stagingDir = await fsp.mkdtemp(path.join(groupDir, 'bridge-tmp-'));
+  const tmpPath = path.join(stagingDir, 'bridge.lbug');
   const bakPath = path.join(groupDir, 'bridge.lbug.bak');
 
   const report: WriteBridgeReport = {
@@ -389,43 +397,42 @@ export async function writeBridge(
     }
   };
 
-  // Clean up stale tmp files left behind by previously crashed writeBridge
-  // runs.  With randomBytes-based names each run picks a unique path, so
-  // the old fixed-name `removeLbugFile(tmpPath)` was a no-op — stale
-  // artifacts accumulated.  The glob-based helper finds *all* leftover
-  // `bridge.lbug.tmp.*` entries and removes them (including sidecars).
-  await cleanStaleBridgeTmpFiles(groupDir);
+  // The mkdtemp staging directory above is freshly created with a unique
+  // random suffix, so there are no leftover `bridge.lbug.tmp` / `.wal` /
+  // `.shadow` sidecars from a previous crashed run to clean up here — the
+  // directory is empty by construction.
 
-  // 1. Create temp DB, insert all data.
-  //
-  // Everything after `openBridgeDb` must run inside a try/finally so that
-  // if ANY step before the explicit `closeBridgeDb` throws — schema
-  // creation, a contract insert loop that rethrows, a snapshot write, the
-  // cross-link loop, or anything else — the handle is still released. A
-  // leaked handle holds the native LadybugDB file lock on tmpPath, which
-  // (a) leaks a FD and (b) prevents the next writeBridge call from
-  // reusing the same tmp slot.
-  const handle = await openBridgeDb(tmpPath);
-  let handleClosed = false;
   try {
-    await ensureBridgeSchema(handle);
+    // 1. Create temp DB, insert all data.
+    //
+    // Everything after `openBridgeDb` must run inside a try/finally so that
+    // if ANY step before the explicit `closeBridgeDb` throws — schema
+    // creation, a contract insert loop that rethrows, a snapshot write, the
+    // cross-link loop, or anything else — the handle is still released. A
+    // leaked handle holds the native LadybugDB file lock on tmpPath, which
+    // (a) leaks a FD and (b) prevents the next writeBridge call from
+    // reusing the same tmp slot.
+    const handle = await openBridgeDb(tmpPath);
+    let handleClosed = false;
+    try {
+      await ensureBridgeSchema(handle);
 
-    // Build the lookup index incrementally as contracts are inserted, so
-    // failed inserts are never in the index (and therefore never resolved
-    // by the cross-link loop below). This replaces a previous N+1 query
-    // pattern where each link made up to 6 DB round-trips to find its
-    // endpoints — see ContractLookupIndex.
-    const lookupIndex = createContractLookupIndex();
+      // Build the lookup index incrementally as contracts are inserted, so
+      // failed inserts are never in the index (and therefore never resolved
+      // by the cross-link loop below). This replaces a previous N+1 query
+      // pattern where each link made up to 6 DB round-trips to find its
+      // endpoints — see ContractLookupIndex.
+      const lookupIndex = createContractLookupIndex();
 
-    // Insert contracts — tolerate individual failures (e.g., a corrupt meta
-    // that can't be serialized). The whole sync must not fail because one
-    // contract is broken.
-    for (const c of contracts) {
-      const id = contractNodeId(c.repo, c.contractId, c.role, c.symbolRef.filePath);
-      try {
-        await queryBridge(
-          handle,
-          `CREATE (n:Contract {
+      // Insert contracts — tolerate individual failures (e.g., a corrupt meta
+      // that can't be serialized). The whole sync must not fail because one
+      // contract is broken.
+      for (const c of contracts) {
+        const id = contractNodeId(c.repo, c.contractId, c.role, c.symbolRef.filePath);
+        try {
+          await queryBridge(
+            handle,
+            `CREATE (n:Contract {
       id: $id,
       contractId: $contractId,
       type: $type,
@@ -438,91 +445,91 @@ export async function writeBridge(
       confidence: $confidence,
       meta: $meta
     })`,
-          {
-            id,
-            contractId: c.contractId,
-            type: c.type,
-            role: c.role,
-            repo: c.repo,
-            service: c.service ?? '',
-            symbolUid: c.symbolUid,
-            filePath: c.symbolRef.filePath,
-            symbolName: c.symbolName,
-            confidence: c.confidence,
-            meta: JSON.stringify(c.meta),
-          },
-        );
-        report.contractsInserted++;
-        // Only index on successful insert — the cross-link loop must never
-        // resolve to a row that isn't actually in the DB.
-        indexContract(lookupIndex, c, id);
-      } catch (err) {
-        report.contractsFailed++;
-        recordError('contract', id, err);
+            {
+              id,
+              contractId: c.contractId,
+              type: c.type,
+              role: c.role,
+              repo: c.repo,
+              service: c.service ?? '',
+              symbolUid: c.symbolUid,
+              filePath: c.symbolRef.filePath,
+              symbolName: c.symbolName,
+              confidence: c.confidence,
+              meta: JSON.stringify(c.meta),
+            },
+          );
+          report.contractsInserted++;
+          // Only index on successful insert — the cross-link loop must never
+          // resolve to a row that isn't actually in the DB.
+          indexContract(lookupIndex, c, id);
+        } catch (err) {
+          report.contractsFailed++;
+          recordError('contract', id, err);
+        }
       }
-    }
 
-    // Insert repo snapshots
-    for (const [repoId, snap] of Object.entries(input.repoSnapshots)) {
-      try {
-        await queryBridge(
-          handle,
-          `CREATE (s:RepoSnapshot {
+      // Insert repo snapshots
+      for (const [repoId, snap] of Object.entries(input.repoSnapshots)) {
+        try {
+          await queryBridge(
+            handle,
+            `CREATE (s:RepoSnapshot {
       id: $id,
       indexedAt: $indexedAt,
       lastCommit: $lastCommit
     })`,
-          {
-            id: repoId,
-            indexedAt: snap.indexedAt,
-            lastCommit: snap.lastCommit,
-          },
-        );
-        report.snapshotsInserted++;
-      } catch (err) {
-        report.snapshotsFailed++;
-        recordError('snapshot', repoId, err);
-      }
-    }
-
-    // Insert cross-links (tolerating missing nodes).
-    //
-    // `findContractNode` consults the in-memory lookup index built above,
-    // not the DB — that's an O(1) pure-function lookup per endpoint instead
-    // of the previous 2-3 DB queries. For M cross-links, the previous code
-    // issued up to 6M round-trips; this version issues zero.
-    //
-    // `link.contractId` may differ between the consumer and provider sides
-    // (e.g. wildcard consumer `grpc::Service/*` → method-level provider
-    // `grpc::Service/Method`) — that's why we resolve each endpoint
-    // independently via its own `(repo, role, symbolUid, filePath, symbolName)`
-    // tuple rather than matching on contractId.
-    for (const link of crossLinks) {
-      const linkId = `${link.from.repo}::${link.contractId}->${link.to.repo}::${link.contractId}`;
-      try {
-        const fromId = findContractNode(
-          lookupIndex,
-          link.from.repo,
-          'consumer',
-          link.from.symbolUid,
-          link.from.symbolRef.filePath,
-          link.from.symbolRef.name,
-        );
-        const toId = findContractNode(
-          lookupIndex,
-          link.to.repo,
-          'provider',
-          link.to.symbolUid,
-          link.to.symbolRef.filePath,
-          link.to.symbolRef.name,
-        );
-        if (!fromId || !toId) {
-          report.linksDroppedMissingNode++;
-          continue;
+            {
+              id: repoId,
+              indexedAt: snap.indexedAt,
+              lastCommit: snap.lastCommit,
+            },
+          );
+          report.snapshotsInserted++;
+        } catch (err) {
+          report.snapshotsFailed++;
+          recordError('snapshot', repoId, err);
         }
-        await queryBridge(
-          handle,
-          `
+      }
+
+      // Insert cross-links (tolerating missing nodes).
+      //
+      // `findContractNode` consults the in-memory lookup index built above,
+      // not the DB — that's an O(1) pure-function lookup per endpoint instead
+      // of the previous 2-3 DB queries. For M cross-links, the previous code
+      // issued up to 6M round-trips; this version issues zero.
+      //
+      // `link.contractId` may differ between the consumer and provider sides
+      // (e.g. wildcard consumer `grpc::Service/*` → method-level provider
+      // `grpc::Service/Method`) — that's why we resolve each endpoint
+      // independently via its own `(repo, role, symbolUid, filePath, symbolName)`
+      // tuple rather than matching on contractId.
+      for (const link of crossLinks) {
+        const linkId = `${link.from.repo}::${link.contractId}->${link.to.repo}::${link.contractId}`;
+        try {
+          const fromId = findContractNode(
+            lookupIndex,
+            link.from.repo,
+            'consumer',
+            link.from.symbolUid,
+            link.from.symbolRef.filePath,
+            link.from.symbolRef.name,
+          );
+          const toId = findContractNode(
+            lookupIndex,
+            link.to.repo,
+            'provider',
+            link.to.symbolUid,
+            link.to.symbolRef.filePath,
+            link.to.symbolRef.name,
+          );
+          if (!fromId || !toId) {
+            report.linksDroppedMissingNode++;
+            continue;
+          }
+          await queryBridge(
+            handle,
+            `
       MATCH (a:Contract), (b:Contract)
       WHERE a.id = $fromId AND b.id = $toId
       CREATE (a)-[:ContractLink {
@@ -533,83 +540,93 @@ export async function writeBridge(
         toRepo: $toRepo
       }]->(b)
     `,
-          {
-            fromId,
-            toId,
-            matchType: link.matchType,
-            confidence: link.confidence,
-            contractId: link.contractId,
-            fromRepo: link.from.repo,
-            toRepo: link.to.repo,
-          },
-        );
-        report.linksInserted++;
-      } catch (err) {
-        report.linksFailed++;
-        recordError('link', linkId, err);
+            {
+              fromId,
+              toId,
+              matchType: link.matchType,
+              confidence: link.confidence,
+              contractId: link.contractId,
+              fromRepo: link.from.repo,
+              toRepo: link.to.repo,
+            },
+          );
+          report.linksInserted++;
+        } catch (err) {
+          report.linksFailed++;
+          recordError('link', linkId, err);
+        }
+      }
+
+      // 2. Close temp DB (happy path). The finally block also calls
+      //    closeBridgeDb if we threw above; `handleClosed` prevents a
+      //    double-close on the native handle.
+      await closeBridgeDb(handle);
+      handleClosed = true;
+    } finally {
+      if (!handleClosed) {
+        await closeBridgeDb(handle).catch(() => {
+          /* ignore: cleanup path, best effort */
+        });
       }
     }
 
-    // 2. Close temp DB (happy path). The finally block also calls
-    //    closeBridgeDb if we threw above; `handleClosed` prevents a
-    //    double-close on the native handle.
-    await closeBridgeDb(handle);
-    handleClosed = true;
-  } finally {
-    if (!handleClosed) {
-      await closeBridgeDb(handle).catch(() => {
-        /* ignore: cleanup path, best effort */
-      });
+    // 3. Atomic swap: old→.bak, tmp→final, rm .bak
+    //
+    // The current database file (with its `.wal` / `.shadow` sidecars) is
+    // moved aside, then the freshly built tmp database takes its place.
+    // We move the sidecars together with the main file so the open below
+    // and any external readers see a consistent set; orphan sidecars from
+    // the tmp namespace are then removed because LadybugDB looks for them
+    // under the renamed-to base name and would reject mismatching IDs.
+    try {
+      await fsp.access(finalPath);
+      await retryRename(finalPath, bakPath);
+      for (const suffix of LBUG_SIDECAR_SUFFIXES) {
+        try {
+          await fsp.access(`${finalPath}${suffix}`);
+          await retryRename(`${finalPath}${suffix}`, `${bakPath}${suffix}`);
+        } catch {
+          /* sidecar absent — nothing to move */
+        }
+      }
+    } catch {
+      /* no existing db */
     }
-  }
-
-  // 3. Atomic swap: old→.bak, tmp→final, rm .bak
-  //
-  // The current database file (with its `.wal` / `.shadow` sidecars) is
-  // moved aside, then the freshly built tmp database takes its place.
-  // We move the sidecars together with the main file so the open below
-  // and any external readers see a consistent set; orphan sidecars from
-  // the tmp namespace are then removed because LadybugDB looks for them
-  // under the renamed-to base name and would reject mismatching IDs.
-  try {
-    await fsp.access(finalPath);
-    await retryRename(finalPath, bakPath);
+    await retryRename(tmpPath, finalPath);
     for (const suffix of LBUG_SIDECAR_SUFFIXES) {
+      // Rename — not delete — so the WAL (which may carry uncommitted-at-
+      // close-time pages on a graceful close, depending on
+      // `autoCheckpoint` / `checkpointThreshold`) and the `.shadow`
+      // checkpoint snapshot stay paired with the database file under its
+      // final name. LadybugDB 0.16.0's database-id check rejects an open
+      // when the sidecars belong to a different base name.
       try {
-        await fsp.access(`${finalPath}${suffix}`);
-        await retryRename(`${finalPath}${suffix}`, `${bakPath}${suffix}`);
+        await fsp.access(`${tmpPath}${suffix}`);
+        await retryRename(`${tmpPath}${suffix}`, `${finalPath}${suffix}`);
       } catch {
         /* sidecar absent — nothing to move */
       }
     }
-  } catch {
-    /* no existing db */
-  }
-  await retryRename(tmpPath, finalPath);
-  for (const suffix of LBUG_SIDECAR_SUFFIXES) {
-    // Rename — not delete — so the WAL (which may carry uncommitted-at-
-    // close-time pages on a graceful close, depending on
-    // `autoCheckpoint` / `checkpointThreshold`) and the `.shadow`
-    // checkpoint snapshot stay paired with the database file under its
-    // final name. LadybugDB 0.16.0's database-id check rejects an open
-    // when the sidecars belong to a different base name.
-    try {
-      await fsp.access(`${tmpPath}${suffix}`);
-      await retryRename(`${tmpPath}${suffix}`, `${finalPath}${suffix}`);
-    } catch {
-      /* sidecar absent — nothing to move */
-    }
-  }
-  await removeLbugFile(bakPath);
+    await removeLbugFile(bakPath);
 
-  // 4. Write meta.json
-  await writeBridgeMeta(groupDir, {
-    version: BRIDGE_SCHEMA_VERSION,
-    generatedAt: new Date().toISOString(),
-    missingRepos: input.missingRepos,
-  });
+    // 4. Write meta.json
+    await writeBridgeMeta(groupDir, {
+      version: BRIDGE_SCHEMA_VERSION,
+      generatedAt: new Date().toISOString(),
+      missingRepos: input.missingRepos,
+    });
 
-  return report;
+    return report;
+  } finally {
+    // Always remove the mkdtemp staging directory. On the happy path the
+    // main file and sidecars have been renamed out of it, so it's empty;
+    // on any error path it may still contain a partial database — either
+    // way `recursive: true, force: true` removes it without surfacing
+    // "directory not empty" or ENOENT.
+    await fsp.rm(stagingDir, { recursive: true, force: true }).catch(() => {
+      /* best-effort cleanup */
+    });
+  }
 }
 
 /* ------------------------------------------------------------------ */
@@ -705,8 +722,15 @@ export async function openBridgeDbReadOnly(groupDir: string): Promise<BridgeHand
       await new Promise((r) => setTimeout(r, delay));
     }
   }
+  // 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/cross-impact.ts

@@ -91,6 +91,25 @@ function clampCrossDepth(raw: unknown): { depth: number; warning?: string } {
   return { depth: d };
 }
 
+/**
+ * Clamp the impact timeout to a sane bounded range. Callers can feed this
+ * via tool params, so an unclamped value lets a single request hold a
+ * timer slot for an arbitrarily long duration (CodeQL js/resource-
+ * exhaustion). 100ms lower bound preserves test-suite scenarios that
+ * exercise tight timeouts; 5min upper bound is well above any legitimate
+ * single-impact compute. Applied at the validate boundary so the
+ * downstream `deadline` (Date.now() + timeoutMs) and the local-leg
+ * `setTimeout` see the same clamped value — earlier shapes had a 1hr
+ * outer cap and a 5min inner clamp that disagreed.
+ */
+export const IMPACT_TIMEOUT_MIN_MS = 100;
+export const IMPACT_TIMEOUT_MAX_MS = 5 * 60 * 1_000;
+
+export function clampTimeout(timeoutMs: number): number {
+  if (!Number.isFinite(timeoutMs) || timeoutMs <= 0) return IMPACT_TIMEOUT_MIN_MS;
+  return Math.min(IMPACT_TIMEOUT_MAX_MS, Math.max(IMPACT_TIMEOUT_MIN_MS, Math.trunc(timeoutMs)));
+}
+
 export function validateGroupImpactParams(params: Record<string, unknown>):
   | {
       ok: true;
@@ -143,13 +162,19 @@ export function validateGroupImpactParams(params: Record<string, unknown>):
   const service = normalizeServicePrefix(params.service);
   const subgroup = typeof params.subgroup === 'string' ? params.subgroup : undefined;
 
-  let timeoutMs =
+  // Clamp at the validate boundary so the downstream `deadline` (line
+  // ~366) and `safeLocalImpact`'s `setTimeout` both see a single
+  // bounded value. Without this, the outer deadline budgeted Phase-2
+  // cross-repo fanout up to 1hr while only the inner setTimeout was
+  // capped to 5min — the two halves of CodeQL #184's mitigation
+  // disagreed.
+  const rawTimeoutMs =
     typeof params.timeoutMs === 'number' && params.timeoutMs > 0
       ? params.timeoutMs
       : typeof params.timeout === 'number' && params.timeout > 0
         ? params.timeout
         : DEFAULT_LOCAL_IMPACT_TIMEOUT_MS;
-  if (timeoutMs > 3_600_000) timeoutMs = 3_600_000;
+  const timeoutMs = clampTimeout(rawTimeoutMs);
 
   return {
     ok: true,
@@ -191,12 +216,13 @@ async function safeLocalImpact(
   impactParams: Parameters<GroupToolPort['impact']>[1],
   timeoutMs: number,
 ): Promise<{ value: unknown; timedOut: boolean }> {
+  const safeTimeoutMs = clampTimeout(timeoutMs);
   let timer: ReturnType<typeof setTimeout> | undefined;
   const impactP = port.impact(repo, impactParams).catch((err) => ({
     error: err instanceof Error ? err.message : String(err),
   }));
   const timeoutP = new Promise<'timeout'>((resolve) => {
-    timer = setTimeout(() => resolve('timeout'), timeoutMs);
+    timer = setTimeout(() => resolve('timeout'), safeTimeoutMs);
   });
   const won = await Promise.race([
     impactP.then((v) => ({ tag: 'impact' as const, v })),
@@ -212,6 +238,65 @@ async function safeLocalImpact(
   return { value: won.v, timedOut: false };
 }
 
+/**
+ * Race a single Phase-2 `impactByUid` call against a remaining-budget
+ * timer. The Codex adversarial review on PR #1331 surfaced that the
+ * fanout loop only checked `Date.now() > deadline` *between* neighbor
+ * calls — once `await port.impactByUid(...)` was reached, a hung
+ * neighbor could pin the request indefinitely, and slow neighbors
+ * could compound past the 5-min `IMPACT_TIMEOUT_MAX_MS` cap.
+ *
+ * This helper wraps each call: a `setTimeout(remainingMs)` aborts an
+ * `AbortController` whose signal is forwarded to `impactByUid`, and a
+ * `Promise.race` resolves to `{ timedOut: true }` when the timer
+ * fires before the call completes. Implementors that ignore the
+ * signal (current local backend) still see their await resolved by
+ * the race; full cooperative cancellation inside the BFS is a future
+ * follow-up. On rejection, the value is `null` (matching the
+ * fanout's existing `if (fan == null)` truncation contract).
+ *
+ * Exported for direct unit testing — the helper IS the load-bearing
+ * mitigation surface, so the U3 regression test pins it directly
+ * rather than driving the full `runGroupImpact` path.
+ */
+export async function safeNeighborImpact(
+  port: GroupToolPort,
+  repoId: string,
+  uid: string,
+  direction: string,
+  opts: {
+    maxDepth: number;
+    relationTypes: string[];
+    minConfidence: number;
+    includeTests: boolean;
+  },
+  remainingMs: number,
+): Promise<{ value: unknown; timedOut: boolean }> {
+  const controller = new AbortController();
+  let timer: ReturnType<typeof setTimeout> | undefined;
+  const callP = port
+    .impactByUid(repoId, uid, direction, { ...opts, signal: controller.signal })
+    .catch(() => null);
+  const timeoutP = new Promise<'timeout'>((resolve) => {
+    timer = setTimeout(
+      () => {
+        controller.abort();
+        resolve('timeout');
+      },
+      Math.max(0, remainingMs),
+    );
+  });
+  const won = await Promise.race([
+    callP.then((v) => ({ tag: 'impact' as const, v })),
+    timeoutP.then(() => ({ tag: 'timeout' as const })),
+  ]);
+  if (timer !== undefined) clearTimeout(timer);
+  if (won.tag === 'timeout') {
+    return { value: null, timedOut: true };
+  }
+  return { value: won.v, timedOut: false };
+}
+
 export function collectImpactSymbolUids(
   local: unknown,
   servicePrefix: string | undefined,
@@ -476,7 +561,8 @@ export async function runGroupImpact(
       if (seen.has(key)) continue;
       seen.add(key);
 
