chore: release v1.6.6 (#2075)

Bump gitnexus 1.6.5 -> 1.6.6 and add the 1.6.6 CHANGELOG section
covering ~190 PRs merged since v1.6.5 (range v1.6.5..main).

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.claude/skills/gitnexus/gitnexus-debugging/SKILL.md

@@ -16,10 +16,10 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 ## Workflow
 
 ```
-1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
-2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
+1. query({query: "<error or symptom>"})            → Find related execution flows
+2. context({name: "<suspect>"})                    → See callers/callees/processes
 3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
-4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
+4. cypher({query: "MATCH path..."})                 → Custom traces if needed
 ```
 
 > If "Index is stale" → run `node .gitnexus/run.cjs analyze` in terminal.
@@ -28,11 +28,11 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ```
 - [ ] Understand the symptom (error message, unexpected behavior)
-- [ ] gitnexus_query for error text or related code
+- [ ] query for error text or related code
 - [ ] Identify the suspect function from returned processes
-- [ ] gitnexus_context to see callers and callees
+- [ ] context to see callers and callees
 - [ ] Trace execution flow via process resource if applicable
-- [ ] gitnexus_cypher for custom call chain traces if needed
+- [ ] cypher for custom call chain traces if needed
 - [ ] Read source files to confirm root cause
 ```
 
@@ -40,7 +40,7 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 | Symptom              | GitNexus Approach                                          |
 | -------------------- | ---------------------------------------------------------- |
-| Error message        | `gitnexus_query` for error text → `context` on throw sites |
+| Error message        | `query` for error text → `context` on throw sites |
 | Wrong return value   | `context` on the function → trace callees for data flow    |
 | Intermittent failure | `context` → look for external calls, async deps            |
 | Performance issue    | `context` → find symbols with many callers (hot paths)     |
@@ -48,24 +48,24 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ## Tools
 
-**gitnexus_query** — find code related to error:
+**query** — find code related to error:
 
 ```
-gitnexus_query({query: "payment validation error"})
+query({query: "payment validation error"})
 → Processes: CheckoutFlow, ErrorHandling
 → Symbols: validatePayment, handlePaymentError, PaymentException
 ```
 
-**gitnexus_context** — full context for a suspect:
+**context** — full context for a suspect:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates (external API!)
 → Processes: CheckoutFlow (step 3/7)
 ```
 
-**gitnexus_cypher** — custom call chain traces:
+**cypher** — custom call chain traces:
 
 ```cypher
 MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
@@ -75,11 +75,11 @@ RETURN [n IN nodes(path) | n.name] AS chain
 ## Example: "Payment endpoint returns 500 intermittently"
 
 ```
-1. gitnexus_query({query: "payment error handling"})
+1. query({query: "payment error handling"})
    → Processes: CheckoutFlow, ErrorHandling
    → Symbols: validatePayment, handlePaymentError
 
-2. gitnexus_context({name: "validatePayment"})
+2. context({name: "validatePayment"})
    → Outgoing calls: verifyCard, fetchRates (external API!)
 
 3. READ gitnexus://repo/my-app/process/CheckoutFlow

.claude/skills/gitnexus/gitnexus-exploring/SKILL.md

@@ -18,8 +18,8 @@ description: "Use when the user asks how code works, wants to understand archite
 ```
 1. READ gitnexus://repos                          → Discover indexed repos
 2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
-3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
-4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
+3. query({query: "<what you want to understand>"})  → Find related execution flows
+4. context({name: "<symbol>"})            → Deep dive on specific symbol
 5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
 ```
 
@@ -29,9 +29,9 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ```
 - [ ] READ gitnexus://repo/{name}/context
-- [ ] gitnexus_query for the concept you want to understand
+- [ ] query for the concept you want to understand
 - [ ] Review returned processes (execution flows)
-- [ ] gitnexus_context on key symbols for callers/callees
+- [ ] context on key symbols for callers/callees
 - [ ] READ process resource for full execution traces
 - [ ] Read source files for implementation details
 ```
@@ -47,18 +47,18 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ## Tools
 
-**gitnexus_query** — find execution flows related to a concept:
+**query** — find execution flows related to a concept:
 
 ```
-gitnexus_query({query: "payment processing"})
+query({query: "payment processing"})
 → Processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Symbols grouped by flow with file locations
 ```
 
-**gitnexus_context** — 360-degree view of a symbol:
+**context** — 360-degree view of a symbol:
 
 ```
-gitnexus_context({name: "validateUser"})
+context({name: "validateUser"})
 → Incoming calls: loginHandler, apiMiddleware
 → Outgoing calls: checkToken, getUserById
 → Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
@@ -68,10 +68,10 @@ gitnexus_context({name: "validateUser"})
 
 ```
 1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
-2. gitnexus_query({query: "payment processing"})
+2. query({query: "payment processing"})
    → CheckoutFlow: processPayment → validateCard → chargeStripe
    → RefundFlow: initiateRefund → calculateRefund → processRefund
-3. gitnexus_context({name: "processPayment"})
+3. context({name: "processPayment"})
    → Incoming: checkoutHandler, webhookHandler
    → Outgoing: validateCard, chargeStripe, saveTransaction
 4. Read src/payments/processor.ts for implementation details

.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md

@@ -17,9 +17,9 @@ description: "Use when the user wants to know what will break if they change som
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
+1. impact({target: "X", direction: "upstream"})  → What depends on this
 2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
-3. gitnexus_detect_changes()                               → Map current git changes to affected flows
+3. detect_changes()                               → Map current git changes to affected flows
 4. Assess risk and report to user
 ```
 
@@ -28,11 +28,11 @@ description: "Use when the user wants to know what will break if they change som
 ## Checklist
 
 ```
-- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
+- [ ] impact({target, direction: "upstream"}) to find dependents
 - [ ] Review d=1 items first (these WILL BREAK)
 - [ ] Check high-confidence (>0.8) dependencies
 - [ ] READ processes to check affected execution flows
-- [ ] gitnexus_detect_changes() for pre-commit check
+- [ ] detect_changes() for pre-commit check
 - [ ] Assess risk level and report to user
 ```
 
@@ -55,10 +55,10 @@ description: "Use when the user wants to know what will break if they change som
 
 ## Tools
 
-**gitnexus_impact** — the primary tool for symbol blast radius:
+**impact** — the primary tool for symbol blast radius:
 
 ```
-gitnexus_impact({
+impact({
   target: "validateUser",
   direction: "upstream",
   minConfidence: 0.8,
@@ -73,10 +73,10 @@ gitnexus_impact({
   - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_detect_changes** — git-diff based impact analysis:
+**detect_changes** — git-diff based impact analysis:
 
 ```
-gitnexus_detect_changes({scope: "staged"})
+detect_changes({scope: "staged"})
 
 → Changed: 5 symbols in 3 files
 → Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
@@ -86,7 +86,7 @@ gitnexus_detect_changes({scope: "staged"})
 ## Example: "What breaks if I change validateUser?"
 
 ```
-1. gitnexus_impact({target: "validateUser", direction: "upstream"})
+1. impact({target: "validateUser", direction: "upstream"})
    → d=1: loginHandler, apiMiddleware (WILL BREAK)
    → d=2: authRouter, sessionManager (LIKELY AFFECTED)
 

.claude/skills/gitnexus/gitnexus-pr-review/SKILL.md

@@ -18,10 +18,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 1. gh pr diff <number>                                    → Get the raw diff
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+2. detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
 3. For each changed symbol:
-   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
-4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+   impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. context({name: "<key symbol>"})               → Understand callers/callees
 5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
 6. Summarize findings with risk assessment
 ```
@@ -32,10 +32,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 - [ ] Fetch PR diff (gh pr diff or git diff base...head)
-- [ ] gitnexus_detect_changes to map changes to affected execution flows
-- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] detect_changes to map changes to affected execution flows
+- [ ] impact on each non-trivial changed symbol
 - [ ] Review d=1 items (WILL BREAK) — are callers updated?
-- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] context on key changed symbols to understand full picture
 - [ ] Check if affected processes have test coverage
 - [ ] Assess overall risk level
 - [ ] Write review summary with findings
@@ -63,20 +63,20 @@ description: "Use when the user wants to review a pull request, understand what
 