-      if (Date.now() > deadline) {
+      const remainingMs = deadline - Date.now();
+      if (remainingMs <= 0) {
         truncatedRepos.push(n.neighborRepo);
         continue;
       }
@@ -492,13 +578,25 @@ export async function runGroupImpact(
         continue;
       }
 
-      const fan = await deps.port.impactByUid(neighborHandle.id, n.neighborUid, direction, {
-        maxDepth,
-        relationTypes: relationTypes ?? [],
-        minConfidence,
-        includeTests,
-      });
-      if (fan == null) {
+      // Phase-2 hardening: race each impactByUid against a per-call
+      // timeout derived from the remaining budget. Without this wrap a
+      // single hung neighbor would pin the request past the clamped
+      // timeout, which Codex's adversarial review on PR #1331 flagged
+      // as the still-open half of CodeQL #184 / js/resource-exhaustion.
+      const { value: fan, timedOut: neighborTimedOut } = await safeNeighborImpact(
+        deps.port,
+        neighborHandle.id,
+        n.neighborUid,
+        direction,
+        {
+          maxDepth,
+          relationTypes: relationTypes ?? [],
+          minConfidence,
+          includeTests,
+        },
+        remainingMs,
+      );
+      if (neighborTimedOut || fan == null) {
         truncatedRepos.push(n.neighborRepo);
         continue;
       }

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

@@ -0,0 +1,610 @@
+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 { 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 = parser.parse(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/rust-workspace-extractor.ts

@@ -31,6 +31,32 @@ interface ImportedSymbol {
   filePath: string;
 }
 
+/**
+ * Linear-time `[package].name = "..."` lookup. The previous regex
+ * `^\[package\]\s*\n(?:[^\[]*?\n)*?name\s*=\s*"([^"]+)"` had a nested
+ * lazy quantifier on `\n` that CodeQL js/redos flagged as exponential
+ * on inputs like `[package]\n` + many bare `\n`. We walk lines
+ * explicitly: scan from the first `[package]` header until we hit the
+ * next `[...]` section header, looking for the `name = "..."` line.
+ * O(n) with the line count.
+ *
+ * Exported so the U8 ReDoS regression test can drive the production
+ * line-walk directly with adversarial fixtures (multi-line strings,
+ * trailing sections, etc.) instead of duplicating it inline.
+ */
+export function parseCargoPackageName(content: string): string | null {
+  const lines = content.split('\n');
+  const packageStart = lines.findIndex((l) => l.trim() === '[package]');
+  if (packageStart < 0) return null;
+  for (let i = packageStart + 1; i < lines.length; i++) {
+    const line = lines[i].trimStart();
+    if (line.startsWith('[')) break; // hit the next section header
+    const m = /^name\s*=\s*"([^"]+)"/.exec(line);
+    if (m) return m[1];
+  }
+  return null;
+}
+
 /**
  * Parse a Cargo.toml to extract the crate name and workspace dependency
  * names. Uses simple line-based parsing — no TOML library needed for
@@ -47,12 +73,9 @@ async function parseCrateManifest(
     return null;
   }
 
-  let name = '';
+  const name = parseCargoPackageName(content) ?? '';
   const workspaceDeps: string[] = [];
 
-  const nameMatch = content.match(/^\[package\]\s*\n(?:[^\[]*?\n)*?name\s*=\s*"([^"]+)"/m);
-  if (nameMatch) name = nameMatch[1];
-
   // Match dependencies that use workspace = true, which indicates they
   // are workspace-internal deps:
   //   dep_name = { workspace = true }

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

@@ -217,6 +217,10 @@ 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 +294,10 @@ 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/**'],
     });
 

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/service.ts

@@ -65,6 +65,15 @@ export interface GroupToolPort {
       relationTypes: string[];
       minConfidence: number;
       includeTests: boolean;
+      // Optional cancellation signal. Callers (notably the cross-impact
+      // Phase-2 fanout) wrap this call in a Promise.race against a
+      // setTimeout-driven AbortController so a single hung neighbor
+      // cannot exceed the request's clamped timeout budget. Implementors
+      // may honor the signal cooperatively or simply let the caller's
+      // race resolve the await — the latter is sufficient for the
+      // resource-exhaustion mitigation. When the signal is absent or
+      // already aborted at call time, behavior is unchanged.
+      signal?: AbortSignal;
     },
   ): Promise<unknown | null>;
   context(

gitnexus/src/core/group/storage.ts

@@ -4,6 +4,16 @@ 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
+ * previous `Date.now()` pattern which CodeQL flagged as
+ * js/insecure-temporary-file: a guessable suffix in a writable directory
+ * lets a co-located attacker pre-create or symlink the tmp path before the
+ * write lands.
+ */
+const tmpSuffix = (): string => randomBytes(8).toString('hex');
 
 const CONTRACTS_FILE = 'contracts.json';
 
@@ -35,10 +45,28 @@ export async function writeContractRegistry(
   registry: ContractRegistry,
 ): Promise<void> {
   const targetPath = path.join(groupDir, CONTRACTS_FILE);
-  const tmpPath = `${targetPath}.tmp.${randomBytes(8).toString('hex')}`;
+  const tmpPath = `${targetPath}.tmp.${tmpSuffix()}`;
 
-  await fsp.writeFile(tmpPath, JSON.stringify(registry, null, 2), 'utf-8');
-  await fsp.rename(tmpPath, targetPath);
+  // O_EXCL via `'wx'` flag + explicit `0o600` mode — closes both halves
+  // of the CodeQL js/insecure-temporary-file finding: `'wx'` rejects a
+  // pre-planted symlink at the path, and `0o600` (user-only) prevents
+  // the file from being created group/world readable while it briefly
+  // contains contract data en route to the rename. The query's
+  // `isSecureMode` predicate inspects ONLY the mode argument, not the
+  // flags, so the explicit mode is what credits the fix.
+  const handle = await fsp.open(tmpPath, 'wx', 0o600);
+  try {
+    await handle.writeFile(JSON.stringify(registry, null, 2), 'utf-8');
+  } finally {
+    await handle.close();
+  }
+  // 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> {
@@ -107,6 +135,38 @@ matching:
   # exclude_links_paths: [/ping, /health, /healthcheck]
   # exclude_links_param_only_paths: false
 `;
-  await fsp.writeFile(path.join(groupDir, 'group.yaml'), template, 'utf-8');
+  // Always write group.yaml with O_EXCL via `fsp.open(..., 'wx')` —
+  // refuses to follow a pre-planted symlink at the target path, closing
+  // the TOCTOU window between the existence check (line ~98) and the
+  // write that CodeQL js/insecure-temporary-file flags. Under
+  // `force=true` we unlink the existing file first (best-effort, no-op
+  // when absent) so the subsequent O_EXCL open succeeds AND the same
+  // symlink-rejection guarantee holds — this is strictly safer than
+  // the previous `flag: force ? 'w' : 'wx'` shape, which silently
+  // followed symlinks under force. CodeQL's rule does not recognize
+  // the `writeFile(path, content, { flag: 'wx' })` shape as O_EXCL;
+  // the explicit open() handle below is what credits the mitigation.
+  const yamlPath = path.join(groupDir, 'group.yaml');
+  if (force) {
+    try {
+      await fsp.unlink(yamlPath);
+    } catch (err) {
+      // ENOENT (file absent) is expected on first run; rethrow anything
+      // else so we don't silently mask permission/EBUSY failures.
+      if ((err as NodeJS.ErrnoException).code !== 'ENOENT') throw err;
+    }
+  }
+  // `'wx'` rejects a pre-planted symlink at the path; `0o600` is
+  // user-only (no group/world bits) — gitnexus storage is per-user
+  // (`~/.gitnexus/...`), so any "other user wants to read this" case is
+  // a misconfiguration, not a feature. Keeping the file user-only also
+  // satisfies CodeQL's `isSecureMode` predicate (low 6 bits == 0) and
+  // closes the js/insecure-temporary-file alert at this site.
+  const handle = await fsp.open(yamlPath, 'wx', 0o600);
+  try {
+    await handle.writeFile(template, 'utf-8');
+  } finally {
+    await handle.close();
+  }
   return groupDir;
 }

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/ingestion/call-processor.ts

@@ -769,9 +769,10 @@ 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 = parser.parse(parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         continue;
@@ -3280,9 +3281,10 @@ 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 = parser.parse(parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch {
         continue;

gitnexus/src/core/ingestion/cobol/cobol-preprocessor.ts

@@ -369,9 +369,20 @@ const RE_USE_AFTER =
   /\bUSE\s+(?:AFTER\s+)?(?:STANDARD\s+)?(?:EXCEPTION|ERROR)\s+ON\s+([A-Z][A-Z0-9-]+|INPUT|OUTPUT|I-O|EXTEND)\b/i;
 
 // SET statement (condition, index)
-const RE_SET_TO_TRUE = /\bSET\s+((?:[A-Z][A-Z0-9-]+(?:\s+OF\s+[A-Z][A-Z0-9-]+)?\s+)+)TO\s+TRUE\b/i;
-const RE_SET_INDEX =
-  /\bSET\s+((?:[A-Z][A-Z0-9-]+\s+)+)(TO|UP\s+BY|DOWN\s+BY)\s+(\d+|[A-Z][A-Z0-9-]+)/i;
+//
+// Catastrophic-backtracking note (CodeQL js/redos): the previous shape
+// `((?:[A-Z][A-Z0-9-]+(?:\s+OF\s+[A-Z][A-Z0-9-]+)?\s+)+)TO\s+TRUE`
+// nested `\s+` quantifiers across alternations and was exponential on
+// inputs like "SET a OF a OF a ... TO TRUE". Replaced with a lazy
+// dot-match bounded by the explicit `\s+TO\s+TRUE` suffix — `.+?` is
+// O(n) with the trailing anchor, and the captured group is parsed
+// downstream the same way as before.
+// Exported so the U8 ReDoS regression test can pin the exact production
+// pattern. Direct import is the only way to ensure the test's
+// pathological-input timing assertion exercises the production regex
+// instead of an inline copy that drifts.
+export const RE_SET_TO_TRUE = /\bSET\s+(.+?)\s+TO\s+TRUE\b/i;
+export const RE_SET_INDEX = /\bSET\s+(.+?)\s+(TO|UP\s+BY|DOWN\s+BY)\s+(\d+|[A-Z][A-Z0-9-]+)/i;
 
 // INITIALIZE statement — data reset (captures targets before REPLACING/WITH clause)
 const RE_INITIALIZE = /\bINITIALIZE\s+([\s\S]*?)(?=\bREPLACING\b|\bWITH\b|\.\s*$|$)/i;

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

@@ -219,9 +219,13 @@ 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 = parser.parse(parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         // Skip files that can't be parsed
@@ -413,9 +417,10 @@ 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 = parser.parse(parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch {
         continue;

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

@@ -305,9 +305,10 @@ 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 = parser.parse(parseContent, undefined, {
+          bufferSize: getTreeSitterBufferSize(parseContent),
         });
       } catch (parseError) {
         continue;

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 +45,7 @@ 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';
 
 const C_BUILT_INS: ReadonlySet<string> = new Set([
   'printf',
@@ -410,6 +411,7 @@ export const cppProvider = defineLanguage({
     },
   ] satisfies AstFrameworkPatternConfig[],
   treeSitterQueries: CPP_QUERIES,
+  preprocessSource: stripUeMacros,
   typeConfig: cCppConfig,
   exportChecker: cCppExportChecker,
   importResolver: createImportResolver(cppImportConfig),

gitnexus/src/core/ingestion/languages/csharp/captures.ts

@@ -42,6 +42,39 @@ const FUNCTION_NODE_TYPES = [
   'local_function_statement',
 ] as const;
 
+const BUILTIN_TYPE_NAMES = new Set([
+  'bool',
+  'byte',
+  'char',
+  'decimal',
+  'double',
+  'float',
+  'int',
+  'long',
+  'object',
+  'sbyte',
+  'short',
+  'string',
+  'uint',
+  'ulong',
+  'ushort',
+  'void',
+]);
+
+function shouldEmitReadMember(memberNode: SyntaxNode): boolean {
+  const parent = memberNode.parent;
+  if (parent === null) return true;
+
+  switch (parent.type) {
+    case 'invocation_expression':
+      return parent.childForFieldName('function')?.id !== memberNode.id;
+    case 'assignment_expression':
+      return parent.childForFieldName('left')?.id !== memberNode.id;
+    default:
+      return true;
+  }
+}
+
 export function emitCsharpScopeCaptures(
   sourceText: string,
   _filePath: string,
@@ -94,6 +127,14 @@ export function emitCsharpScopeCaptures(
       continue;
     }
 
+    if (grouped['@reference.read.member'] !== undefined) {
+      const anchor = grouped['@reference.read.member'];
+      const memberNode = findNodeAtRange(tree.rootNode, anchor.range, 'member_access_expression');
+      if (memberNode === null || !shouldEmitReadMember(memberNode)) {
+        continue;
+      }
+    }
+
     // Synthesize `this` / `base` receiver type-bindings on every
     // instance method-like. Tree-sitter can't cleanly express "the
     // implicit receiver of a non-static member of a class/struct/
@@ -209,9 +250,63 @@ export function emitCsharpScopeCaptures(
     }
   }
 
+  out.push(...synthesizeGenericTypeArgumentReferences(tree.rootNode));
+
   return out;
 }
 
+function synthesizeGenericTypeArgumentReferences(root: SyntaxNode): CaptureMatch[] {
+  const out: CaptureMatch[] = [];
+  // Treat all generic type arguments as static type references, including
+  // declaration signatures and call-site generic instantiations.
+  visit(root, (node) => {
+    if (node.type !== 'generic_name') return;
+    const args = findNamedChild(node, 'type_argument_list');
+    if (args === null) return;
+
+    for (const arg of args.namedChildren) {
+      if (arg === null) continue;
+      const nameNode = terminalTypeNameNode(arg);
+      if (nameNode === null) continue;
+      if (BUILTIN_TYPE_NAMES.has(nameNode.text)) continue;
+      out.push({
+        '@reference.type': nodeToCapture('@reference.type', nameNode),
+        '@reference.name': nodeToCapture('@reference.name', nameNode),
+      });
+    }
+  });
+  return out;
+}
+
+function terminalTypeNameNode(node: SyntaxNode): SyntaxNode | null {
+  switch (node.type) {
+    case 'identifier':
+      return node;
+    case 'nullable_type':
+      return node.firstNamedChild === null ? null : terminalTypeNameNode(node.firstNamedChild);
+    case 'qualified_name':
+      return node.lastNamedChild;
+    case 'generic_name':
+      return node.childForFieldName('name') ?? node.firstNamedChild;
+    default:
+      return null;
+  }
+}
+
+function findNamedChild(node: SyntaxNode, type: string): SyntaxNode | null {
+  for (const child of node.namedChildren) {
+    if (child !== null && child.type === type) return child;
+  }
+  return null;
+}
+
+function visit(node: SyntaxNode, cb: (node: SyntaxNode) => void): void {
+  cb(node);
+  for (const child of node.namedChildren) {
+    if (child !== null) visit(child, cb);
+  }
+}
+
 /** C# 12 primary constructor: `class X(a, b) { }` / `record X(a, b)`.
  *  The parameters are a bare `parameter_list` named child of the type
  *  declaration (no `constructor_declaration` node). Emit a synthetic

gitnexus/src/core/ingestion/languages/csharp/query.ts

@@ -499,6 +499,12 @@ const CSHARP_SCOPE_QUERY = `
   left: (member_access_expression
     expression: "base" @reference.receiver
     name: (identifier) @reference.name)) @reference.write.member
+
+;; References — field/property reads: \`obj.Name\`
+;; Emit-side filtering drops call targets and assignment left-hand sides.
+(member_access_expression
+  expression: (_) @reference.receiver
+  name: (identifier) @reference.name) @reference.read.member
 `;
 
 let _parser: Parser | null = null;

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

@@ -371,6 +371,11 @@ const processParsingSequential = async (
       isVueSetup = extracted.isSetup;
     }
 
+    // Per-language source-text transform (e.g., UE macro stripping for C++).
+    // Length-preserving — see LanguageProvider.preprocessSource contract.
+    parseContent =
+      getProvider(language).preprocessSource?.(parseContent, file.path) ?? parseContent;
+
     try {
       await loadLanguage(language, file.path);
     } catch {

gitnexus/src/core/ingestion/vue-sfc-extractor.ts

@@ -23,7 +23,24 @@ interface ScriptBlock {
   lang: string;
 }
 
-const SCRIPT_RE = /<script(\s[^>]*)?>([^]*?)<\/script>/g;
+// Closing-tag pattern accepts:
+//   - whitespace before `>`            — `</script >`, `</script\t\n>`
+//   - attribute-like junk after `script` — `</script foo="bar">`,
+//                                          `</script\t\n bar>`
+//   - any case                          — `</SCRIPT>`, `</Script>`
+//
+// HTML5 parses `</script foo>` as a valid close tag (attributes on
+// close tags are ignored by the parser but still terminate the script
+// block). A strict `<\/script\s*>` would miss those forms and let a
+// crafted Vue file hide content from this extractor — exactly the
+// CodeQL `js/bad-tag-filter` failure mode (the published test cases
+// it checks include `</script foo="bar">` and `</script\t\n bar>`).
+//
+// `[^>]*` after `</script` accepts everything up to the next `>`,
+// matching the HTML parser's actual close-tag behaviour. The `i` flag
+// covers the case axis. PR #1330 CI surfaced both the case and
+// attribute axes; this expression closes both at once.
+const SCRIPT_RE = /<script(\s[^>]*)?>([^]*?)<\/script[^>]*>/gi;
 const TEMPLATE_COMPONENT_RE = /<([A-Z][A-Za-z0-9]+)/g;
 // Greedy: matches from the first <template> to the *last* </template>.
 // This is intentional — nested <template v-slot:...> tags are valid Vue

gitnexus/src/core/ingestion/workers/parse-worker.ts

@@ -1407,6 +1407,11 @@ const processFileGroup = (
       isVueSetup = extracted.isSetup;
     }
 
+    // Per-language source-text transform (e.g., UE macro stripping for C++).
+    // Length-preserving — see LanguageProvider.preprocessSource contract.
+    parseContent =
+      getProvider(language).preprocessSource?.(parseContent, file.path) ?? parseContent;
+
     clearCaches(); // Reset memoization before each new file
 
     let tree;

gitnexus/src/core/lbug/csv-generator.ts

@@ -301,11 +301,15 @@ export const streamAllCSVsToDisk = async (
     'Template',
     'Module',
   ] as const;
+  const propertyHeader = 'id,name,filePath,startLine,endLine,content,description,declaredType';
   const multiLangWriters = new Map<string, BufferedCSVWriter>();
   for (const t of MULTI_LANG_TYPES) {
     multiLangWriters.set(
       t,
-      new BufferedCSVWriter(path.join(csvDir, `${t.toLowerCase()}.csv`), multiLangHeader),
+      new BufferedCSVWriter(
+        path.join(csvDir, `${t.toLowerCase()}.csv`),
+        t === 'Property' ? propertyHeader : multiLangHeader,
+      ),
     );
   }
 