 ## Tools
 
-**gitnexus_detect_changes** — map PR diff to affected execution flows:
+**detect_changes** — map PR diff to affected execution flows:
 
 ```
-gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+detect_changes({scope: "compare", base_ref: "main"})
 
 → Changed: 8 symbols in 4 files
 → Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Risk: MEDIUM
 ```
 
-**gitnexus_impact** — blast radius per changed symbol:
+**impact** — blast radius per changed symbol:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream"})
+impact({target: "validatePayment", direction: "upstream"})
 
 → d=1 (WILL BREAK):
   - processCheckout (src/checkout.ts:42) [CALLS, 100%]
@@ -86,20 +86,20 @@ gitnexus_impact({target: "validatePayment", direction: "upstream"})
   - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_impact with tests** — check test coverage:
+**impact with tests** — check test coverage:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+impact({target: "validatePayment", direction: "upstream", includeTests: true})
 
 → Tests that cover this symbol:
   - validatePayment.test.ts [direct]
   - checkout.integration.test.ts [via processCheckout]
 ```
 
-**gitnexus_context** — understand a changed symbol's role:
+**context** — understand a changed symbol's role:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates
@@ -112,20 +112,20 @@ gitnexus_context({name: "validatePayment"})
 1. gh pr diff 42 > /tmp/pr42.diff
    → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
 
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+2. detect_changes({scope: "compare", base_ref: "main"})
    → Changed symbols: validatePayment, PaymentInput, formatAmount
    → Affected processes: CheckoutFlow, RefundFlow
    → Risk: MEDIUM
 
-3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+3. impact({target: "validatePayment", direction: "upstream"})
    → d=1: processCheckout, webhookHandler (WILL BREAK)
    → webhookHandler is NOT in the PR diff — potential breakage!
 
-4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+4. impact({target: "PaymentInput", direction: "upstream"})
    → d=1: validatePayment (in PR), createPayment (NOT in PR)
    → createPayment uses the old PaymentInput shape — breaking change!
 
-5. gitnexus_context({name: "formatAmount"})
+5. context({name: "formatAmount"})
    → Called by 12 functions — but change is backwards-compatible (added optional param)
 
 6. Review summary:

.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md

@@ -16,9 +16,9 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
-2. gitnexus_query({query: "X"})                            → Find execution flows involving X
-3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
+1. impact({target: "X", direction: "upstream"})  → Map all dependents
+2. query({query: "X"})                            → Find execution flows involving X
+3. context({name: "X"})                           → See all incoming/outgoing refs
 4. Plan update order: interfaces → implementations → callers → tests
 ```
 
@@ -29,65 +29,65 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ### Rename Symbol
 
 ```
-- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
+- [ ] rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
 - [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
-- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
-- [ ] gitnexus_detect_changes() — verify only expected files changed
+- [ ] If satisfied: rename({..., dry_run: false}) — apply edits
+- [ ] detect_changes() — verify only expected files changed
 - [ ] Run tests for affected processes
 ```
 
 ### Extract Module
 
 ```
-- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
-- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
+- [ ] context({name: target}) — see all incoming/outgoing refs
+- [ ] impact({target, direction: "upstream"}) — find all external callers
 - [ ] Define new module interface
 - [ ] Extract code, update imports
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ### Split Function/Service
 
 ```
-- [ ] gitnexus_context({name: target}) — understand all callees
+- [ ] context({name: target}) — understand all callees
 - [ ] Group callees by responsibility
-- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
+- [ ] impact({target, direction: "upstream"}) — map callers to update
 - [ ] Create new functions/services
 - [ ] Update callers
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ## Tools
 
-**gitnexus_rename** — automated multi-file rename:
+**rename** — automated multi-file rename:
 
 ```
-gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
 → 12 edits across 8 files
 → 10 graph edits (high confidence), 2 ast_search edits (review)
 → Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
 ```
 
-**gitnexus_impact** — map all dependents first:
+**impact** — map all dependents first:
 
 ```
-gitnexus_impact({target: "validateUser", direction: "upstream"})
+impact({target: "validateUser", direction: "upstream"})
 → d=1: loginHandler, apiMiddleware, testUtils
 → Affected Processes: LoginFlow, TokenRefresh
 ```
 