@@ -478,6 +482,9 @@ export const streamAllCSVsToDisk = async (
                 escapeCSVNumber(node.properties.endLine, -1),
                 escapeCSVField(content),
                 escapeCSVField(node.properties.description || ''),
+                ...(node.label === 'Property'
+                  ? [escapeCSVField(node.properties.declaredType || '')]
+                  : []),
               ].join(','),
             );
           }

gitnexus/src/core/lbug/lbug-adapter.ts

@@ -19,7 +19,10 @@ import type { CachedEmbedding } from '../embeddings/types.js';
 import { extensionManager, type ExtensionEnsureOptions } from './extension-loader.js';
 import {
   closeLbugConnection,
+  isDbBusyError,
+  isOpenRetryExhausted,
   openLbugConnection,
+  waitForWindowsHandleRelease,
   type LbugConnectionHandle,
 } from './lbug-config.js';
 import { isVectorExtensionSupportedByPlatform } from '../platform/capabilities.js';
@@ -185,21 +188,6 @@ const DB_LOCK_RETRY_ATTEMPTS = 3;
 /** Base back-off in ms between BUSY retries (multiplied by attempt number). */
 const DB_LOCK_RETRY_DELAY_MS = 500;
 
-/**
- * Return true when the error message indicates that another process holds
- * an exclusive lock on the LadybugDB file (e.g. `gitnexus analyze` or
- * `gitnexus serve` running at the same time).
- */
-export const isDbBusyError = (err: unknown): boolean => {
-  const msg = (err instanceof Error ? err.message : String(err)).toLowerCase();
-  return (
-    msg.includes('busy') ||
-    msg.includes('lock') ||
-    msg.includes('already in use') ||
-    msg.includes('could not set lock')
-  );
-};
-
 /**
  * Return true when the error message indicates a write was attempted against
  * a read-only LadybugDB connection. The MCP query pool opens DBs read-only,
@@ -252,7 +240,11 @@ export const withLbugDb = async <T>(dbPath: string, operation: () => Promise<T>)
       });
     } catch (err) {
       lastError = err;
-      if (!isDbBusyError(err) || attempt === DB_LOCK_RETRY_ATTEMPTS) {
+      // Skip outer retry when the inner open-retry already exhausted: the
+      // ~1.5s open-time budget was just spent, repeating the full reset+
+      // reopen cycle would only add 4-5s of tail latency without changing
+      // the outcome (both layers consult the same isDbBusyError matcher).
+      if (!isDbBusyError(err) || isOpenRetryExhausted(err) || attempt === DB_LOCK_RETRY_ATTEMPTS) {
         throw err;
       }
       // Close stale connection inside the session lock to prevent race conditions
@@ -330,7 +322,16 @@ const doInitLbug = async (dbPath: string) => {
       await conn.query(schemaQuery);
     } catch (err) {
       const msg = err instanceof Error ? err.message : String(err);
-      if (!msg.includes('already exists')) {
+      // Suppression list:
+      //   - "already exists": expected idempotent re-create on existing DBs
+      //   - "could not set lock on file": LadybugDB v0.16.1 emits this on
+      //     Windows when CREATE NODE TABLE runs against a path that was
+      //     just opened (the WAL handle from a fresh Database briefly
+      //     contests the table's first-write lock). The table is created
+      //     anyway and any genuine cross-process lock contention surfaces
+      //     on the next operation via withLbugDb's retry. Logging it here
+      //     would just be noise in CI.
+      if (!msg.includes('already exists') && !isDbBusyError(err)) {
         logger.warn(`⚠️ Schema creation warning: ${msg.slice(0, 120)}`);
       }
     }
@@ -607,6 +608,9 @@ const getCopyQuery = (table: NodeTableName, filePath: string): string => {
   if (table === 'Method') {
     return `COPY ${t}(id, name, filePath, startLine, endLine, isExported, content, description, parameterCount, returnType) FROM "${filePath}" ${COPY_CSV_OPTS}`;
   }
+  if (table === 'Property') {
+    return `COPY ${t}(id, name, filePath, startLine, endLine, content, description, declaredType) FROM "${filePath}" ${COPY_CSV_OPTS}`;
+  }
   // TypeScript/JS code element tables have isExported; multi-language tables do not
   if (TABLES_WITH_EXPORTED.has(table)) {
     return `COPY ${t}(id, name, filePath, startLine, endLine, isExported, content, description) FROM "${filePath}" ${COPY_CSV_OPTS}`;
@@ -658,6 +662,11 @@ export const insertNodeToLbug = async (
         ? `, description: ${escapeValue(properties.description)}`
         : '';
       query = `CREATE (n:${t} {id: ${escapeValue(properties.id)}, name: ${escapeValue(properties.name)}, filePath: ${escapeValue(properties.filePath)}, startLine: ${properties.startLine || 0}, endLine: ${properties.endLine || 0}, isExported: ${!!properties.isExported}, content: ${escapeValue(properties.content || '')}${descPart}})`;
+    } else if (label === 'Property') {
+      const descPart = properties.description
+        ? `, description: ${escapeValue(properties.description)}`
+        : '';
+      query = `CREATE (n:${t} {id: ${escapeValue(properties.id)}, name: ${escapeValue(properties.name)}, filePath: ${escapeValue(properties.filePath)}, startLine: ${properties.startLine || 0}, endLine: ${properties.endLine || 0}, content: ${escapeValue(properties.content || '')}${descPart}, declaredType: ${escapeValue(properties.declaredType || '')}})`;
     } else {
       // Multi-language tables (Struct, Impl, Trait, Macro, etc.) — no isExported
       const descPart = properties.description
@@ -736,6 +745,11 @@ export const batchInsertNodesToLbug = async (
             ? `, n.description = ${escapeValue(properties.description)}`
             : '';
           query = `MERGE (n:${t} {id: ${escapeValue(properties.id)}}) SET n.name = ${escapeValue(properties.name)}, n.filePath = ${escapeValue(properties.filePath)}, n.startLine = ${properties.startLine || 0}, n.endLine = ${properties.endLine || 0}, n.isExported = ${!!properties.isExported}, n.content = ${escapeValue(properties.content || '')}${descPart}`;
+        } else if (label === 'Property') {
+          const descPart = properties.description
+            ? `, n.description = ${escapeValue(properties.description)}`
+            : '';
+          query = `MERGE (n:${t} {id: ${escapeValue(properties.id)}}) SET n.name = ${escapeValue(properties.name)}, n.filePath = ${escapeValue(properties.filePath)}, n.startLine = ${properties.startLine || 0}, n.endLine = ${properties.endLine || 0}, n.content = ${escapeValue(properties.content || '')}${descPart}, n.declaredType = ${escapeValue(properties.declaredType || '')}`;
         } else {
           const descPart = properties.description
             ? `, n.description = ${escapeValue(properties.description)}`
@@ -1064,6 +1078,9 @@ export const flushWAL = async (): Promise<void> => {
  */
 export const safeClose = async (): Promise<void> => {
   await flushWAL();
+  // Capture before close — currentDbPath stays set so the Windows post-close
+  // probe below knows which file to wait on.
+  const closingDbPath = currentDbPath;
   if (conn) {
     try {
       // eslint-disable-next-line no-restricted-syntax -- sole authorised close site
@@ -1082,6 +1099,24 @@ export const safeClose = async (): Promise<void> => {
     }
     db = null;
   }
+  // Windows: libuv reports `db.close()` resolved before the kernel has
+  // released the file handle. A subsequent `new Database(samePath)` in
+  // the same process can race the release. The probe (lbug-config.ts)
+  // forces any residual lock to surface as EBUSY/EPERM/EACCES so the
+  // open-time retry absorbs the lag.
+  if (process.platform === 'win32' && closingDbPath) {
+    const released = await waitForWindowsHandleRelease(closingDbPath);
+    if (!released) {
+      // Probe exhausted with a lock code still in flight. The next
+      // openLbugConnection will absorb whatever residual lag remains, but
+      // a chronic warning helps operators spot AV interference (Windows
+      // Defender holding the file far past the 250ms budget).
+      logger.warn(
+        { dbPath: closingDbPath },
+        '⚠️ LadybugDB file handle still locked after close (Windows). If this repeats, check antivirus/Defender exclusions for the GitNexus storage directory.',
+      );
+    }
+  }
 };
 
 export const closeLbug = async (): Promise<void> => {

gitnexus/src/core/lbug/lbug-config.ts

@@ -1,3 +1,6 @@
+import fs from 'fs/promises';
+import os from 'os';
+import path from 'path';
 import type lbug from '@ladybugdb/core';
 
 /**
@@ -42,10 +45,23 @@ export const LBUG_MAX_DB_SIZE: number = (() => {
   return 16 * 1024 * 1024 * 1024;
 })();
 
+/** Matches WAL corruption errors from the LadybugDB engine. */
+const WAL_CORRUPTION_RE = /corrupt(ed)?\s+wal|invalid\s+wal\s+record|wal.*corrupt|checksum.*wal/i;
+
+export const WAL_RECOVERY_SUGGESTION =
+  'WAL corruption detected. Run `gitnexus analyze` to rebuild the index.';
+
+export function isWalCorruptionError(err: unknown): boolean {
+  if (!err) return false;
+  const msg = err instanceof Error ? err.message : String(err);
+  return WAL_CORRUPTION_RE.test(msg);
+}
+
 type LbugModule = typeof lbug;
 
 export interface LbugDatabaseOptions {
   readOnly?: boolean;
+  throwOnWalReplayFailure?: boolean;
 }
 
 export interface LbugConnectionHandle {
@@ -53,20 +69,200 @@ export interface LbugConnectionHandle {
   conn: lbug.Connection;
 }
 
+/**
+ * Return true when the error message indicates that a LadybugDB file lock
+ * could not be acquired — either at construction time
+ * (`new lbug.Database(...)` raises from `local_file_system.cpp`) or during
+ * a query (another writer holds the exclusive lock).
+ *
+ * Lives here (not in `lbug-adapter.ts`) so both the construction-time
+ * retry (`openWithLockRetry` in this file) and the query-time retry
+ * (`withLbugDb` in `lbug-adapter.ts`) consult the same matcher. Callers
+ * import directly from this module — no re-export to keep in sync.
+ */
+export const isDbBusyError = (err: unknown): boolean => {
+  const msg = (err instanceof Error ? err.message : String(err)).toLowerCase();
+  // `lock` already subsumes `could not set lock`; the broader term is kept
+  // because graph-DB transient errors include "deadlock", "lock contention",
+  // and the LadybugDB native module's "could not set lock on file" — all of
+  // which deserve a retry. If a non-transient lock-shaped error ever
+  // surfaces (e.g., "lock file missing" during recovery), tighten this
+  // matcher rather than raising the retry budget.
+  return msg.includes('busy') || msg.includes('lock') || msg.includes('already in use');
+};
+
 export function createLbugDatabase(
   lbugModule: LbugModule,
   databasePath: string,
   options: LbugDatabaseOptions = {},
 ): lbug.Database {
-  return new lbugModule.Database(
+  // .d.ts declares fewer args than the native constructor accepts.
+  return new (lbugModule.Database as any)(
     databasePath,
-    0,
-    false,
+    0, // bufferManagerSize
+    false, // enableCompression (pinned for v0.16.0)
     options.readOnly ?? false,
     LBUG_MAX_DB_SIZE,
-  );
+    true, // autoCheckpoint
+    -1, // checkpointThreshold
+    options.throwOnWalReplayFailure ?? true,
+    true, // enableChecksums
+  ) as lbug.Database;
 }
 
+// ─── Lock-busy retry tuning knobs ───────────────────────────────────────────
+//
+// All four GitNexus retry pairs that touch native LadybugDB locks live with
+// a comment cross-reference here so an SRE tuning Windows flakes finds them
+// in one grep:
+//
+//   1. OPEN_LOCK_RETRY_ATTEMPTS / OPEN_LOCK_RETRY_DELAY_MS  (this file)
+//      → `new lbug.Database()` constructor lock failures
+//   2. HANDLE_RELEASE_PROBE_ATTEMPTS / HANDLE_RELEASE_PROBE_DELAY_MS  (this file)
+//      → post-close fs.open probe to absorb Windows handle-release lag
+//   3. DB_LOCK_RETRY_ATTEMPTS / DB_LOCK_RETRY_DELAY_MS  (lbug-adapter.ts withLbugDb)
+//      → query-time busy/lock retry around already-open connections
+//
+// `new lbug.Database()` calls into the native module which performs an
+// OS-level exclusive lock on `<dbPath>`. On Windows that lock can fail
+// for reasons specific to the OS (Defender briefly opens new files,
+// libuv handle release lags the JS-side close). 5 attempts × 100ms
+// linear back-off (max sleep 100+200+300+400 = 1s, plus 5 ctor RTTs
+// of 10–50ms each = ~1.0–1.2s worst case) clears the typical
+// AV-scanner hold without masking real cross-process conflicts.
+//
+// Source: https://github.com/LadybugDB/ladybug/blob/v0.16.1/src/common/file_system/local_file_system.cpp#L126
+const OPEN_LOCK_RETRY_ATTEMPTS = 5;
+const OPEN_LOCK_RETRY_DELAY_MS = 100;
+
+const HANDLE_RELEASE_PROBE_ATTEMPTS = 5;
+const HANDLE_RELEASE_PROBE_DELAY_MS = 50;
+const HANDLE_RELEASE_LOCK_CODES = new Set(['EBUSY', 'EPERM', 'EACCES']);
+
+/**
+ * Test-fixture directory prefixes recognized by `isTestFixturePath`.
+ *
+ * IMPORTANT: this list must stay in sync with the prefixes passed to
+ * `createTempDir` in `gitnexus/test/helpers/test-db.ts` and the prefixes
+ * used by `withTestLbugDB` (`gitnexus/test/helpers/test-indexed-db.ts`).
+ * If you add a new test that passes a custom prefix to `createTempDir`,
+ * add it here too — otherwise the stale-sidecar sweep silently won't
+ * fire for that fixture and CI flakes return.
+ *
+ * The default `createTempDir('gitnexus-test-')` and the lbug variant
+ * `'gitnexus-lbug-'` cover today's call sites.
+ */
+const TEST_FIXTURE_PREFIXES = ['gitnexus-lbug-', 'gitnexus-test-'];
+
+/**
+ * Marker symbol attached to lock errors after `openWithLockRetry` exhausts
+ * its budget. `withLbugDb`'s outer query-time retry consults this so it
+ * does not re-retry a path that just spent up to ~1.5s in the open-time
+ * loop — preventing 6s tail latencies (3× outer × 5× inner attempts).
+ *
+ * The symbol is internal to GitNexus; consumers should treat the underlying
+ * error message as the user-visible signal.
+ */
+export const LBUG_OPEN_RETRY_EXHAUSTED = Symbol.for('gitnexus.lbug.openRetryExhausted');
+
+export const isOpenRetryExhausted = (err: unknown): boolean => {
+  if (err === null || err === undefined || typeof err !== 'object') return false;
+  return (err as { [LBUG_OPEN_RETRY_EXHAUSTED]?: boolean })[LBUG_OPEN_RETRY_EXHAUSTED] === true;
+};
+
+const tagOpenRetryExhausted = (err: unknown): unknown => {
+  if (err && typeof err === 'object') {
+    (err as { [LBUG_OPEN_RETRY_EXHAUSTED]?: boolean })[LBUG_OPEN_RETRY_EXHAUSTED] = true;
+  }
+  return err;
+};
+
+/**
+ * True when `dbPath` resolves to a recognized test fixture under the OS
+ * temp directory. Used to gate the stale-sidecar sweep so production
+ * paths never have their `.wal` / `.lock` files deleted.
+ *
+ * Defensive shape:
+ *   - `path.resolve` normalizes `..` segments before the prefix check, so
+ *     `<tmp>/gitnexus-lbug-x/../../etc/passwd` is rejected.
+ *   - The tmpRoot check trims any trailing separator returned by some
+ *     Windows TMP configurations (`C:\Users\X\Temp\`) so the startsWith
+ *     comparison stays correct.
+ *   - Only the IMMEDIATE parent directory is matched against the prefix
+ *     list. An ancestor walk would let a tmpdir whose own basename starts
+ *     with `gitnexus-lbug-` accept arbitrary nested paths under it.
+ */
+const isTestFixturePath = (dbPath: string): boolean => {
+  const tmpRoot = os.tmpdir().replace(new RegExp(`${path.sep === '\\' ? '\\\\' : path.sep}+$`), '');
+  const resolved = path.resolve(dbPath);
+  if (!resolved.startsWith(tmpRoot + path.sep) && resolved !== tmpRoot) return false;
+  const parentBase = path.basename(path.dirname(resolved));
+  return TEST_FIXTURE_PREFIXES.some((p) => parentBase.startsWith(p));
+};
+
+/** Exported only for direct unit testing — production callers use `openWithLockRetry`. */
+export const _isTestFixturePathForTest = isTestFixturePath;
+
+const sleep = (ms: number): Promise<void> => new Promise((resolve) => setTimeout(resolve, ms));
+
+/**
+ * Attempt to remove stale `.wal` / `.lock` sidecars that a previous aborted
+ * test run may have left behind. Best-effort: ENOENT is normal, anything
+ * else is swallowed so the caller's retry can surface the original error.
+ */
+const sweepStaleSidecars = async (dbPath: string): Promise<void> => {
+  for (const suffix of ['.wal', '.lock']) {
+    try {
+      await fs.unlink(dbPath + suffix);
+    } catch {
+      /* missing sidecar or permission error — let the open retry surface it */
+    }
+  }
+};
+
+/**
+ * Run `construct` with bounded retries when `new lbug.Database(...)` throws
+ * a busy/lock error. The original (loop-captured) error is preferred over
+ * any post-sweep error so triage sees the real LadybugDB lock message.
+ * On exhaustion the rethrown error is tagged via
+ * `LBUG_OPEN_RETRY_EXHAUSTED` so the outer query-time retry in
+ * `withLbugDb` skips re-retrying a freshly-exhausted path.
+ */
+const openWithLockRetry = async (
+  construct: () => lbug.Database,
+  dbPath: string,
+): Promise<lbug.Database> => {
+  let originalLockError: unknown;
+  for (let attempt = 1; attempt <= OPEN_LOCK_RETRY_ATTEMPTS; attempt++) {
+    try {
+      return construct();
+    } catch (err) {
+      if (!isDbBusyError(err)) throw err;
+      originalLockError = err;
+      if (attempt === OPEN_LOCK_RETRY_ATTEMPTS) break;
+      await sleep(OPEN_LOCK_RETRY_DELAY_MS * attempt);
+    }
+  }
+
+  // Final defense: only for recognized test fixtures, sweep stale sidecars
+  // (a prior aborted test run can leave a `.wal` lock that survives the
+  // tmp dir cleanup). Production paths never reach this branch — the guard
+  // requires the immediate parent dir to match a test prefix AND the
+  // resolved path to live under the OS temp directory.
+  if (isTestFixturePath(dbPath)) {
+    await sweepStaleSidecars(dbPath);
+    try {
+      return construct();
+    } catch {
+      // Intentionally do NOT overwrite originalLockError. The user-actionable
+      // signal is "we exhausted lock retries" — a different error from the
+      // post-sweep attempt is less useful than the lock failure that drove
+      // the sweep in the first place.
+    }
+  }
+  throw tagOpenRetryExhausted(originalLockError);
+};
+
 export async function openLbugConnection(
   lbugModule: LbugModule,
   databasePath: string,
@@ -74,7 +270,10 @@ export async function openLbugConnection(
 ): Promise<LbugConnectionHandle> {
   let db: lbug.Database | undefined;
   try {
-    db = createLbugDatabase(lbugModule, databasePath, options);
+    db = await openWithLockRetry(
+      () => createLbugDatabase(lbugModule, databasePath, options),
+      databasePath,
+    );
     return { db, conn: new lbugModule.Connection(db) };
   } catch (err) {
     if (db) await db.close().catch(() => {});
@@ -86,3 +285,60 @@ export async function closeLbugConnection(handle: LbugConnectionHandle): Promise
   await handle.conn.close().catch(() => {});
   await handle.db.close().catch(() => {});
 }
+
+/**
+ * Probe `dbPath` AND its `.wal` sidecar after `db.close()` so any
+ * residual native file handle surfaces as EBUSY/EPERM/EACCES and the
+ * bounded retry absorbs the release lag. Windows-only — Linux/macOS do
+ * not exhibit this race.
+ *
+ * Both files matter. Empirically, on rapid open→close→reopen cycles the
+ * main `dbPath` handle releases first; the `.wal` handle from the
+ * previous Database lingers and the new Database's first write (CREATE
+ * NODE TABLE during schema init) fails with "Could not set lock on
+ * file". Probing both makes safeClose actually return when the kernel
+ * is fully done with the path.
+ *
+ * Returns `true` when both probes succeeded (or skipped on non-lock
+ * errors / missing files). Returns `false` when either probe exhausted
+ * its budget with a lock code still in flight.
+ *
+ * Defensive shape:
+ *   - Opens read+write (`'r+'`) so the probe actually surfaces exclusive
+ *     locks held by the previous Database. A read-only probe (`'r'`) is
+ *     insufficient — Windows will grant read access while the previous
+ *     handle's exclusive write lock is still in flight, which lets
+ *     `safeClose` return before the next CREATE NODE TABLE can lock the
+ *     file.
+ *   - `try/finally` around `handle.close()` guarantees no fd leak even
+ *     if close itself throws.
+ */
+export const waitForWindowsHandleRelease = async (dbPath: string): Promise<boolean> => {
+  const mainReleased = await probeSinglePath(dbPath);
+  const walReleased = await probeSinglePath(dbPath + '.wal');
+  return mainReleased && walReleased;
+};
+
+const probeSinglePath = async (filePath: string): Promise<boolean> => {
+  for (let attempt = 1; attempt <= HANDLE_RELEASE_PROBE_ATTEMPTS; attempt++) {
+    let handle: fs.FileHandle | undefined;
+    try {
+      handle = await fs.open(filePath, 'r+');
+      return true;
+    } catch (err) {
+      const code = (err as NodeJS.ErrnoException | undefined)?.code;
+      if (!code || !HANDLE_RELEASE_LOCK_CODES.has(code)) return true; // ENOENT / unrelated → not our problem
+      if (attempt === HANDLE_RELEASE_PROBE_ATTEMPTS) return false;
+      await sleep(HANDLE_RELEASE_PROBE_DELAY_MS * attempt);
+    } finally {
+      if (handle) {
+        try {
+          await handle.close();
+        } catch {
+          /* swallow — caller cannot do anything useful with a probe-close failure */
+        }
+      }
+    }
+  }
+  return false;
+};

gitnexus/src/core/lbug/pool-adapter.ts

@@ -18,7 +18,7 @@
 import fs from 'fs/promises';
 import lbug from '@ladybugdb/core';
 import { loadFTSExtension } from './lbug-adapter.js';
-import { createLbugDatabase } from './lbug-config.js';
+import { createLbugDatabase, isWalCorruptionError } from './lbug-config.js';
 
 /** Per-repo pool: one Database, many Connections */
 interface PoolEntry {
@@ -97,7 +97,7 @@ let idleTimer: ReturnType<typeof setInterval> | null = null;
 // @ladybugdb/core), corrupting stdout in the pre-sentinel window. Routing
 // through the leaf breaks that chain.
 export { realStdoutWrite, realStderrWrite, setActiveStdoutWrite } from '../../mcp/stdio-capture.js';
-import { getActiveStdoutWrite } from '../../mcp/stdio-capture.js';
+import { getActiveStdoutWrite, realStderrWrite } from '../../mcp/stdio-capture.js';
 
 let stdoutSilenceCount = 0;
 /** True while pre-warming connections — prevents watchdog from prematurely restoring stdout */
@@ -263,6 +263,46 @@ const WAITER_TIMEOUT_MS = 15_000;
 const LOCK_RETRY_ATTEMPTS = 3;
 const LOCK_RETRY_DELAY_MS = 2000;
 
+async function openReadOnlyDatabase(dbPath: string): Promise<lbug.Database> {
+  let db: lbug.Database | undefined;
+  silenceStdout();
+  try {
+    db = createLbugDatabase(lbug, dbPath, {
+      readOnly: true,
+      throwOnWalReplayFailure: false,
+    });
+    await db.init();
+    return db;
+  } catch (err) {
+    if (db) await db.close().catch(() => {});
+    throw err;
+  } finally {
+    restoreStdout();
+  }
+}
+
+/**
+ * Quarantine the .wal file and retry opening the database.
+ * Used when the initial open fails with a WAL corruption error.
+ */
+async function tryQuarantineAndReopen(dbPath: string, repoId: string): Promise<lbug.Database> {
+  const walPath = dbPath + '.wal';
+  const quarantineName = `${walPath}.corrupt.${Date.now()}-${Math.random().toString(36).slice(2)}`;
+  try {
+    await fs.rename(walPath, quarantineName);
+  } catch {
+    throw new Error(
+      `LadybugDB WAL corruption detected for ${repoId}. ` +
+        `Run \`gitnexus analyze\` to rebuild the index. (quarantine failed)`,
+    );
+  }
+  realStderrWrite(
+    `GitNexus: LadybugDB WAL quarantined for ${repoId}; graph may be stale. ` +
+      `Run \`gitnexus analyze\` to rebuild the index.\n`,
+  );
+  return await openReadOnlyDatabase(dbPath);
+}
+
 /** Deduplicates concurrent initLbug calls for the same repoId */
 const initPromises = new Map<string, Promise<void>>();
 
@@ -319,16 +359,29 @@ async function doInitLbug(repoId: string, dbPath: string): Promise<void> {
     // avoids lock conflicts when `gitnexus analyze` is writing.
     let lastError: Error | null = null;
     for (let attempt = 1; attempt <= LOCK_RETRY_ATTEMPTS; attempt++) {
-      silenceStdout();
       try {
-        const db = createLbugDatabase(lbug, dbPath, { readOnly: true });
-        restoreStdout();
+        const db = await openReadOnlyDatabase(dbPath);
         shared = { db, refCount: 0, ftsLoaded: false };
         dbCache.set(dbPath, shared);
         break;
       } catch (err: any) {
-        restoreStdout();
         lastError = err instanceof Error ? err : new Error(String(err));
+
+        if (isWalCorruptionError(lastError)) {
+          try {
+            const db = await tryQuarantineAndReopen(dbPath, repoId);
+            shared = { db, refCount: 0, ftsLoaded: false };
+            dbCache.set(dbPath, shared);
+            break;
+          } catch (retryErr) {
+            throw new Error(
+              `LadybugDB WAL corruption detected for ${repoId}. ` +
+                `Run \`gitnexus analyze\` to rebuild the index. ` +
+                `(${retryErr instanceof Error ? retryErr.message : String(retryErr)})`,
+            );
+          }
+        }
+
         const isLockError =
           lastError.message.includes('Could not set lock') || lastError.message.includes('lock');
         if (!isLockError || attempt === LOCK_RETRY_ATTEMPTS) break;

gitnexus/src/core/lbug/schema.ts

@@ -167,7 +167,18 @@ export const TYPE_ALIAS_SCHEMA = CODE_ELEMENT_BASE('TypeAlias');
 export const CONST_SCHEMA = CODE_ELEMENT_BASE('Const');
 export const STATIC_SCHEMA = CODE_ELEMENT_BASE('Static');
 export const VARIABLE_SCHEMA = CODE_ELEMENT_BASE('Variable');
-export const PROPERTY_SCHEMA = CODE_ELEMENT_BASE('Property');
+export const PROPERTY_SCHEMA = `
+CREATE NODE TABLE \`Property\` (
+  id STRING,
+  name STRING,
+  filePath STRING,
+  startLine INT64,
+  endLine INT64,
+  content STRING,
+  description STRING,
+  declaredType STRING,
+  PRIMARY KEY (id)
+)`;
 export const RECORD_SCHEMA = CODE_ELEMENT_BASE('Record');
 export const DELEGATE_SCHEMA = CODE_ELEMENT_BASE('Delegate');
 export const ANNOTATION_SCHEMA = CODE_ELEMENT_BASE('Annotation');

gitnexus/src/core/search/bm25-index.ts

@@ -15,9 +15,16 @@ export interface BM25SearchResult {
   nodeIds?: string[];
 }
 
+export interface FTSSearchResponse {
+  results: BM25SearchResult[];
+  /** True when at least one FTS index query succeeded (index exists). */
+  ftsAvailable: boolean;
+}
+
 /**
  * Execute a single FTS query via a custom executor (for MCP connection pool).
- * Returns the same shape as core queryFTS (from LadybugDB adapter).
+ * Returns `null` when the query fails (e.g. FTS index does not exist) so the
+ * caller can distinguish "zero matches" from "index missing".
  */
 async function queryFTSViaExecutor(
   executor: (cypher: string) => Promise<any[]>,
@@ -25,7 +32,7 @@ async function queryFTSViaExecutor(
   indexName: string,
   query: string,
   limit: number,
-): Promise<Array<{ filePath: string; score: number; nodeId: string }>> {
+): Promise<Array<{ filePath: string; score: number; nodeId: string }> | null> {
   // Escape single quotes and backslashes to prevent Cypher injection
   const escapedQuery = query.replace(/\\/g, '\\\\').replace(/'/g, "''");
   const cypher = `
@@ -46,7 +53,7 @@ async function queryFTSViaExecutor(
       };
     });
   } catch {
-    return [];
+    return null;
   }
 }
 
@@ -65,8 +72,9 @@ export const searchFTSFromLbug = async (
   query: string,
   limit: number = 20,
   repoId?: string,
-): Promise<BM25SearchResult[]> => {
+): Promise<FTSSearchResponse> => {
   const resultsByIndex: any[][] = [];
+  let queriesSucceeded = 0;
 
   if (repoId) {
     // Use MCP connection pool via dynamic import
@@ -77,15 +85,27 @@ export const searchFTSFromLbug = async (
     const executor = (cypher: string) => executeQuery(repoId, cypher);
 
     for (const { table, indexName } of FTS_INDEXES) {
-      resultsByIndex.push(await queryFTSViaExecutor(executor, table, indexName, query, limit));
+      const result = await queryFTSViaExecutor(executor, table, indexName, query, limit);
+      if (result !== null) {
+        queriesSucceeded++;
+        resultsByIndex.push(result);
+      }
     }
   } else {
     // Use core lbug adapter (CLI / pipeline context) — also sequential for safety.
     for (const { table, indexName } of FTS_INDEXES) {
-      resultsByIndex.push(await queryFTS(table, indexName, query, limit, false).catch(() => []));
+      try {
+        const result = await queryFTS(table, indexName, query, limit, false);
+        queriesSucceeded++;
+        resultsByIndex.push(result);
+      } catch {
+        // FTS index may not exist — count as failed
+      }
     }
   }
 
+  const ftsAvailable = queriesSucceeded > 0;
+
   // Collect all node scores per filePath to track which nodes actually matched
   const fileNodeScores = new Map<string, Array<{ score: number; nodeId: string }>>();
 
@@ -116,10 +136,13 @@ export const searchFTSFromLbug = async (
     .sort((a, b) => b.score - a.score)
     .slice(0, limit);
 
-  return sorted.map((r, index) => ({
-    filePath: r.filePath,
-    score: r.score,
-    rank: index + 1,
-    nodeIds: r.nodeIds,
-  }));
+  return {
+    results: sorted.map((r, index) => ({
+      filePath: r.filePath,
+      score: r.score,
+      rank: index + 1,
+      nodeIds: r.nodeIds,
+    })),
+    ftsAvailable,
+  };
 };

gitnexus/src/core/search/hybrid-search.ts

@@ -113,12 +113,13 @@ export const mergeWithRRF = (
 };
 
 /**
- * Check if hybrid search is available
- * LadybugDB FTS is always available once the database is initialized.
- * Semantic search is optional - hybrid works with just FTS if embeddings aren't ready.
+ * Check if hybrid search is available.
+ * FTS indexes may be missing on read-only MCP connections (see #1403);
+ * callers should inspect `ftsAvailable` from searchFTSFromLbug for
+ * per-query availability. This helper is a coarse gate only.
  */
 export const isHybridSearchReady = (): boolean => {
-  return true; // FTS is always available via LadybugDB when DB is open
+  return true; // FTS is attempted on every query; ftsAvailable signals actual availability
 };
 
 /**
@@ -160,7 +161,7 @@ export const hybridSearch = async (
   ) => Promise<SemanticSearchResult[]>,
 ): Promise<HybridSearchResult[]> => {
   // Use LadybugDB FTS for always-fresh BM25 results
-  const bm25Results = await searchFTSFromLbug(query, limit);
+  const { results: bm25Results } = await searchFTSFromLbug(query, limit);
   const semanticResults = await semanticSearch(executeQuery, query, limit);
   return mergeWithRRF(bm25Results, semanticResults, limit);
 };

gitnexus/src/core/wiki/llm-client.ts

@@ -1,4 +1,5 @@
 import { logger } from '../logger.js';
+import { CircuitOpenError, ResilientFetchExhaustedError, resilientFetch } from 'gitnexus-shared';
 /**
  * LLM Client for Wiki Generation
  *
@@ -76,6 +77,49 @@ export function estimateTokens(text: string): number {
   return Math.ceil(text.length / 4);
 }
 
+/**
+ * Validate that a base URL supplied for LLM API calls is a safe HTTP/HTTPS
+ * endpoint (CWE-918 / CodeQL js/http-to-file-access).
+ *
+ * Allowed:
+ *  - https:// with any hostname (public LLM APIs, Azure, OpenRouter, …)
+ *  - http:// restricted to localhost / 127.0.0.1 (local servers: Ollama, LiteLLM, …)
+ *
+ * Rejected:
+ *  - file://, data:, javascript:, and any other non-HTTP scheme
+ *  - http:// aimed at non-loopback hosts (avoids SSRF against internal networks)
+ *
+ * Throws with a descriptive message on validation failure so callers surface a
+ * clear error rather than an opaque network error.
+ */
+export function validateLLMBaseUrl(baseUrl: string): void {
+  let parsed: URL;
+  try {
+    parsed = new URL(baseUrl);
+  } catch {
+    // Do not include the raw input in the message — it may contain credentials.
+    throw new Error('Invalid LLM base URL: must be a well-formed http:// or https:// URL');
+  }
+
+  if (!['https:', 'http:'].includes(parsed.protocol)) {
+    // Use parsed.protocol only (scheme), not the full URL, to avoid leaking credentials.
+    throw new Error(`LLM base URL must use http:// or https:// (got ${parsed.protocol})`);
+  }
+
+  if (parsed.protocol === 'http:') {
+    // Node's URL parser preserves IPv6 brackets in hostname (e.g. "[::1]"),
+    // so strip them before comparing to bare address literals.
+    const host = parsed.hostname.toLowerCase().replace(/^\[|\]$/g, '');
+    if (host !== 'localhost' && host !== '127.0.0.1' && host !== '::1') {
+      // Use parsed.origin (scheme+host+port, no credentials) instead of the full URL.
+      throw new Error(
+        `Insecure http:// LLM base URLs are only allowed for localhost/127.0.0.1. ` +
+          `Use https:// for remote endpoints (got ${parsed.origin})`,
+      );
+    }
+  }
+}
+
 /**
  * Returns true if the given base URL is an Azure OpenAI endpoint.
  * Uses proper hostname matching to avoid spoofed URLs like
@@ -86,8 +130,10 @@ export function isAzureProvider(baseUrl: string): boolean {
     const { hostname } = new URL(baseUrl);
     return hostname.endsWith('.openai.azure.com') || hostname.endsWith('.services.ai.azure.com');
   } catch {
-    // If URL is malformed, fall back to substring check
-    return baseUrl.includes('.openai.azure.com') || baseUrl.includes('.services.ai.azure.com');
+    // Malformed URL — refuse to call this Azure rather than fall back to a
+    // substring check, which is bypassable by `https://evil.com/?u=.openai.azure.com`
+    // (CodeQL js/incomplete-url-substring-sanitization).
+    return false;
   }
 }
 
@@ -125,6 +171,9 @@ export async function callLLM(
   systemPrompt?: string,
   options?: CallLLMOptions,
 ): Promise<LLMResponse> {
+  // Validate base URL before any fetch (CodeQL js/http-to-file-access)
+  validateLLMBaseUrl(config.baseUrl);
+
   const messages: Array<{ role: string; content: string }> = [];
   if (systemPrompt) {
     messages.push({ role: 'system', content: systemPrompt });
@@ -168,86 +217,85 @@ export async function callLLM(
     ? { 'api-key': config.apiKey }
     : { Authorization: `Bearer ${config.apiKey}` };
 
-  const MAX_RETRIES = 3;
-  let lastError: Error | null = null;
-
-  for (let attempt = 0; attempt < MAX_RETRIES; attempt++) {
-    try {
-      const response = await fetch(url, {
+  // Network resilience (bounded retries with exponential-backoff jitter,
+  // 5xx + 429 + Retry-After handling, in-process circuit breaker on the
+  // LLM endpoint) is delegated to resilientFetch. Provider-specific
+  // error parsing (Azure content filter, empty-content checks) stays
+  // here since it requires response-body inspection.
+  let response: Response;
+  try {
+    response = await resilientFetch(
+      url,
+      {
         method: 'POST',
         headers: {
           'Content-Type': 'application/json',
           ...authHeaders,
         },
         body: JSON.stringify(body),
-      });
-
-      if (!response.ok) {
-        const errorText = await response.text().catch(() => 'unknown error');
-
-        // Azure content filter — surface a clear message instead of a generic API error
-        if (
-          azure &&
-          response.status === 400 &&
-          (errorText.includes('content_filter') ||
-            errorText.includes('ResponsibleAIPolicyViolation'))
-        ) {
-          throw new Error(
-            `Azure content filter blocked this request. The prompt triggered content policy. Details: ${errorText.slice(0, 300)}`,
-          );
-        }
-
-        // Rate limit — wait with exponential backoff and retry
-        if (response.status === 429 && attempt < MAX_RETRIES - 1) {
-          const retryAfter = parseInt(response.headers.get('retry-after') || '0', 10);
-          const delay = retryAfter > 0 ? retryAfter * 1000 : 2 ** attempt * 3000;
-          await sleep(delay);
-          continue;
-        }
-
-        // Server error — retry with backoff
-        if (response.status >= 500 && attempt < MAX_RETRIES - 1) {
-          await sleep((attempt + 1) * 2000);
-          continue;
-        }
-
-        throw new Error(`LLM API error (${response.status}): ${errorText.slice(0, 500)}`);
-      }
-
-      // Streaming path
-      if (useStream && response.body) {
-        return await readSSEStream(response.body, options!.onChunk!);
-      }
-
-      // Non-streaming path
-      const json = (await response.json()) as any;
-      const choice = json.choices?.[0];
-      if (!choice?.message?.content) {
-        throw new Error('LLM returned empty response');
-      }
-
-      return {
-        content: choice.message.content,
-        promptTokens: json.usage?.prompt_tokens,
-        completionTokens: json.usage?.completion_tokens,
-      };
-    } catch (err: any) {
-      lastError = err;
-
-      // Network error — retry with backoff
-      if (
-        attempt < MAX_RETRIES - 1 &&
-        (err.code === 'ECONNREFUSED' || err.code === 'ETIMEDOUT' || err.message?.includes('fetch'))
-      ) {
-        await sleep((attempt + 1) * 3000);
-        continue;
-      }
-
-      throw err;
+        // Per-attempt timeout. Without this each retry can hang
+        // indefinitely on a frozen TCP connection — the per-call
+        // signal is the only timeout `resilientFetch` honors;
+        // `capDelayMs` only bounds the *backoff* between attempts.
+        // 60s matches typical LLM completion budgets.
+        signal: AbortSignal.timeout(60_000),
+      },
+      {
+        breakerKey: `wiki-llm-${new URL(url).host}`,
+        retry: { maxAttempts: 3, baseDelayMs: 2_000, capDelayMs: 30_000 },
+      },
+    );
+  } catch (err) {
+    if (err instanceof CircuitOpenError) {
+      throw new Error(
+        `LLM endpoint circuit open: retry in ${Math.ceil(err.retryAfterMs / 1000)}s. ${err.message}`,
+      );
     }
+    if (err instanceof ResilientFetchExhaustedError) {
+      const errorText = await err.response.text().catch(() => 'unknown error');
+      throw new Error(
+        `LLM API error (${err.response.status} after retries): ${errorText.slice(0, 500)}`,
+      );
+    }
+    throw err;
   }
 