-**gitnexus_detect_changes** — verify your changes after refactoring:
+**detect_changes** — verify your changes after refactoring:
 
 ```
-gitnexus_detect_changes({scope: "all"})
+detect_changes({scope: "all"})
 → Changed: 8 files, 12 symbols
 → Affected processes: LoginFlow, TokenRefresh
 → Risk: MEDIUM
 ```
 
-**gitnexus_cypher** — custom reference queries:
+**cypher** — custom reference queries:
 
 ```cypher
 MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
@@ -98,24 +98,24 @@ RETURN caller.name, caller.filePath ORDER BY caller.filePath
 
 | Risk Factor         | Mitigation                                |
 | ------------------- | ----------------------------------------- |
-| Many callers (>5)   | Use gitnexus_rename for automated updates |
+| Many callers (>5)   | Use rename for automated updates |
 | Cross-area refs     | Use detect_changes after to verify scope  |
-| String/dynamic refs | gitnexus_query to find them               |
+| String/dynamic refs | query to find them               |
 | External/public API | Version and deprecate properly            |
 
 ## Example: Rename `validateUser` to `authenticateUser`
 
 ```
-1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+1. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
    → 12 edits: 10 graph (safe), 2 ast_search (review)
    → Files: validator.ts, login.ts, middleware.ts, config.json...
 
 2. Review ast_search edits (config.json: dynamic reference!)
 
-3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
+3. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
    → Applied 12 edits across 8 files
 