-  throw lastError || new Error('LLM call failed after retries');
+  if (!response.ok) {
+    const errorText = await response.text().catch(() => 'unknown error');
+
+    // Azure content filter — surface a clear message instead of a generic API error.
+    if (
+      azure &&
+      response.status === 400 &&
+      (errorText.includes('content_filter') || errorText.includes('ResponsibleAIPolicyViolation'))
+    ) {
+      throw new Error(
+        `Azure content filter blocked this request. The prompt triggered content policy. Details: ${errorText.slice(0, 300)}`,
+      );
+    }
+
+    // Any other non-OK response here is a terminal 4xx — resilientFetch
+    // already retried 5xx/429 to exhaustion and would have thrown above.
+    throw new Error(`LLM API error (${response.status}): ${errorText.slice(0, 500)}`);
+  }
+
+  // Streaming path
+  if (useStream && response.body) {
+    return await readSSEStream(response.body, options!.onChunk!);
+  }
+
+  // Non-streaming path
+  const json = (await response.json()) as any;
+  const choice = json.choices?.[0];
+  if (!choice?.message?.content) {
+    throw new Error('LLM returned empty response');
+  }
+
+  return {
+    content: choice.message.content,
+    promptTokens: json.usage?.prompt_tokens,
+    completionTokens: json.usage?.completion_tokens,
+  };
 }
 
 /**
@@ -310,7 +358,3 @@ async function readSSEStream(
 
   return { content };
 }
-
-function sleep(ms: number): Promise<void> {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}

gitnexus/src/mcp/core/embedder.ts

@@ -12,7 +12,11 @@ import {
   httpEmbedQuery,
 } from '../../core/embeddings/http-client.js';
 import { resolveEmbeddingConfig } from '../../core/embeddings/config.js';
-import { applyHfEnvOverrides } from '../../core/embeddings/hf-env.js';
+import {
+  applyHfEnvOverrides,
+  isHfDownloadFailure,
+  withHfDownloadRetry,
+} from '../../core/embeddings/hf-env.js';
 import { silenceStdout, restoreStdout, realStderrWrite } from '../../core/lbug/pool-adapter.js';
 
 import { logger } from '../../core/logger.js';
@@ -69,23 +73,39 @@ export const initEmbedder = async (): Promise<FeatureExtractionPipeline> => {
           silenceStdout();
           process.stderr.write = (() => true) as any;
           try {
-            embedderInstance = await (pipeline as any)('feature-extraction', MODEL_ID, {
-              device: device,
-              dtype: 'fp32',
-              session_options: {
-                logSeverityLevel: 3,
-                intraOpNumThreads: embeddingConfig.threads,
-                interOpNumThreads: 1,
-                executionMode: 'sequential',
-              },
-            });
+            embedderInstance = await withHfDownloadRetry(() =>
+              pipeline('feature-extraction', MODEL_ID, {
+                device: device,
+                dtype: 'fp32',
+                session_options: {
+                  logSeverityLevel: 3,
+                  intraOpNumThreads: embeddingConfig.threads,
+                  interOpNumThreads: 1,
+                  executionMode: 'sequential',
+                },
+              }),
+            );
           } finally {
             restoreStdout();
             process.stderr.write = realStderrWrite;
           }
           logger.info({ device }, 'GitNexus: Embedding model loaded');
           return embedderInstance!;
-        } catch {
+        } catch (deviceError) {
+          // Network errors and circuit-open errors are not device-specific —
+          // they will fail the same way on every device. Rethrow immediately
+          // with actionable HF_ENDPOINT guidance rather than silently falling
+          // back to the next device.
+          const errMsg = deviceError instanceof Error ? deviceError.message : String(deviceError);
+          if (isHfDownloadFailure(errMsg)) {
+            const endpointHint = process.env.HF_ENDPOINT
+              ? `The configured endpoint (${process.env.HF_ENDPOINT}) may be unreachable.`
+              : `huggingface.co may be unreachable from your network.\n` +
+                `  Set HF_ENDPOINT to a mirror and retry:\n` +
+                `    HF_ENDPOINT=https://hf-mirror.com npx gitnexus analyze --embeddings\n` +
+                `    (Windows: set HF_ENDPOINT=https://hf-mirror.com && npx gitnexus analyze --embeddings)`;
+            throw new Error(`Failed to download embedding model: ${errMsg}\n  ${endpointHint}`);
+          }
           if (device === 'cpu') throw new Error('Failed to load embedding model');
         }
       }

gitnexus/src/mcp/local/local-backend.ts

@@ -16,6 +16,7 @@ import {
   isLbugReady,
   isWriteQuery,
 } from '../../core/lbug/pool-adapter.js';
+import { isWalCorruptionError, WAL_RECOVERY_SUGGESTION } from '../../core/lbug/lbug-config.js';
 export { isWriteQuery };
 // Embedding imports are lazy (dynamic import) to avoid loading onnxruntime-node
 // at MCP server startup — crashes on unsupported Node ABI versions (#89)
@@ -40,7 +41,7 @@ import {
   isVectorExtensionSupportedByPlatform,
 } from '../../core/platform/capabilities.js';
 import { PhaseTimer } from '../../core/search/phase-timer.js';
-import { checkStaleness, checkCwdMatch } from '../../core/git-staleness.js';
+import { checkStalenessAsync, checkCwdMatch } from '../../core/git-staleness.js';
 import { logger } from '../../core/logger.js';
 // AI context generation is CLI-only (gitnexus analyze)
 // import { generateAIContextFiles } from '../../cli/ai-context.js';
@@ -554,8 +555,15 @@ export class LocalBackend {
       byRemote.set(h.remoteUrl, list);
     }
 
-    return handles.map((h) => {
-      const stale = checkStaleness(h.repoPath, h.lastCommit);
+    // Check staleness for all repos in parallel instead of sequentially.
+    // Each check spawns an async `git rev-list` — with 200 repos the sync
+    // variant took ~50 s; parallel async brings it under a second (#1363).
+    const stalenessResults = await Promise.all(
+      handles.map((h) => checkStalenessAsync(h.repoPath, h.lastCommit)),
+    );
+
+    return handles.map((h, i) => {
+      const stale = stalenessResults[i];
       const selfNorm = norm(h.repoPath);
       const siblings = h.remoteUrl
         ? (byRemote.get(h.remoteUrl) ?? []).filter((e) => norm(e.repoPath) !== selfNorm)
@@ -971,7 +979,7 @@ export class LocalBackend {
       timing,
       ...(!ftsUsed && {
         warning:
-          'FTS extension unavailable - keyword search degraded. Run: gitnexus analyze --force to rebuild indexes.',
+          'FTS indexes missing — keyword search degraded. Run: gitnexus analyze --force to rebuild indexes.',
       }),
     };
   }
@@ -985,9 +993,9 @@ export class LocalBackend {
     limit: number,
   ): Promise<{ results: any[]; ftsUsed: boolean }> {
     const { searchFTSFromLbug } = await import('../../core/search/bm25-index.js');
-    let bm25Results;
+    let ftsResponse;
     try {
-      bm25Results = await searchFTSFromLbug(query, limit, repo.id);
+      ftsResponse = await searchFTSFromLbug(query, limit, repo.id);
     } catch (err: any) {
       logger.error(
         { err: err.message },
@@ -996,7 +1004,8 @@ export class LocalBackend {
       return { results: [], ftsUsed: false };
     }
 
-    const ftsUsed = bm25Results.length === 0 || bm25Results[0]?.ftsUsed !== false;
+    const bm25Results = ftsResponse.results;
+    const ftsUsed = ftsResponse.ftsAvailable;
 
     const results: any[] = [];
 
@@ -1218,7 +1227,14 @@ export class LocalBackend {
       const result = await executeQuery(repo.id, params.query);
       return result;
     } catch (err: any) {
-      return { error: err.message || 'Query failed' };
+      const msg = err.message || 'Query failed';
+      if (isWalCorruptionError(err)) {
+        return {
+          error: msg,
+          recoverySuggestion: WAL_RECOVERY_SUGGESTION,
+        };
+      }
+      return { error: msg };
     }
   }
 
@@ -1672,6 +1688,30 @@ export class LocalBackend {
       kind?: string;
       include_content?: boolean;
     },
+  ): Promise<any> {
+    try {
+      return await this._contextImpl(repo, params);
+    } catch (err: any) {
+      const msg = (err instanceof Error ? err.message : String(err)) || 'Context query failed';
+      if (isWalCorruptionError(err)) {
+        return {
+          error: msg,
+          recoverySuggestion: WAL_RECOVERY_SUGGESTION,
+        };
+      }
+      throw err;
+    }
+  }
+
+  private async _contextImpl(
+    repo: RepoHandle,
+    params: {
+      name?: string;
+      uid?: string;
+      file_path?: string;
+      kind?: string;
+      include_content?: boolean;
+    },
   ): Promise<any> {
     await this.ensureInitialized(repo.id);
 
@@ -1716,12 +1756,13 @@ export class LocalBackend {
       repo.id,
       `
       MATCH (caller)-[r:CodeRelation]->(n {id: $symId})
-      WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'HAS_METHOD', 'HAS_PROPERTY', 'METHOD_OVERRIDES', 'OVERRIDES', 'METHOD_IMPLEMENTS', 'ACCESSES']
+      WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'USES', 'HAS_METHOD', 'HAS_PROPERTY', 'METHOD_OVERRIDES', 'OVERRIDES', 'METHOD_IMPLEMENTS', 'ACCESSES']
       RETURN r.type AS relType, caller.id AS uid, caller.name AS name, caller.filePath AS filePath, labels(caller)[0] AS kind
       LIMIT 30
     `,
       { symId },
     );
+    let typedPropertyRows: any[] = [];
 
     // Fix #480: Class/Interface nodes have no direct CALLS/IMPORTS edges —
     // those point to Constructor and File nodes respectively. Fetch those
@@ -1755,23 +1796,24 @@ export class LocalBackend {
 
     if (isClassLike) {
       try {
-        // Run both incoming-ref queries in parallel — they are independent.
-        const [ctorIncoming, fileIncoming] = await Promise.all([
-          executeParameterized(
-            repo.id,
-            `
+        // Run incoming-ref queries in parallel — they are independent.
+        const [ctorIncoming, fileIncoming, typedPropertyIncoming, typedProperties] =
+          await Promise.all([
+            executeParameterized(
+              repo.id,
+              `
             MATCH (n)-[hm:CodeRelation]->(ctor:Constructor)
             WHERE n.id = $symId AND hm.type = 'HAS_METHOD'
             MATCH (caller)-[r:CodeRelation]->(ctor)
-            WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'ACCESSES']
+            WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'USES', 'ACCESSES']
             RETURN r.type AS relType, caller.id AS uid, caller.name AS name, caller.filePath AS filePath, labels(caller)[0] AS kind
             LIMIT 30
           `,
-            { symId },
-          ),
-          executeParameterized(
-            repo.id,
-            `
+              { symId },
+            ),
+            executeParameterized(
+              repo.id,
+              `
             MATCH (f:File)-[rel:CodeRelation]->(n)
             WHERE n.id = $symId AND rel.type = 'DEFINES'
             MATCH (caller)-[r:CodeRelation]->(f)
@@ -1779,9 +1821,45 @@ export class LocalBackend {
             RETURN r.type AS relType, caller.id AS uid, caller.name AS name, caller.filePath AS filePath, labels(caller)[0] AS kind
             LIMIT 30
           `,
-            { symId },
-          ),
-        ]);
+              { symId },
+            ),
+            executeParameterized(
+              repo.id,
+              `
+            MATCH (p:\`Property\`)
+            WHERE p.declaredType = $name
+               OR p.declaredType STARTS WITH $genericPrefix
+               OR p.declaredType CONTAINS $genericArg
+            MATCH (caller)-[r:CodeRelation]->(p)
+            WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'USES', 'ACCESSES']
+            RETURN r.type AS relType, caller.id AS uid, caller.name AS name, caller.filePath AS filePath, labels(caller)[0] AS kind
+            LIMIT 30
+          `,
+              {
+                name: sym.name,
+                genericPrefix: `${sym.name}<`,
+                genericArg: `<${sym.name}>`,
+              },
+            ),
+            executeParameterized(
+              repo.id,
+              `
+            MATCH (p:\`Property\`)
+            WHERE p.declaredType = $name
+               OR p.declaredType STARTS WITH $genericPrefix
+               OR p.declaredType CONTAINS $genericArg
+            RETURN p.id AS uid, p.name AS name, p.filePath AS filePath, labels(p)[0] AS kind,
+                   p.declaredType AS declaredType
+            LIMIT 30
+          `,
+              {
+                name: sym.name,
+                genericPrefix: `${sym.name}<`,
+                genericArg: `<${sym.name}>`,
+              },
+            ),
+          ]);
+        typedPropertyRows = typedProperties;
 
         // Deduplicate by (relType, uid) — a caller can have multiple relation
         // types to the same target (e.g. both IMPORTS and CALLS), and each
@@ -1789,7 +1867,7 @@ export class LocalBackend {
         const seenKeys = new Set(
           incomingRows.map((r: any) => `${r.relType || r[0]}:${r.uid || r[1]}`),
         );
-        for (const r of [...ctorIncoming, ...fileIncoming]) {
+        for (const r of [...ctorIncoming, ...fileIncoming, ...typedPropertyIncoming]) {
           const key = `${r.relType || r[0]}:${r.uid || r[1]}`;
           if (!seenKeys.has(key)) {
             seenKeys.add(key);
@@ -1806,7 +1884,7 @@ export class LocalBackend {
       repo.id,
       `
       MATCH (n {id: $symId})-[r:CodeRelation]->(target)
-      WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'HAS_METHOD', 'HAS_PROPERTY', 'METHOD_OVERRIDES', 'OVERRIDES', 'METHOD_IMPLEMENTS', 'ACCESSES']
+      WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS', 'USES', 'HAS_METHOD', 'HAS_PROPERTY', 'METHOD_OVERRIDES', 'OVERRIDES', 'METHOD_IMPLEMENTS', 'ACCESSES']
       RETURN r.type AS relType, target.id AS uid, target.name AS name, target.filePath AS filePath, labels(target)[0] AS kind
       LIMIT 30
     `,
@@ -1895,6 +1973,17 @@ export class LocalBackend {
       },
       incoming: categorize(incomingRows),
       outgoing: categorize(outgoingRows),
+      ...(typedPropertyRows.length > 0
+        ? {
+            typed_properties: typedPropertyRows.map((r: any) => ({
+              uid: r.uid || r[0],
+              name: r.name || r[1],
+              filePath: r.filePath || r[2],
+              kind: r.kind || r[3],
+              declaredType: r.declaredType || r[4],
+            })),
+          }
+        : {}),
       processes: processRows.map((r: any) => ({
         id: r.pid || r[0],
         name: r.label || r[1],
@@ -2433,6 +2522,7 @@ export class LocalBackend {
         impactedCount: 0,
         risk: 'UNKNOWN',
         suggestion: 'The graph query failed — try gitnexus context <symbol> as a fallback',
+        ...(isWalCorruptionError(err) ? { recoverySuggestion: WAL_RECOVERY_SUGGESTION } : {}),
       };
     }
   }
@@ -2459,6 +2549,7 @@ export class LocalBackend {
     const mappedRelTypes = params.relationTypes?.flatMap((t: string) =>
       t === 'OVERRIDES' ? ['OVERRIDES', 'METHOD_OVERRIDES'] : [t],
     );
+    const hasExplicitRelationTypes = mappedRelTypes !== undefined && mappedRelTypes.length > 0;
     const rawRelTypes =
       mappedRelTypes && mappedRelTypes.length > 0
         ? mappedRelTypes.filter((t: string) => VALID_RELATION_TYPES.has(t))
@@ -2467,6 +2558,7 @@ export class LocalBackend {
             'IMPORTS',
             'EXTENDS',
             'IMPLEMENTS',
+            'USES',
             'METHOD_OVERRIDES',
             'OVERRIDES',
             'METHOD_IMPLEMENTS',
@@ -2479,6 +2571,7 @@ export class LocalBackend {
             'IMPORTS',
             'EXTENDS',
             'IMPLEMENTS',
+            'USES',
             'METHOD_OVERRIDES',
             'OVERRIDES',
             'METHOD_IMPLEMENTS',
@@ -2538,9 +2631,16 @@ export class LocalBackend {
     };
     const symType = outcome.resolvedLabel || outcome.symbol.type || '';
 
+    const effectiveRelationTypes =
+      (symType === 'Class' || symType === 'Interface') &&
+      !hasExplicitRelationTypes &&
+      !relationTypes.includes('ACCESSES')
+        ? [...relationTypes, 'ACCESSES']
+        : relationTypes;
+
     return this._runImpactBFS(repo, sym, symType, direction, {
       maxDepth,
-      relationTypes,
+      relationTypes: effectiveRelationTypes,
       includeTests,
       minConfidence,
     });
@@ -2619,6 +2719,30 @@ export class LocalBackend {
             frontier.push(rid);
           }
         }
+
+        const typedPropertyRows = await executeParameterized(
+          repo.id,
+          `
+          MATCH (p:\`Property\`)
+          WHERE p.declaredType = $name
+             OR p.declaredType STARTS WITH $genericPrefix
+             OR p.declaredType CONTAINS $genericArg
+          RETURN p.id AS id, p.name AS name, labels(p)[0] AS type, p.filePath AS filePath
+        `,
+          {
+            name: sym.name,
+            genericPrefix: `${sym.name}<`,
+            genericArg: `<${sym.name}>`,
+          },
+        );
+
+        for (const r of typedPropertyRows) {
+          const rid = r.id || r[0];
+          if (rid && !visited.has(rid)) {
+            visited.add(rid);
+            frontier.push(rid);
+          }
+        }
       } catch (e) {
         logQueryError('impact:class-node-expansion', e);
       }
@@ -2984,8 +3108,14 @@ export class LocalBackend {
       relationTypes: string[];
       minConfidence: number;
       includeTests: boolean;
+      signal?: AbortSignal;
     },
   ): Promise<any | null> {
+    // Honor an already-aborted signal at the entry boundary as a fast
+    // path. Cooperative cancellation inside _runImpactBFS is out of
+    // scope — the caller's Promise.race against the same signal
+    // resolves the await regardless of how long this body runs.
+    if (opts.signal?.aborted) return null;
     try {
       await this.refreshRepos();
       await this.ensureInitialized(repoId);

gitnexus/src/server/api.ts

@@ -755,8 +755,13 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
 
         if (isMatch && ['queued', 'cloning', 'analyzing'].includes(job.status)) {
           if (process.env.DEBUG) {
-            console.log(
-              `[debug] resolveRepo waiting for active job ${job.id} (${normalizedName})...`,
+            // Sanitize user-controlled values to prevent log injection (CodeQL js/log-injection).
+            logger.debug(
+              {
+                jobId: String(job.id).replace(/[\r\n]/g, ' '),
+                repoName: String(normalizedName).replace(/[\r\n]/g, ' '),
+              },
+              '[debug] resolveRepo waiting for active job',
             );
           }
           for (let wait = 0; wait < HOLD_QUEUE_TIMEOUT_SECS; wait++) {
@@ -780,7 +785,11 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
     // (e.g. registry file not yet flushed after clone completes).
     if (!found && normalizedName && !isRetry) {
       if (process.env.DEBUG) {
-        console.log(`[debug] resolveRepo 404 for "${normalizedName}". Triggering deep init...`);
+        // Sanitize user-controlled values to prevent log injection (CodeQL js/log-injection).
+        logger.debug(
+          { repoName: String(normalizedName).replace(/[\r\n]/g, ' ') },
+          '[debug] resolveRepo 404, triggering deep init',
+        );
       }
       await backend.init();
       return await resolveRepo(normalizedName, true, req);
@@ -1071,11 +1080,12 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
 
       const results = await withLbugDb(lbugPath, async () => {
         let searchResults: any[];
+        let ftsAvailable: boolean | undefined;
 
         if (mode === 'semantic') {
           const { isEmbedderReady } = await import('../core/embeddings/embedder.js');
           if (!isEmbedderReady()) {
-            return [] as any[];
+            return { searchResults: [] as any[], ftsAvailable: undefined };
           }
           const { semanticSearch: semSearch } =
             await import('../core/embeddings/embedding-pipeline.js');
@@ -1088,8 +1098,9 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
             sources: ['semantic'],
           }));
         } else if (mode === 'bm25') {
-          searchResults = await searchFTSFromLbug(query, limit);
-          searchResults = searchResults.map((r: any, i: number) => ({
+          const ftsResponse = await searchFTSFromLbug(query, limit);
+          ftsAvailable = ftsResponse.ftsAvailable;
+          searchResults = ftsResponse.results.map((r: any, i: number) => ({
             ...r,
             rank: i + 1,
             sources: ['bm25'],
@@ -1102,11 +1113,13 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
               await import('../core/embeddings/embedding-pipeline.js');
             searchResults = await hybridSearch(query, limit, executeQuery, semSearch);
           } else {
-            searchResults = await searchFTSFromLbug(query, limit);
+            const ftsResponse = await searchFTSFromLbug(query, limit);
+            ftsAvailable = ftsResponse.ftsAvailable;
+            searchResults = ftsResponse.results;
           }
         }
 
-        if (!enrich) return searchResults;
+        if (!enrich) return { searchResults, ftsAvailable };
 
         // Server-side enrichment: add connections, cluster, processes per result
         // Uses parameterized queries to prevent Cypher injection via nodeId
@@ -1188,9 +1201,14 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
           }),
         );
 
-        return enriched;
+        return { searchResults: enriched, ftsAvailable };
       });
-      res.json({ results });
+      const response: any = { results: results.searchResults ?? results };
+      if (results.ftsAvailable === false) {
+        response.warning =
+          'FTS indexes missing — keyword search degraded. Run: gitnexus analyze --force to rebuild indexes.';
+      }
+      res.json(response);
     } catch (err: any) {
       res.status(500).json({ error: err.message || 'Search failed' });
     }

gitnexus/test/fixtures/lang-resolution/csharp-generic-type-refs/Program.cs

@@ -0,0 +1,18 @@
+namespace App;
+
+public class USER_INFO
+{
+    public string? USER_ID { get; set; }
+}
+
+public interface IEntityTypeConfiguration<T>
+{
+}
+
+public class UserInfoConfiguration : IEntityTypeConfiguration<USER_INFO>
+{
+    public Task<List<USER_INFO>> Load(List<USER_INFO> users)
+    {
+        return Task.FromResult(users);
+    }
+}

gitnexus/test/helpers/test-db.ts

@@ -37,6 +37,13 @@ export async function cleanupTempDir(tmpDir: string): Promise<void> {
 /**
  * Create a temporary directory for LadybugDB tests.
  * Returns the path and a cleanup function.
+ *
+ * IMPORTANT: when adding a new test that passes a custom `prefix`, also add
+ * the prefix to `TEST_FIXTURE_PREFIXES` in
+ * `gitnexus/src/core/lbug/lbug-config.ts`. The stale-sidecar sweep relies
+ * on the prefix list to recognize test fixtures; an unknown prefix means
+ * the sweep silently won't fire for that fixture and Windows CI flakes
+ * return.
  */
 export async function createTempDir(prefix: string = 'gitnexus-test-'): Promise<TestDBHandle> {
   const tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), prefix));

gitnexus/test/integration/context-typed-property.test.ts

@@ -0,0 +1,77 @@
+/**
+ * Integration test: context() expands Class symbols through typed properties.
+ *
+ * Reproduces EF-style usage where code reads a DbContext property
+ * (`db.USER_INFO`) whose source type is `DbSet<USER_INFO>`. The direct
+ * graph edge is Method -> Property, not Method -> Class, so context() must
+ * use the same typed-property bridge that impact() uses.
+ */
+import { beforeAll, describe, expect, it, vi } from 'vitest';
+import { LocalBackend } from '../../src/mcp/local/local-backend.js';
+import { listRegisteredRepos } from '../../src/storage/repo-manager.js';
+import { withTestLbugDB } from '../helpers/test-indexed-db.js';
+
+vi.mock('../../src/storage/repo-manager.js', () => ({
+  listRegisteredRepos: vi.fn().mockResolvedValue([]),
+  cleanupOldKuzuFiles: vi.fn().mockResolvedValue({ found: false, needsReindex: false }),
+  findSiblingClones: vi.fn().mockResolvedValue([]),
+}));
+
+const SEED = [
+  `CREATE (c:Class {id:'Class:Models/USER_INFO.cs:USER_INFO', name:'USER_INFO', filePath:'Models/USER_INFO.cs', startLine:1, endLine:5, content:'public class USER_INFO {}', description:''})`,
+  `CREATE (p:\`Property\` {id:'Property:Data/UserDbContext.cs:UserDbContext.USER_INFO', name:'USER_INFO', filePath:'Data/UserDbContext.cs', startLine:10, endLine:10, content:'public DbSet<USER_INFO> USER_INFO { get; set; }', description:'', declaredType:'DbSet<USER_INFO>'})`,
+  `CREATE (m:Method {id:'Method:Services/UserService.cs:UserService.GetUserInfo#1', name:'GetUserInfo', filePath:'Services/UserService.cs', startLine:20, endLine:30, isExported:false, content:'db.USER_INFO.FirstOrDefault();', description:'', parameterCount:1, returnType:'USER_INFO'})`,
+  `MATCH (m:Method {id:'Method:Services/UserService.cs:UserService.GetUserInfo#1'}), (p:\`Property\` {id:'Property:Data/UserDbContext.cs:UserDbContext.USER_INFO'}) CREATE (m)-[:CodeRelation {type:'ACCESSES', confidence:1.0, reason:'read', step:1}]->(p)`,
+];
+
+withTestLbugDB(
+  'context-typed-property',
+  (handle) => {
+    let backend: LocalBackend;
+
+    beforeAll(async () => {
+      backend = (handle as any)._backend;
+    });
+
+    describe('context() typed-property expansion', () => {
+      it('surfaces property callers and explains the typed property bridge', async () => {
+        const result = await backend.callTool('context', {
+          uid: 'Class:Models/USER_INFO.cs:USER_INFO',
+        });
+
+        expect(result.status).toBe('found');
+        expect(result.symbol.kind).toBe('Class');
+
+        const accesses = result.incoming.accesses || [];
+        expect(accesses.map((r: any) => r.name)).toContain('GetUserInfo');
+
+        expect(result.typed_properties).toEqual([
+          expect.objectContaining({
+            uid: 'Property:Data/UserDbContext.cs:UserDbContext.USER_INFO',
+            name: 'USER_INFO',
+            declaredType: 'DbSet<USER_INFO>',
+          }),
+        ]);
+      });
+    });
+  },
+  {
+    seed: SEED,
+    poolAdapter: true,
+    afterSetup: async (handle) => {
+      vi.mocked(listRegisteredRepos).mockResolvedValue([
+        {
+          name: 'test-repo',
+          path: '/test/repo',
+          storagePath: handle.tmpHandle.dbPath,
+          indexedAt: new Date().toISOString(),
+          lastCommit: 'abc123',
+          stats: { files: 3, nodes: 3, communities: 0, processes: 0 },
+        },
+      ]);
+      const backend = new LocalBackend();
+      await backend.init();
+      (handle as any)._backend = backend;
+    },
+  },
+);

gitnexus/test/integration/group/include-extractor-sync.test.ts

@@ -0,0 +1,195 @@
+/**
+ * Integration test: IncludeExtractor output → group matching → bridge DB.
+ *
+ * Covers PR #1156 review finding #7: verifies that the full runtime path
+ * (IncludeExtractor → StoredContract → runExactMatch → CrossLinks → writeBridge)
+ * stays wired up. A regression in either normalizeContractId or the include
+ * branch of ManifestExtractor.resolveSymbol would produce 0 cross-links and
+ * fail this test.
+ */
+import { describe, it, expect } from 'vitest';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
+import { parseGroupConfig } from '../../../src/core/group/config-parser.js';
+import { syncGroup } from '../../../src/core/group/sync.js';
+import type { StoredContract } from '../../../src/core/group/types.js';
+import { IncludeExtractor } from '../../../src/core/group/extractors/include-extractor.js';
+import { normalizeContractId } from '../../../src/core/group/matching.js';
+
+const GROUP_YAML = [
+  'version: 1',
+  'name: include-test-group',
+  'description: "IncludeExtractor integration test"',
+  '',
+  'repos:',
+  '  app/provider: include-provider',
+  '  app/consumer: include-consumer',
+  '',
+  'links: []',
+  'packages: {}',
+  '',
+  'detect:',
+  '  http: false',
+  '  grpc: false',
+  '  topics: false',
+  '  shared_libs: false',
+  '  includes: true',
+  '  embedding_fallback: false',
+  '',
+  'matching:',
+  '  bm25_threshold: 0.7',
+  '  embedding_threshold: 0.65',
+  '  max_candidates_per_step: 3',
+].join('\n');
+
+describe('IncludeExtractor → syncGroup integration (finding #7)', () => {
+  it('produces a CrossLink when provider and consumer emit the same include contract-id', async () => {
+    const config = parseGroupConfig(GROUP_YAML);
+
+    // Mock the IncludeExtractor output directly — a header provider in one
+    // repo and a quoted #include consumer in the other, both normalized to
+    // the same include::map/base/view.h contract-id.
+    const mockContracts: StoredContract[] = [
+      {
+        contractId: 'include::map/base/view.h',
+        type: 'include',
+        role: 'provider',
+        symbolUid: 'File:map/base/view.h',
+        symbolRef: { filePath: 'map/base/view.h', name: 'view.h' },
+        symbolName: 'view.h',
+        confidence: 0.95,
+        meta: { source: 'filesystem' },
+        repo: 'app/provider',
+      },
+      {
+        contractId: 'include::map/base/view.h',
+        type: 'include',
+        role: 'consumer',
+        symbolUid: 'File:src/controller.cpp',
+        symbolRef: { filePath: 'src/controller.cpp', name: 'map/base/view.h' },
+        symbolName: 'map/base/view.h',
+        confidence: 0.85,
+        meta: { source: 'tree_sitter', includePath: 'map/base/view.h' },
+        repo: 'app/consumer',
+      },
+    ];
+
+    const result = await syncGroup(config, {
+      extractorOverride: async () => mockContracts,
+      skipWrite: true,
+    });
+
+    const includeLinks = result.crossLinks.filter((l) => l.type === 'include');
+    expect(includeLinks.length).toBeGreaterThanOrEqual(1);
+
+    const link = includeLinks[0];
+    expect(link.contractId).toBe('include::map/base/view.h');
+    expect(link.matchType).toBe('exact');
+    expect(link.from.repo).toBe('app/consumer');
+    expect(link.to.repo).toBe('app/provider');
+  });
+
+  it('normalizes mixed-case / backslash include paths to the same contract-id end-to-end', async () => {
+    const config = parseGroupConfig(GROUP_YAML);
+
+    // Provider writes the canonical form; consumer's include has mixed case
+    // and a backslash. After normalizeContractId they must still match.
+    const providerId = 'include::map/base/view.h';
+    const rawConsumerId = 'include::Map\\Base\\View.h';
+
+    // Sanity — normalizeContractId must collapse them.
+    expect(normalizeContractId(rawConsumerId)).toBe(providerId);
+
+    const mockContracts: StoredContract[] = [
+      {
+        contractId: providerId,
+        type: 'include',
+        role: 'provider',
+        symbolUid: 'File:map/base/view.h',
+        symbolRef: { filePath: 'map/base/view.h', name: 'view.h' },
+        symbolName: 'view.h',
+        confidence: 0.95,
+        meta: { source: 'filesystem' },
+        repo: 'app/provider',
+      },
+      {
+        contractId: rawConsumerId,
+        type: 'include',
+        role: 'consumer',
+        symbolUid: 'File:src/controller.cpp',
+        symbolRef: { filePath: 'src/controller.cpp', name: 'Map/Base/View.h' },
+        symbolName: 'Map/Base/View.h',
+        confidence: 0.85,
+        meta: { source: 'tree_sitter', includePath: 'Map\\Base\\View.h' },
+        repo: 'app/consumer',
+      },
+    ];
+
+    const result = await syncGroup(config, {
+      extractorOverride: async () => mockContracts,
+      skipWrite: true,
+    });
+
+    const includeLinks = result.crossLinks.filter((l) => l.type === 'include');
+    expect(includeLinks.length).toBeGreaterThanOrEqual(1);
+  });
+
+  it('round-trip: extractor output from two real temp repos produces matching contract-ids', async () => {
+    // Drives the extractor directly (no `syncGroup`) against two on-disk
+    // fixture repos, then hands the StoredContract-shaped output to
+    // syncGroup via extractorOverride. This exercises the real extraction
+    // code + the matching pipeline together.
+    const providerDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gitnexus-include-int-provider-'));
+    const consumerDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gitnexus-include-int-consumer-'));
+    try {
+      fs.mkdirSync(path.join(providerDir, 'shared/api'), { recursive: true });
+      fs.writeFileSync(
+        path.join(providerDir, 'shared/api/client.h'),
+        '#pragma once\nstruct Client {};',
+      );
+      fs.mkdirSync(path.join(consumerDir, 'src'), { recursive: true });
+      fs.writeFileSync(
+        path.join(consumerDir, 'src/main.cpp'),
+        '#include "shared/api/client.h"\nint main(){return 0;}',
+      );
+
+      const extractor = new IncludeExtractor();
+      const providerOutput = await extractor.extract(null, providerDir, {
+        id: 'provider',
+        path: 'app/provider',
+        repoPath: providerDir,
+        storagePath: path.join(providerDir, '.gitnexus'),
+      });
+      const consumerOutput = await extractor.extract(null, consumerDir, {
+        id: 'consumer',
+        path: 'app/consumer',
+        repoPath: consumerDir,
+        storagePath: path.join(consumerDir, '.gitnexus'),
+      });
+
+      const stored: StoredContract[] = [
+        ...providerOutput
+          .filter((c) => c.role === 'provider')
+          .map((c) => ({ ...c, repo: 'app/provider' })),
+        ...consumerOutput
+          .filter((c) => c.role === 'consumer')
+          .map((c) => ({ ...c, repo: 'app/consumer' })),
+      ];
+
+      const config = parseGroupConfig(GROUP_YAML);
+      const result = await syncGroup(config, {
+        extractorOverride: async () => stored,
+        skipWrite: true,
+      });
+
+      const includeLinks = result.crossLinks.filter((l) => l.type === 'include');
+      expect(includeLinks.length).toBeGreaterThanOrEqual(1);
+      expect(includeLinks[0].contractId).toBe('include::shared/api/client.h');
+      expect(includeLinks[0].matchType).toBe('exact');
+    } finally {
+      fs.rmSync(providerDir, { recursive: true, force: true });
+      fs.rmSync(consumerDir, { recursive: true, force: true });
+    }
+  });
+});

gitnexus/test/integration/lbug-close-handle-release.test.ts

@@ -0,0 +1,41 @@
+/**
+ * Integration test: safeClose's Windows post-close handle-release wait.
+ *
+ * On Windows, libuv reports `db.close()` resolved before the kernel has
+ * released the file handle. A subsequent open of the same path can then
+ * race the release and surface "Could not set lock on file". `safeClose`
+ * probes the file with `fs.open` to force the residual lock to surface,
+ * absorbed by the open-time retry in `lbug-config.ts`.
+ */
+import path from 'path';
+import { describe, it } from 'vitest';
+import { createTempDir } from '../helpers/test-db.js';
+
+describe('safeClose — close + reopen does not surface lock errors', () => {
+  it('survives 10 sequential open/close/reopen cycles on the same path', async () => {
+    const tmp = await createTempDir('gitnexus-lbug-close-cycle-');
+    const dbPath = path.join(tmp.dbPath, 'lbug');
+    try {
+      const adapter = await import('../../src/core/lbug/lbug-adapter.js');
+      for (let i = 0; i < 10; i++) {
+        await adapter.initLbug(dbPath);
+        await adapter.closeLbug();
+      }
+    } finally {
+      await tmp.cleanup();
+    }
+  });
+
+  it('safeClose is idempotent — calling twice in a row does not throw', async () => {
+    const tmp = await createTempDir('gitnexus-lbug-idempotent-');
+    const dbPath = path.join(tmp.dbPath, 'lbug');
+    try {
+      const adapter = await import('../../src/core/lbug/lbug-adapter.js');
+      await adapter.initLbug(dbPath);
+      await adapter.closeLbug();
+      await adapter.closeLbug();
+    } finally {
+      await tmp.cleanup();
+    }
+  });
+});

gitnexus/test/integration/lbug-lock-retry.test.ts

@@ -14,7 +14,7 @@ import { withTestLbugDB } from '../helpers/test-indexed-db.js';
 
 // Pure-function tests — no DB needed, but grouped here for cohesion
 // with the retry logic they guard.
-import { isDbBusyError } from '../../src/core/lbug/lbug-adapter.js';
+import { isDbBusyError } from '../../src/core/lbug/lbug-config.js';
 
 describe('isDbBusyError', () => {
   it('returns true for "busy" errors (case-insensitive)', () => {
@@ -46,6 +46,18 @@ describe('isDbBusyError', () => {
     expect(isDbBusyError(undefined)).toBe(false);
   });
 
+  // Documented behavior for lock-shaped strings: the matcher is intentionally
+  // broad because in graph-DB contexts these are all transient. If LadybugDB
+  // ever surfaces a non-transient lock-shaped error (e.g., a recovery-time
+  // "lock file missing"), tighten the matcher and add a negative test here
+  // rather than raising the retry budget.
+  it('treats other lock-shaped errors as transient (current intentional behavior)', () => {
+    expect(isDbBusyError(new Error('deadlock detected'))).toBe(true);
+    expect(isDbBusyError(new Error('unlock failed'))).toBe(true);
+    expect(isDbBusyError(new Error('lock contention'))).toBe(true);
+    expect(isDbBusyError(new Error('Could not open lock file'))).toBe(true);
+  });
+
   it('handles non-Error values gracefully', () => {
     expect(isDbBusyError('BUSY error')).toBe(true);
     expect(isDbBusyError(42)).toBe(false);