-4. gitnexus_detect_changes({scope: "all"})
+4. detect_changes({scope: "all"})
    → Affected: LoginFlow, TokenRefresh
    → Risk: MEDIUM — run tests for these flows
 ```

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# Code owners
+
+* @Arvuno
+* @magyargergo

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

@@ -1,87 +0,0 @@
-name: Scope Resolution Parity
-
-# Reusable workflow — called from ci.yml. Does NOT declare concurrency;
-# it inherits the caller's concurrency group per the convention documented
-# in CONTRIBUTING.md → "GitHub Actions — Concurrency Convention".
-#
-# ── Purpose (RFC #909 Ring 3, §6.4 "Observability gates") ──────────────
-# For every language in `MIGRATED_LANGUAGES` (exported from
-# `gitnexus/src/core/ingestion/registry-primary-flag.ts`), run the
-# resolver integration test at `test/integration/resolvers/<slug>.test.ts`
-# TWICE on every PR:
-#
-#   1. `REGISTRY_PRIMARY_<LANG>=0` — legacy DAG path (guarantees we haven't
-#      broken the old path while migrating). Known legacy gaps may be skipped
-#      through the resolver test helper's expected-failure list.
-#   2. `REGISTRY_PRIMARY_<LANG>=1` — registry-primary path (guarantees the
-#      new path carries the same behavior — the parity gate).
-#
-# BOTH must pass. The source of truth is the TypeScript constant — adding
-# a language to that `Set` is the ONLY contributor action; CI auto-
-# discovers it, runs parity, and the language's default production path
-# flips to registry-primary in the same change.
-#
-# When the set is empty (e.g. mid-Ring-3 for every language), the parity
-# matrix is skipped and the workflow reports success — no-op until a
-# language is explicitly claimed migrated.
-#
-# ── Consolidation (chore/vitest-speed-strategy) ────────────────────────
-# Previously each language was a separate GitHub Actions matrix job,
-# meaning N languages × 1 checkout+install+build per shard. The build
-# cost dwarfed the test cost (~5 min setup for ~15 sec test execution).
-#
-# Now a single job runs `scripts/run-parity.ts` which loops through all
-# migrated languages sequentially (2 vitest invocations per language:
-# legacy + registry-primary). All failures are collected and reported
-# at the end (equivalent to the old fail-fast: false behavior).
-#
-# Adding a new language to MIGRATED_LANGUAGES still requires no workflow
-# edit — the script auto-discovers the set at runtime.
-
-on:
-  workflow_call:
-
-permissions:
-  contents: read
-
-jobs:
-  discover:
-    name: Discover migrated languages
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    outputs:
-      has-any: ${{ steps.read.outputs.has-any }}
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: ./.github/actions/setup-gitnexus
-
-      - name: Extract MIGRATED_LANGUAGES from registry-primary-flag.ts
-        id: read
-        shell: bash
-        working-directory: gitnexus
-        run: |
-          set -euo pipefail
-          LANGS=$(npx tsx scripts/ci-list-migrated-languages.ts)
-          COUNT=$(printf '%s' "$LANGS" | jq 'length')
-          HAS_ANY="false"
-          if [[ "$COUNT" -gt 0 ]]; then HAS_ANY="true"; fi
-          echo "has-any=$HAS_ANY" >> "$GITHUB_OUTPUT"
-          echo "Discovered $COUNT migrated language(s): $LANGS"
-          echo "Parity will run: $HAS_ANY"
-
-  parity:
-    name: scope-resolution parity
-    needs: discover
-    if: needs.discover.outputs.has-any == 'true'
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: ./.github/actions/setup-gitnexus
-        with:
-          build: 'true'
-
-      - name: Run parity for all migrated languages
-        shell: bash
-        working-directory: gitnexus
-        run: npx tsx scripts/run-parity.ts

.github/workflows/ci.yml

@@ -27,9 +27,8 @@ concurrency:
 # Each concern lives in its own workflow file for maintainability:
 #   ci-quality.yml       — typecheck (tsc --noEmit)
 #   ci-tests.yml         — unit + integration tests with coverage + cross-platform
+#                          (includes the scope-resolution resolver tests)
 #   ci-e2e.yml           — E2E tests (only when gitnexus-web/ changes)
-#   ci-scope-parity.yml  — RFC #909 Ring 3 parity gate: legacy DAG + registry-primary
-#                          both pass, per migrated language in the JSON registry
 #
 # Shared setup is DRY via .github/actions/setup-gitnexus composite action.
 
@@ -49,11 +48,6 @@ jobs:
     permissions:
       contents: read
 
-  scope-parity:
-    uses: ./.github/workflows/ci-scope-parity.yml
-    permissions:
-      contents: read
-
   # ── Save PR metadata for the reporting workflow ─────────────────
   # The ci-report.yml workflow (triggered by workflow_run) needs the
   # PR number and job results to post a comment.  We save them as an
@@ -62,7 +56,7 @@ jobs:
   save-pr-meta:
     name: Save PR Metadata
     if: always() && github.event_name == 'pull_request'
-    needs: [quality, tests, e2e, scope-parity]
+    needs: [quality, tests, e2e]
     runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
@@ -73,14 +67,12 @@ jobs:
           QUALITY: ${{ needs.quality.result }}
           TESTS: ${{ needs.tests.result }}
           E2E: ${{ needs.e2e.result }}
-          SCOPE_PARITY: ${{ needs.scope-parity.result }}
         run: |
           mkdir -p pr-meta
           echo "$PR_NUMBER"      > pr-meta/pr_number
           echo "$QUALITY"        > pr-meta/quality_result