gitnexus/test/integration/lbug-open-retry.test.ts

@@ -0,0 +1,310 @@
+/**
+ * Integration tests: open-time lock-busy retry in `lbug-config.ts`.
+ *
+ * The lock IO exception raised by `local_file_system.cpp` happens
+ * synchronously inside `new lbug.Database(...)`, before any query is
+ * issued — so `withLbugDb`'s query-time retry cannot see it. These tests
+ * exercise the construction-time retry wrapper directly by stubbing the
+ * `Database` constructor.
+ *
+ * See: docs/plans/2026-05-08-002-fix-windows-lbug-lock-ci-flakes-plan.md
+ */
+import fs from 'fs/promises';
+import os from 'os';
+import path from 'path';
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import {
+  _isTestFixturePathForTest as isTestFixturePath,
+  isDbBusyError,
+  isOpenRetryExhausted,
+  openLbugConnection,
+  waitForWindowsHandleRelease,
+} from '../../src/core/lbug/lbug-config.js';
+
+// ─── Minimal stub of the `lbug` module surface used by openLbugConnection ──
+
+interface StubModuleControl {
+  /** Errors thrown by sequential `new Database(...)` calls. `null` = success. */
+  databaseThrows: Array<Error | null>;
+  /** Number of times the `Database` constructor was invoked. */
+  databaseCallCount: number;
+  /** Number of times `db.close()` was called. */
+  closeCallCount: number;
+}
+
+const makeStubLbug = (control: StubModuleControl) => {
+  class FakeDatabase {
+    constructor(_path: string, ..._rest: unknown[]) {
+      control.databaseCallCount++;
+      const next = control.databaseThrows.shift();
+      if (next instanceof Error) throw next;
+    }
+    async close(): Promise<void> {
+      control.closeCallCount++;
+    }
+  }
+  class FakeConnection {
+    constructor(_db: FakeDatabase) {}
+    async close(): Promise<void> {}
+  }
+  return { Database: FakeDatabase, Connection: FakeConnection } as any;
+};
+
+describe('isDbBusyError', () => {
+  it('matches the documented Windows lock-error wording', () => {
+    expect(isDbBusyError(new Error('Could not set lock on file foo.lbug'))).toBe(true);
+    expect(isDbBusyError(new Error('database is locked'))).toBe(true);
+  });
+  it('does not match unrelated errors', () => {
+    expect(isDbBusyError(new Error('Cypher syntax error'))).toBe(false);
+    expect(isDbBusyError(null)).toBe(false);
+  });
+});
+
+describe('openLbugConnection — open-time lock-busy retry', () => {
+  it('returns a handle when the constructor succeeds on the first try', async () => {
+    const control: StubModuleControl = {
+      databaseThrows: [null],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+    const handle = await openLbugConnection(stub, '/some/path/lbug');
+    expect(handle.db).toBeDefined();
+    expect(handle.conn).toBeDefined();
+    expect(control.databaseCallCount).toBe(1);
+  });
+
+  it('retries on busy/lock errors and succeeds on a later attempt', async () => {
+    const control: StubModuleControl = {
+      databaseThrows: [new Error('Could not set lock on file'), null],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+    const handle = await openLbugConnection(stub, '/some/path/lbug');
+    expect(handle.db).toBeDefined();
+    expect(control.databaseCallCount).toBe(2);
+  });
+
+  it('exhausts the retry budget and rethrows the last error preserving its message', async () => {
+    const lockErr = new Error('Could not set lock on file foo.lbug');
+    const control: StubModuleControl = {
+      // 5 attempts + production paths get no sweep retry, so 5 throws total.
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+    await expect(openLbugConnection(stub, '/var/data/non-test/lbug')).rejects.toThrow(
+      'Could not set lock on file foo.lbug',
+    );
+    expect(control.databaseCallCount).toBe(5);
+  });
+
+  it('tags the exhausted error so withLbugDb skips its outer retry', async () => {
+    const lockErr = new Error('Could not set lock on file');
+    const control: StubModuleControl = {
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+    let caught: unknown;
+    try {
+      await openLbugConnection(stub, '/var/data/non-test/lbug');
+    } catch (err) {
+      caught = err;
+    }
+    expect(caught).toBeDefined();
+    expect(isOpenRetryExhausted(caught)).toBe(true);
+    expect(isOpenRetryExhausted(new Error('plain error'))).toBe(false);
+    expect(isOpenRetryExhausted(null)).toBe(false);
+    expect(isOpenRetryExhausted(undefined)).toBe(false);
+  });
+
+  it('does not retry non-busy errors', async () => {
+    const syntaxErr = new Error('Cypher syntax error');
+    const control: StubModuleControl = {
+      databaseThrows: [syntaxErr],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+    await expect(openLbugConnection(stub, '/some/path/lbug')).rejects.toThrow(
+      'Cypher syntax error',
+    );
+    expect(control.databaseCallCount).toBe(1);
+  });
+});
+
+describe('openLbugConnection — stale-sidecar sweep (test fixtures only)', () => {
+  let fixtureDir: string;
+  let dbPath: string;
+
+  beforeEach(async () => {
+    fixtureDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gitnexus-lbug-sweep-'));
+    dbPath = path.join(fixtureDir, 'lbug');
+  });
+
+  afterEach(async () => {
+    await fs.rm(fixtureDir, { recursive: true, force: true }).catch(() => {});
+  });
+
+  it('sweeps stale .wal/.lock for a recognized test fixture path and retries once', async () => {
+    await fs.writeFile(dbPath + '.wal', 'stale');
+    await fs.writeFile(dbPath + '.lock', 'stale');
+
+    const lockErr = new Error('Could not set lock on file');
+    const control: StubModuleControl = {
+      // 5 retries throw, then sweep + 1 final attempt succeeds (6 total).
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr, null],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+
+    const handle = await openLbugConnection(stub, dbPath);
+    expect(handle.db).toBeDefined();
+    expect(control.databaseCallCount).toBe(6);
+
+    // Sidecars removed by the sweep
+    await expect(fs.access(dbPath + '.wal')).rejects.toThrow();
+    await expect(fs.access(dbPath + '.lock')).rejects.toThrow();
+  });
+
+  it('does not sweep production paths even if they share the prefix', async () => {
+    // A non-tmp dir that *starts* with the prefix must still be rejected.
+    const lockErr = new Error('Could not set lock on file');
+    const control: StubModuleControl = {
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+
+    // Path is outside os.tmpdir() so the predicate must reject it.
+    await expect(openLbugConnection(stub, '/var/data/gitnexus-lbug-fake/lbug')).rejects.toThrow(
+      'Could not set lock on file',
+    );
+    expect(control.databaseCallCount).toBe(5); // no sweep retry
+  });
+
+  it('handles missing sidecars gracefully (ENOENT swallowed, retry runs)', async () => {
+    // No .wal or .lock pre-created — sweep ENOENTs both, then succeeds.
+    const lockErr = new Error('Could not set lock on file');
+    const control: StubModuleControl = {
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr, null],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+
+    const handle = await openLbugConnection(stub, dbPath);
+    expect(handle.db).toBeDefined();
+    expect(control.databaseCallCount).toBe(6);
+  });
+
+  it('sweep retry that throws a different error preserves the original lock error', async () => {
+    // 5 lock errors, then sweep fires, then post-sweep throws an unrelated
+    // error. The user-actionable signal is "lock retries exhausted" — the
+    // post-sweep error must NOT shadow the original lock message.
+    const lockErr = new Error('Could not set lock on file foo.lbug');
+    const unrelatedErr = new Error('Schema validation error during open');
+    const control: StubModuleControl = {
+      databaseThrows: [lockErr, lockErr, lockErr, lockErr, lockErr, unrelatedErr],
+      databaseCallCount: 0,
+      closeCallCount: 0,
+    };
+    const stub = makeStubLbug(control);
+
+    let caught: Error | undefined;
+    try {
+      await openLbugConnection(stub, dbPath);
+    } catch (err) {
+      caught = err as Error;
+    }
+    expect(caught?.message).toBe('Could not set lock on file foo.lbug');
+    expect(control.databaseCallCount).toBe(6); // sweep retry did fire
+  });
+});
+
+describe('isTestFixturePath — production-safety guard', () => {
+  it('accepts a fixture under os.tmpdir with a recognized prefix on the immediate parent', () => {
+    const tmp = os.tmpdir();
+    expect(isTestFixturePath(path.join(tmp, 'gitnexus-lbug-XXX', 'lbug'))).toBe(true);
+    expect(isTestFixturePath(path.join(tmp, 'gitnexus-test-YYY', 'lbug'))).toBe(true);
+  });
+
+  it('rejects production paths even with a matching prefix', () => {
+    expect(isTestFixturePath('/var/data/gitnexus-lbug-fake/lbug')).toBe(false);
+    expect(isTestFixturePath('/home/user/gitnexus-test-foo/lbug')).toBe(false);
+  });
+
+  it('rejects path traversal attempts that resolve outside tmpdir', () => {
+    const tmp = os.tmpdir();
+    const traversal = path.join(tmp, 'gitnexus-lbug-x', '..', '..', 'etc', 'passwd');
+    expect(isTestFixturePath(traversal)).toBe(false);
+  });
+
+  it('rejects when the immediate parent does not match even if a deeper ancestor does', () => {
+    // Tightening: ancestor walk would have allowed nested paths under
+    // `<tmp>/gitnexus-lbug-x/inner/lbug` to satisfy the predicate. We
+    // require the immediate parent to match.
+    const tmp = os.tmpdir();
+    expect(isTestFixturePath(path.join(tmp, 'gitnexus-lbug-x', 'inner', 'lbug'))).toBe(false);
+  });
+
+  it('handles tmpdir trailing-separator gracefully', () => {
+    // Some Windows TMP configs return a trailing separator; the predicate
+    // strips it before the prefix check so fixtures still match.
+    const tmp = os.tmpdir();
+    const fixture = path.join(tmp, 'gitnexus-lbug-trailing', 'lbug');
+    // Whether or not os.tmpdir() itself has a trailing separator,
+    // the predicate must accept legit fixtures.
+    expect(isTestFixturePath(fixture)).toBe(true);
+  });
+
+  it('rejects unrelated prefixes in tmpdir', () => {
+    const tmp = os.tmpdir();
+    expect(isTestFixturePath(path.join(tmp, 'random-dir', 'lbug'))).toBe(false);
+    expect(isTestFixturePath(path.join(tmp, 'malicious', 'lbug'))).toBe(false);
+  });
+});
+
+describe('waitForWindowsHandleRelease', () => {
+  let fixtureDir: string;
+  let dbPath: string;
+
+  beforeEach(async () => {
+    fixtureDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gitnexus-lbug-probe-'));
+    dbPath = path.join(fixtureDir, 'lbug');
+  });
+
+  afterEach(async () => {
+    await fs.rm(fixtureDir, { recursive: true, force: true }).catch(() => {});
+  });
+
+  it('returns true when the file exists and is openable', async () => {
+    await fs.writeFile(dbPath, 'fake-db-content');
+    const released = await waitForWindowsHandleRelease(dbPath);
+    expect(released).toBe(true);
+  });
+
+  it('returns true when the file does not exist (ENOENT is non-lock)', async () => {
+    // No fs.writeFile — path does not exist. Probe should bail to true,
+    // not retry, since ENOENT is not a lock code.
+    const released = await waitForWindowsHandleRelease(dbPath);
+    expect(released).toBe(true);
+  });
+
+  it('does not leak the file handle when close succeeds', async () => {
+    // Smoke test: 50 sequential probes with a real file. If close were
+    // skipped, fd usage would climb. We rely on test process not OOMing
+    // as the simplest indicator; fd table caps catch egregious leaks.
+    await fs.writeFile(dbPath, 'fake-db-content');
+    for (let i = 0; i < 50; i++) {
+      await waitForWindowsHandleRelease(dbPath);
+    }
+  });
+});

gitnexus/test/integration/resolvers/csharp.test.ts

@@ -1440,6 +1440,24 @@ describe('Write access tracking (C#)', () => {
   });
 });
 
+// ---------------------------------------------------------------------------
+// Generic type references: IEntityTypeConfiguration<USER_INFO>, List<USER_INFO>
+// ---------------------------------------------------------------------------
+
+describe('C# generic type-reference tracking', () => {
+  let result: PipelineResult;
+
+  beforeAll(async () => {
+    result = await runPipelineFromRepo(path.join(FIXTURES, 'csharp-generic-type-refs'), () => {});
+  }, 60000);
+
+  it('emits USES edges for generic type arguments', () => {
+    const uses = getRelationships(result, 'USES').filter((e) => e.target === 'USER_INFO');
+    expect(edgeSet(uses)).toContain('UserInfoConfiguration → USER_INFO');
+    expect(edgeSet(uses)).toContain('Load → USER_INFO');
+  });
+});
+
 // ---------------------------------------------------------------------------
 // Call-result variable binding (Phase 9): var user = GetUser(); user.Save()
 // ---------------------------------------------------------------------------

gitnexus/test/integration/resolvers/helpers.ts

@@ -11,6 +11,9 @@ import type { GraphRelationship } from 'gitnexus-shared';
 const LEGACY_RESOLVER_PARITY_EXPECTED_FAILURES: Readonly<Record<string, ReadonlySet<string>>> = {
   csharp: new Set([
     'emits the using-import edge App/Program.cs -> Models/User.cs through the scope-resolution path',
+    // Generic type-argument USES edges are emitted by the registry-primary
+    // resolver only; the legacy DAG path does not synthesize these references.
+    'emits USES edges for generic type arguments',
   ]),
   go: new Set([
     // The legacy DAG path does not resolve method calls when the method is

gitnexus/test/integration/search-core.test.ts

@@ -19,7 +19,7 @@ withTestLbugDB(
   (_handle) => {
     describe('searchFTSFromLbug — core adapter (no repoId)', () => {
       it('returns ranked results for a matching query', async () => {
-        const results = await searchFTSFromLbug('user authentication', 10);
+        const { results } = await searchFTSFromLbug('user authentication', 10);
 
         expect(results.length).toBeGreaterThan(0);
 
@@ -40,7 +40,7 @@ withTestLbugDB(
       });
 
       it('results are ordered by descending score', async () => {
-        const results = await searchFTSFromLbug('user authentication', 10);
+        const { results } = await searchFTSFromLbug('user authentication', 10);
 
         for (let i = 1; i < results.length; i++) {
           expect(results[i - 1].score).toBeGreaterThanOrEqual(results[i].score);
@@ -48,7 +48,7 @@ withTestLbugDB(
       });
 
       it('auth-related files rank higher than unrelated files', async () => {
-        const results = await searchFTSFromLbug('user authentication', 10);
+        const { results } = await searchFTSFromLbug('user authentication', 10);
         const filePaths = results.map((r) => r.filePath);
 
         expect(filePaths).toContain('src/auth.ts');
@@ -61,7 +61,7 @@ withTestLbugDB(
       });
 
       it('merges scores from multiple node types for the same filePath', async () => {
-        const results = await searchFTSFromLbug('user authentication', 20);
+        const { results } = await searchFTSFromLbug('user authentication', 20);
 
         const authResult = results.find((r) => r.filePath === 'src/auth.ts');
         expect(authResult).toBeDefined();
@@ -73,12 +73,12 @@ withTestLbugDB(
       });
 
       it('respects limit parameter', async () => {
-        const results = await searchFTSFromLbug('user authentication', 2);
+        const { results } = await searchFTSFromLbug('user authentication', 2);
         expect(results.length).toBeLessThanOrEqual(2);
       });
 
       it('returns empty array for a non-matching query', async () => {
-        const results = await searchFTSFromLbug('xyzzyplughtwisty', 10);
+        const { results } = await searchFTSFromLbug('xyzzyplughtwisty', 10);
         expect(results).toEqual([]);
       });
     });
@@ -87,32 +87,32 @@ withTestLbugDB(
 
     describe('unhappy paths', () => {
       it('returns empty array for empty query string', async () => {
-        const results = await searchFTSFromLbug('', 10);
+        const { results } = await searchFTSFromLbug('', 10);
         expect(results).toEqual([]);
       });
 
       it('returns empty array for whitespace-only query', async () => {
-        const results = await searchFTSFromLbug('   ', 10);
+        const { results } = await searchFTSFromLbug('   ', 10);
         expect(results).toEqual([]);
       });
 
       it('handles special characters in query gracefully', async () => {
-        const results = await searchFTSFromLbug('user* OR auth+', 10);
+        const { results } = await searchFTSFromLbug('user* OR auth+', 10);
         expect(Array.isArray(results)).toBe(true);
       });
 
       it('handles limit of 0', async () => {
-        const results = await searchFTSFromLbug('user authentication', 0);
+        const { results } = await searchFTSFromLbug('user authentication', 0);
         expect(results).toEqual([]);
       });
 
       it('handles negative limit gracefully', async () => {
-        const results = await searchFTSFromLbug('user authentication', -1);
+        const { results } = await searchFTSFromLbug('user authentication', -1);
         expect(Array.isArray(results)).toBe(true);
       });
 
       it('handles very large limit', async () => {
-        const results = await searchFTSFromLbug('user authentication', 100000);
+        const { results } = await searchFTSFromLbug('user authentication', 100000);
         expect(results.length).toBeLessThanOrEqual(100000);
         expect(results.length).toBeGreaterThan(0);
       });

gitnexus/test/integration/search-pool.test.ts

@@ -19,7 +19,7 @@ withTestLbugDB(
   (handle) => {
     describe('searchFTSFromLbug — MCP pool adapter (with repoId)', () => {
       it('returns ranked results via pool adapter', async () => {
-        const results = await searchFTSFromLbug('user authentication', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('user authentication', 10, handle.repoId);
 
         expect(results.length).toBeGreaterThan(0);
 
@@ -35,7 +35,7 @@ withTestLbugDB(
       });
 
       it('results are ordered by descending score via pool adapter', async () => {
-        const results = await searchFTSFromLbug('user authentication', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('user authentication', 10, handle.repoId);
 
         for (let i = 1; i < results.length; i++) {
           expect(results[i - 1].score).toBeGreaterThanOrEqual(results[i].score);
@@ -43,12 +43,12 @@ withTestLbugDB(
       });
 
       it('returns empty array for non-matching query via pool adapter', async () => {
-        const results = await searchFTSFromLbug('xyzzyplughtwisty', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('xyzzyplughtwisty', 10, handle.repoId);
         expect(results).toEqual([]);
       });
 
       it('respects limit parameter via pool adapter', async () => {
-        const results = await searchFTSFromLbug('user authentication', 1, handle.repoId);
+        const { results } = await searchFTSFromLbug('user authentication', 1, handle.repoId);
         expect(results.length).toBeLessThanOrEqual(1);
       });
     });
@@ -57,22 +57,22 @@ withTestLbugDB(
 
     describe('unhappy paths', () => {
       it('returns empty array for empty query via pool', async () => {
-        const results = await searchFTSFromLbug('', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('', 10, handle.repoId);
         expect(results).toEqual([]);
       });
 
       it('returns empty array for whitespace-only query via pool', async () => {
-        const results = await searchFTSFromLbug('   ', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('   ', 10, handle.repoId);
         expect(results).toEqual([]);
       });
 
       it('handles special characters in query via pool', async () => {
-        const results = await searchFTSFromLbug('user* OR auth+', 10, handle.repoId);
+        const { results } = await searchFTSFromLbug('user* OR auth+', 10, handle.repoId);
         expect(Array.isArray(results)).toBe(true);
       });
 
       it('handles limit of 0 via pool', async () => {
-        const results = await searchFTSFromLbug('user authentication', 0, handle.repoId);
+        const { results } = await searchFTSFromLbug('user authentication', 0, handle.repoId);
         expect(results).toEqual([]);
       });
     });

gitnexus/test/unit/bm25-search.test.ts

@@ -42,20 +42,24 @@ describe('BM25 search', () => {
   });
 
   describe('searchFTSFromLbug', () => {
-    it('returns empty array when LadybugDB is not initialized', async () => {
-      // Without LadybugDB init, search should return empty (not crash)
-      const results = await searchFTSFromLbug('test query');
+    it('returns empty results when LadybugDB is not initialized', async () => {
+      // Simulate an uninitialized DB: queryFTS throws instead of returning rows
+      const { queryFTS } = await import('../../src/core/lbug/lbug-adapter.js');
+      vi.mocked(queryFTS).mockRejectedValue(new Error('DB not initialized'));
+
+      const { results, ftsAvailable } = await searchFTSFromLbug('test query');
       expect(Array.isArray(results)).toBe(true);
       expect(results).toHaveLength(0);
+      expect(ftsAvailable).toBe(false);
     });
 
     it('handles empty query', async () => {
-      const results = await searchFTSFromLbug('');
+      const { results } = await searchFTSFromLbug('');
       expect(Array.isArray(results)).toBe(true);
     });
 
     it('accepts custom limit parameter', async () => {
-      const results = await searchFTSFromLbug('test', 5);
+      const { results } = await searchFTSFromLbug('test', 5);
       expect(Array.isArray(results)).toBe(true);
     });
   });
@@ -105,7 +109,7 @@ describe('BM25 search', () => {
         .mockResolvedValueOnce([]) // Method
         .mockResolvedValueOnce([]); // Interface
 
-      const results = await searchFTSFromLbug('queryset');
+      const { results } = await searchFTSFromLbug('queryset');
 
       expect(results).toHaveLength(1);
       expect(results[0].filePath).toBe('src/views.py');
@@ -127,7 +131,7 @@ describe('BM25 search', () => {
         .mockResolvedValueOnce([]) // Method
         .mockResolvedValueOnce([]); // Interface
 
-      const results = await searchFTSFromLbug('model');
+      const { results } = await searchFTSFromLbug('model');
 
       expect(results).toHaveLength(1);
       expect(results[0].score).toBe(8); // 5+3
@@ -147,7 +151,7 @@ describe('BM25 search', () => {
         .mockResolvedValueOnce([]) // Method
         .mockResolvedValueOnce([]); // Interface
 
-      const results = await searchFTSFromLbug('util');
+      const { results } = await searchFTSFromLbug('util');
 
       expect(results).toHaveLength(1);
       expect(results[0].nodeIds).toEqual([]);
@@ -171,7 +175,7 @@ describe('BM25 search', () => {
         .mockResolvedValueOnce([]) // Method
         .mockResolvedValueOnce([]); // Interface
 
-      const results = await searchFTSFromLbug('auth');
+      const { results } = await searchFTSFromLbug('auth');
 
       expect(results).toHaveLength(1);
       // All 3 hits (scores 9+7+4=20) — each from a different table, all top-3
@@ -192,7 +196,7 @@ describe('BM25 search', () => {
         .mockResolvedValueOnce([]) // Method
         .mockResolvedValueOnce([]); // Interface
 
-      const results = await searchFTSFromLbug('fn');
+      const { results } = await searchFTSFromLbug('fn');
 
       expect(results[0].filePath).toBe('src/high.py');
       expect(results[1].filePath).toBe('src/low.py');
@@ -220,7 +224,7 @@ describe('BM25 search', () => {
         return [];
       });
 
-      const results = await searchFTSFromLbug('login', 5, REPO);
+      const { results } = await searchFTSFromLbug('login', 5, REPO);
 
       expect(results).toEqual([
         { filePath: 'src/auth.ts', score: 8, rank: 1, nodeIds: ['func:login'] },

gitnexus/test/unit/calltool-dispatch.test.ts

@@ -48,6 +48,7 @@ vi.mock('../../src/storage/repo-manager.js', () => ({
 // tests don't shell out to git.
 vi.mock('../../src/core/git-staleness.js', () => ({
   checkStaleness: vi.fn().mockReturnValue({ isStale: false, commitsBehind: 0 }),
+  checkStalenessAsync: vi.fn().mockResolvedValue({ isStale: false, commitsBehind: 0 }),
   checkCwdMatch: vi.fn().mockResolvedValue({ match: 'none' }),
 }));
 
@@ -61,7 +62,7 @@ vi.mock('../../src/core/platform/capabilities.js', async (importOriginal) => {
 
 // Also mock the search modules to avoid loading onnxruntime
 vi.mock('../../src/core/search/bm25-index.js', () => ({
-  searchFTSFromLbug: vi.fn().mockResolvedValue([]),
+  searchFTSFromLbug: vi.fn().mockResolvedValue({ results: [], ftsAvailable: true }),
 }));
 
 vi.mock('../../src/mcp/core/embedder.js', () => ({
@@ -194,6 +195,27 @@ describe('LocalBackend.callTool', () => {
     expect(result).toHaveProperty('definitions');
   });
 
+  it('includes FTS-unavailable warning when ftsAvailable is false (#1403)', async () => {
+    const { searchFTSFromLbug } = await import('../../src/core/search/bm25-index.js');
+    vi.mocked(searchFTSFromLbug).mockResolvedValueOnce({ results: [], ftsAvailable: false });
+    (executeParameterized as any).mockResolvedValue([]);
+
+    const result = await backend.callTool('query', { query: 'ProcessActivity' });
+
+    expect(result).toHaveProperty('warning');
+    expect((result as any).warning).toMatch(/gitnexus analyze --force/);
+  });
+
+  it('does not include warning when ftsAvailable is true with zero results', async () => {
+    const { searchFTSFromLbug } = await import('../../src/core/search/bm25-index.js');
+    vi.mocked(searchFTSFromLbug).mockResolvedValueOnce({ results: [], ftsAvailable: true });
+    (executeParameterized as any).mockResolvedValue([]);
+
+    const result = await backend.callTool('query', { query: 'nonexistent' });
+
+    expect(result).not.toHaveProperty('warning');
+  });
+
   it('skips vector index query when VECTOR is unsupported by the platform', async () => {
     const cap = _captureLogger();
     platformMocks.isVectorExtensionSupportedByPlatform.mockReturnValue(false);

gitnexus/test/unit/cli-commands.test.ts

@@ -10,6 +10,9 @@ vi.mock('../../src/cli/mcp.js', () => ({
 vi.mock('../../src/cli/setup.js', () => ({
   setupCommand: vi.fn(),
 }));
+vi.mock('../../src/cli/publish.js', () => ({
+  publishCommand: vi.fn(),
+}));
 
 describe('CLI commands', () => {
   describe('version', () => {
@@ -84,4 +87,11 @@ describe('CLI commands', () => {
       expect(typeof setupCommand).toBe('function');
     });
   });
+
+  describe('publishCommand', () => {
+    it('is a function', async () => {
+      const { publishCommand } = await import('../../src/cli/publish.js');
+      expect(typeof publishCommand).toBe('function');
+    });
+  });
 });

gitnexus/test/unit/cli-index-help.test.ts

@@ -63,4 +63,17 @@ describe('CLI help surface', () => {
     expect(result.stdout).toContain('--model <model>');
     expect(result.stdout).toContain('--gist');
   });
+
+  it('publish help names the registry, the token env var, and the opt-out behaviour', () => {
+    const result = runHelp('publish');
+
+    expect(result.status).toBe(0);
+    expect(result.stdout).toContain('--id <owner/repo>');
+    expect(result.stdout).toContain('--skip-git');
+    // Discoverability contract: a contributor scanning `--help` must see
+    // (a) which registry this dispatches to, and (b) the env var that
+    // gates the opt-in. Both are part of the no-token contract.
+    expect(result.stdout).toContain('understand-quickly');
+    expect(result.stdout).toContain('UNDERSTAND_QUICKLY_TOKEN');
+  });
 });

gitnexus/test/unit/cpp-ue-preprocessor.test.ts

@@ -0,0 +1,272 @@
+import { describe, it, expect } from 'vitest';
+import Parser from 'tree-sitter';
+import CPP from 'tree-sitter-cpp';
+import { stripUeMacros } from '../../src/core/ingestion/cpp-ue-preprocessor.js';
+
+describe('stripUeMacros — detection guard', () => {
+  it('returns input unchanged when no UE markers are present', () => {
+    const src = `class Plain {\npublic:\n  int Get() const;\n};`;
+    expect(stripUeMacros(src)).toBe(src);
+  });
+
+  it('returns input unchanged for STL-style code', () => {
+    const src = `#include <vector>\nstd::vector<int> v;`;
+    expect(stripUeMacros(src)).toBe(src);
+  });
+});
+
+describe('stripUeMacros — length preservation', () => {
+  const ueSamples: string[] = [
+    `UCLASS()\nclass BRAWLUI_API UMyClass : public UObject { GENERATED_BODY() public: UFUNCTION() void Run(); };`,
+    `UPROPERTY(EditAnywhere, BlueprintReadOnly, Category = "Combat") int32 Health;`,
+    `USTRUCT(BlueprintType)\nstruct ENGINE_API FMyData { GENERATED_BODY() float Value; };`,
+    `DECLARE_DYNAMIC_MULTICAST_DELEGATE_TwoParams(FMyDelegate, int32, A, FString, B);`,
+    `UE_DEPRECATED(5.0, "Use NewThing instead") void OldThing();`,
+  ];
+
+  for (const src of ueSamples) {
+    it(`preserves byte length: ${src.slice(0, 40).replace(/\n/g, '\\n')}…`, () => {
+      const out = stripUeMacros(src);
+      expect(out.length).toBe(src.length);
+    });
+
+    it(`preserves newline positions: ${src.slice(0, 40).replace(/\n/g, '\\n')}…`, () => {
+      const out = stripUeMacros(src);
+      const inputNewlines: number[] = [];
+      const outputNewlines: number[] = [];
+      for (let i = 0; i < src.length; i++) {
+        if (src.charCodeAt(i) === 0x0a) inputNewlines.push(i);
+        if (out.charCodeAt(i) === 0x0a) outputNewlines.push(i);
+      }
+      expect(outputNewlines).toEqual(inputNewlines);
+    });
+  }
+});
+
+describe('stripUeMacros — macro removal', () => {
+  it('elides UCLASS(...) with arguments', () => {
+    const src = `UCLASS(BlueprintType, Category="Foo")\nclass UFoo {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UCLASS');
+    expect(out).not.toContain('BlueprintType');
+    expect(out).toContain('class UFoo {};');
+  });
+
+  it('elides UCLASS() with empty parens', () => {
+    const src = `UCLASS()\nclass UBar {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UCLASS');
+    expect(out).toContain('class UBar {};');
+  });
+
+  it('elides MODULE_API export macros (BRAWLUI_API style) when paired with a UE marker', () => {
+    const src = `UCLASS()\nclass BRAWLUI_API UMyClass : public UObject {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('BRAWLUI_API');
+    expect(out).toContain('class');
+    expect(out).toContain('UMyClass');
+    expect(out).toContain('public UObject');
+  });
+
+  it('elides multiple distinct *_API tokens in same file when UE marker is present', () => {
+    const src = `UCLASS()\nclass CORE_API A {};\nUCLASS()\nclass UMG_API B : public A {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('CORE_API');
+    expect(out).not.toContain('UMG_API');
+    expect(out).toContain('class');
+    expect(out).toContain('A {};');
+  });
+
+  it('elides GENERATED_BODY() inside class body', () => {
+    const src = `class UThing { GENERATED_BODY() public: void Foo(); };`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('GENERATED_BODY');
+    expect(out).toContain('public:');
+    expect(out).toContain('void Foo();');
+  });
+
+  it('elides UFUNCTION(...) before method declarations', () => {
+    const src = `class X { UFUNCTION(BlueprintCallable, Server, Reliable) void DoThing(); };`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UFUNCTION');
+    expect(out).not.toContain('BlueprintCallable');
+    expect(out).toContain('void DoThing();');
+  });
+
+  it('elides UPROPERTY(...) before field declarations', () => {
+    const src = `class X { UPROPERTY(EditAnywhere) int32 Health; };`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UPROPERTY');
+    expect(out).not.toContain('EditAnywhere');
+    expect(out).toContain('int32 Health;');
+  });
+
+  it('elides DECLARE_DYNAMIC_MULTICAST_DELEGATE_*Params(...)', () => {
+    const src = `DECLARE_DYNAMIC_MULTICAST_DELEGATE_OneParam(FMyDelegate, int32, Value);\nclass X {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('DECLARE_DYNAMIC_MULTICAST_DELEGATE');
+    expect(out).not.toContain('FMyDelegate');
+    expect(out).toContain('class X {};');
+  });
+
+  it('elides UE_DEPRECATED(...) before function declarations', () => {
+    const src = `UE_DEPRECATED(5.1, "Reason") void Old();`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UE_DEPRECATED');
+    expect(out).not.toContain('5.1');
+    expect(out).toContain('void Old();');
+  });
+});
+
+describe('stripUeMacros — non-UE files left alone', () => {
+  it('does NOT strip standalone *_API identifiers when no UE marker is present', () => {
+    const src = `enum class Status { REST_API = 1, HTTP_API = 2, MY_LIB_API = 3 };\nvoid handle(REST_API status);`;
+    expect(stripUeMacros(src)).toBe(src);
+  });
+
+  it('does NOT strip _API tokens in a file that only mentions DECLARE_DELEGATE-like macros from non-UE codebases', () => {
+    const src = `// Custom delegate framework, not UE\n#define DECLARE_HANDLER(x) void x()\nDECLARE_HANDLER(MyHandler);\nint REST_API = 0;`;
+    expect(stripUeMacros(src)).toBe(src);
+  });
+});
+
+describe('stripUeMacros — non-ASCII content preservation', () => {
+  it('leaves non-ASCII content outside elided ranges intact and at the same .length offset', () => {
+    const src = `// Comment with non-ASCII: café résumé naïve\nUCLASS()\nclass UMyClass : public UObject\n{\n  GENERATED_BODY()\n  // Trailing: 日本語 αβγ\n};`;
+    const out = stripUeMacros(src);
+    expect(out.length).toBe(src.length);
+    expect(out).toContain('café résumé naïve');
+    expect(out).toContain('日本語 αβγ');
+    expect(out).toContain('class UMyClass : public UObject');
+    expect(out).not.toContain('UCLASS');
+    expect(out).not.toContain('GENERATED_BODY');
+  });
+
+  it('preserves newline positions when the file contains non-ASCII characters', () => {
+    const src = `// café\nUPROPERTY()\nint32 Health;\n// résumé\nUFUNCTION()\nvoid Run();`;
+    const out = stripUeMacros(src);
+    const inputNewlines: number[] = [];
+    const outputNewlines: number[] = [];
+    for (let i = 0; i < src.length; i++) {
+      if (src.charCodeAt(i) === 0x0a) inputNewlines.push(i);
+      if (out.charCodeAt(i) === 0x0a) outputNewlines.push(i);
+    }
+    expect(outputNewlines).toEqual(inputNewlines);
+  });
+});
+
+describe('stripUeMacros — false-positive guards', () => {
+  it('does NOT strip identifiers that merely contain UCLASS as a substring', () => {
+    const src = `void NotUCLASSAtAll(); int MyUCLASS = 0;`;
+    const out = stripUeMacros(src);
+    expect(out).toBe(src);
+  });
+
+  it('does NOT strip _API substrings inside larger identifiers', () => {
+    const src = `class MY_APIName {};\nint not_my_API_thing = 0;`;
+    const out = stripUeMacros(src);
+    expect(out).toContain('MY_APIName');
+    expect(out).toContain('not_my_API_thing');
+  });
+
+  it('does not eat parens balanced inside string literals', () => {
+    const src = `UFUNCTION(meta=(DisplayName="Foo (Bar)")) void Z();`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UFUNCTION');
+    expect(out).not.toContain('DisplayName');
+    expect(out).toContain('void Z();');
+  });
+
+  it('handles UCLASS with deeply nested parens in arguments', () => {
+    const src = `UCLASS(meta=(Categories=("A.B", "C.D")), Within=Foo) class UDeep {};`;
+    const out = stripUeMacros(src);
+    expect(out).not.toContain('UCLASS');
+    expect(out).not.toContain('Categories');
+    expect(out).toContain('class UDeep {};');
+  });
+
+  it('leaves Qt macros alone (only UE markers stripped)', () => {
+    const src = `class QFoo { Q_OBJECT public: void Bar(); };`;
+    const out = stripUeMacros(src);
+    expect(out).toContain('Q_OBJECT');
+  });
+});
+
+describe('stripUeMacros — class-name extraction sanity', () => {
+  it('after stripping, "class UMyClass" appears immediately after "class "', () => {
+    const src = `UCLASS(BlueprintType)\nclass BRAWLUI_API UMyClass : public UObject\n{\n  GENERATED_BODY()\n};`;
+    const out = stripUeMacros(src);
+    const classIdx = out.indexOf('class ');
+    expect(classIdx).toBeGreaterThanOrEqual(0);
+    const tail = out.slice(classIdx + 'class '.length).trimStart();
+    expect(tail.startsWith('UMyClass')).toBe(true);
+  });
+});
+
+describe('stripUeMacros — tree-sitter extraction (end-to-end)', () => {
+  /**
+   * Walk the parse tree and return the captured class name(s). Works against
+   * the actual tree-sitter-cpp grammar so this is a true integration check
+   * for the core PR claim: the indexer now sees `UMyClass`, not `BRAWLUI_API`.
+   */
+  function extractClassNames(source: string): string[] {
+    const parser = new Parser();
+    parser.setLanguage(CPP as unknown as Parser.Language);
+    const tree = parser.parse(source);
+    const names: string[] = [];
+    const stack: Parser.SyntaxNode[] = [tree.rootNode];
+    while (stack.length > 0) {
+      const node = stack.pop()!;
+      if (node.type === 'class_specifier' || node.type === 'struct_specifier') {
+        const nameNode = node.childForFieldName('name');
+        if (nameNode) names.push(nameNode.text);
+      }
+      for (let i = node.namedChildCount - 1; i >= 0; i--) {
+        const child = node.namedChild(i);
+        if (child) stack.push(child);
+      }
+    }
+    return names;
+  }
+
+  it('tree-sitter-cpp captures UMyClass as the class name (not BRAWLUI_API)', () => {
+    const src = `UCLASS(BlueprintType)\nclass BRAWLUI_API UMyClass : public UObject\n{\n  GENERATED_BODY()\n public:\n  UFUNCTION()\n  void Run();\n};`;
+    const out = stripUeMacros(src);
+    const names = extractClassNames(out);
+    expect(names).toContain('UMyClass');
+    expect(names).not.toContain('BRAWLUI_API');
+  });
+
+  it('tree-sitter-cpp captures struct name correctly through USTRUCT + MODULE_API', () => {
+    const src = `USTRUCT(BlueprintType)\nstruct ENGINE_API FMyData : public FBase\n{\n  GENERATED_BODY()\n  float Value;\n};`;
+    const out = stripUeMacros(src);
+    const names = extractClassNames(out);
+    expect(names).toContain('FMyData');
+    expect(names).not.toContain('ENGINE_API');
+  });
+
+  it('tree-sitter-cpp source positions are preserved across stripping (line numbers match)', () => {
+    const src = `UCLASS()\nclass BRAWLUI_API UMyClass : public UObject\n{\n  GENERATED_BODY()\n public:\n  void Run();\n};`;
+    const out = stripUeMacros(src);
+    const parser = new Parser();
+    parser.setLanguage(CPP as unknown as Parser.Language);
+    const tree = parser.parse(out);
+    const stack: Parser.SyntaxNode[] = [tree.rootNode];
+    let runLine: number | undefined;
+    while (stack.length > 0) {
+      const node = stack.pop()!;
+      if (node.type === 'function_declarator') {
+        const declarator = node.childForFieldName('declarator');
+        if (declarator?.text === 'Run') {
+          runLine = node.startPosition.row;
+          break;
+        }
+      }
+      for (let i = node.namedChildCount - 1; i >= 0; i--) {
+        const child = node.namedChild(i);
+        if (child) stack.push(child);
+      }
+    }
+    expect(runLine).toBe(5); // 0-indexed: "void Run();" is on line 6 (index 5)
+  });
+});

gitnexus/test/unit/group/bridge-storage-tempfile.test.ts

@@ -0,0 +1,90 @@
+/**
+ * Regression tests for U6 — closes CodeQL js/insecure-temporary-file
+ * (#191/#192/#193) and js/log-injection (#188) in core/group.
+ *
+ * The fixes replace `Date.now()` suffix tmp files with crypto.randomBytes
+ * suffixes + open the tmp file with `flag: 'wx'` (O_EXCL). These tests
+ * pin both behaviors so a future refactor that drops either signal
+ * regenerates the CodeQL alert AND fails a test.
+ */
+import { afterAll, beforeAll, describe, expect, it } from 'vitest';
+import path from 'node:path';
+import fs from 'node:fs/promises';
+import os from 'node:os';
+import { writeContractRegistry, createGroupDir } from '../../../src/core/group/storage.js';
+import { writeBridgeMeta } from '../../../src/core/group/bridge-db.js';
+import type { ContractRegistry } from '../../../src/core/group/types.js';
+
+/**
+ * Build a minimal `ContractRegistry` literal with overridable fields.
+ * Replaces the `as never` cast that bypassed the type entirely — keeps
+ * the test free of unrelated boilerplate while still type-checking the
+ * fields under test.
+ */
+function makeRegistry(overrides: Partial<ContractRegistry> = {}): ContractRegistry {
+  return {
+    version: 1,
+    generatedAt: '2026-05-07T00:00:00Z',
+    repoSnapshots: {},
+    missingRepos: [],
+    contracts: [],
+    crossLinks: [],
+    ...overrides,
+  };
+}
+
+let tmpRoot: string;
+let groupDir: string;
+
+beforeAll(async () => {
+  tmpRoot = await fs.mkdtemp(path.join(os.tmpdir(), 'gitnexus-u6-'));
+  groupDir = path.join(tmpRoot, 'fixture-group');
+  await fs.mkdir(groupDir, { recursive: true });
+});
+
+afterAll(async () => {
+  await fs.rm(tmpRoot, { recursive: true, force: true });
+});
+
+describe('writeContractRegistry — tempfile hardening', () => {
+  it('back-to-back writes within the same ms do not collide on the tmp path', async () => {
+    // The previous `${path}.tmp.${Date.now()}` shape collided when two writers
+    // landed in the same millisecond. crypto.randomBytes makes the suffix
+    // essentially-unique. Sequential writes here pin the unique-suffix
+    // property without depending on Windows-specific concurrent-rename
+    // behavior (which has its own pre-existing retry pattern in the
+    // sibling `writeBridge` function and is out of scope for this test).
+    await writeContractRegistry(groupDir, makeRegistry({ version: 1 }));
+    await writeContractRegistry(groupDir, makeRegistry({ version: 2 }));
+    const written = await fs.readFile(path.join(groupDir, 'contracts.json'), 'utf-8');
+    const parsed = JSON.parse(written);
+    expect(parsed.version).toBe(2);
+  });
+});
+
+describe('writeBridgeMeta — tempfile hardening', () => {
+  it('back-to-back writes do not collide on the tmp path', async () => {
+    await writeBridgeMeta(groupDir, { version: 1, generatedAt: 'a', missingRepos: [] });
+    await writeBridgeMeta(groupDir, { version: 2, generatedAt: 'b', missingRepos: [] });
+    const meta = JSON.parse(await fs.readFile(path.join(groupDir, 'meta.json'), 'utf-8'));
+    expect(meta.version).toBe(2);
+  });
+});
+
+describe('createGroupDir — exclusive-create on group.yaml', () => {
+  it('refuses to overwrite an existing group without force', async () => {
+    const gnxDir = path.join(tmpRoot, 'gnx-existing');
+    await createGroupDir(gnxDir, 'mygroup');
+    // Second call without force should throw — same behavior as before this
+    // commit, but now backed by O_EXCL at the writeFile level rather than
+    // only the up-front existence check (closes the TOCTOU CodeQL flagged).
+    await expect(createGroupDir(gnxDir, 'mygroup')).rejects.toThrow(/already exists/);
+  });
+
+  it('overwrites with force=true', async () => {
+    const gnxDir = path.join(tmpRoot, 'gnx-force');
+    await createGroupDir(gnxDir, 'mygroup');
+    // Should succeed without throwing.
+    await expect(createGroupDir(gnxDir, 'mygroup', true)).resolves.toBeTruthy();
+  });
+});