           echo "$TESTS"          > pr-meta/tests_result
           echo "$E2E"            > pr-meta/e2e_result
-          echo "$SCOPE_PARITY"   > pr-meta/scope_parity_result
           # TODO(post-merge): remove backward-compat copies once ci-report.yml
           # on main reads underscore names.
           # Backward-compat: ci-report.yml on main still reads hyphenated
@@ -103,7 +95,7 @@ jobs:
   # Single required check for branch protection.
   ci-status:
     name: CI Gate
-    needs: [quality, tests, e2e, scope-parity]
+    needs: [quality, tests, e2e]
     if: always()
     runs-on: ubuntu-latest
     timeout-minutes: 5
@@ -117,14 +109,15 @@ jobs:
           # reusable workflow, so `needs.tests.result` below blocks the merge
           # on an ABI mismatch. (`jobs.<id>.result` cannot be exposed as a
           # workflow_call output, so the gate is enforced transitively here.)
+          # The scope-resolution resolver tests also run inside the `tests`
+          # workflow (RING4-1 #942 removed the separate scope-parity gate),
+          # so a resolver regression makes TESTS != success and blocks here.
           TESTS: ${{ needs.tests.result }}
           E2E: ${{ needs.e2e.result }}
-          SCOPE_PARITY: ${{ needs.scope-parity.result }}
         run: |
           echo "Quality:        $QUALITY"
           echo "Tests:          $TESTS"
           echo "E2E:            $E2E"
-          echo "Scope parity:   $SCOPE_PARITY"
           # A failed `abi-assert` job (#1922) inside the tests reusable
           # workflow makes TESTS != success, so this clause also blocks the
           # merge on a tree-sitter ABI mismatch.
@@ -137,14 +130,3 @@ jobs:
             echo "::error::E2E job failed"
             exit 1
           fi
-          # scope-parity is a reusable workflow. With an empty migrated-
-          # languages list, its parity matrix is skipped and the outer
-          # workflow still reports `success`. If any entry's legacy-DAG or
-          # registry-primary run fails, the workflow reports `failure`.
-          # Accept only `success`; `skipped` would mean the entire
-          # discover job was skipped too (upstream failure), which should
-          # still block.
-          if [[ "$SCOPE_PARITY" != "success" ]]; then
-            echo "::error::Scope-resolution parity gate failed (RFC #909 Ring 3)"
-            exit 1
-          fi

.github/workflows/codeql.yml

@@ -48,7 +48,7 @@ jobs:
           persist-credentials: false
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4.35.5
+        uses: github/codeql-action/init@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4.36.0
         with:
           languages: ${{ matrix.language }}
           queries: security-and-quality
@@ -69,6 +69,6 @@ jobs:
               - '**/test/fixtures/**'
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4.35.5
+        uses: github/codeql-action/analyze@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4.36.0
         with:
           category: '/language:${{ matrix.language }}'

.github/workflows/docker.yml

@@ -141,14 +141,14 @@ jobs:
         uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4.0.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0
+        uses: docker/setup-buildx-action@d7f5e7f509e45cec5c76c4d5afdd7de93d0b3df5 # v4.1.0
 
       - name: Install Cosign
         uses: sigstore/cosign-installer@6f9f17788090df1f26f669e9d70d6ae9567deba6 # v4.1.2
 
       - name: Log in to GitHub Container Registry
         if: ${{ github.event_name != 'pull_request' && !inputs.dry_run }}
-        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4.1.0
+        uses: docker/login-action@650006c6eb7dba73a995cc03b0b2d7f5ca915bee # v4.2.0
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -163,7 +163,7 @@ jobs:
       # `akonlabs/gitnexus` and `akonlabs/gitnexus-web` repos.
       - name: Log in to Docker Hub
         if: ${{ github.event_name != 'pull_request' && !inputs.dry_run }}
-        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4.1.0
+        uses: docker/login-action@650006c6eb7dba73a995cc03b0b2d7f5ca915bee # v4.2.0
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -183,7 +183,7 @@ jobs:
       # `github.event_name` would still be "push", not "workflow_call".
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@030e881283bb7a6894de51c315a6bfe6a94e05cf # v6.0.0
+        uses: docker/metadata-action@80c7e94dd9b9319bd5eb7a0e0fe9291e23a2a2e9 # v6.1.0
         with:
           # Dual-registry publish. metadata-action expands the same tag set
           # against every image ref listed here, and build-push-action pushes

.github/workflows/gitleaks.yml

@@ -38,6 +38,18 @@ jobs:
           # steps (and Gitleaks itself) don't need it for repo operations.
           persist-credentials: false
 
+      # gitleaks-action builds `base^..head` for pull_request events; both SHAs
+      # must exist locally (fork PRs and shallow checkouts otherwise fail with
+      # "unknown revision" — see gitleaks/gitleaks-action#199).
+      - name: Fetch PR refs for gitleaks range
+        if: github.event_name == 'pull_request'
+        env:
+          BASE_SHA: ${{ github.event.pull_request.base.sha }}
+          HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+        run: |
+          git fetch --no-tags origin "$BASE_SHA"
+          git fetch --no-tags origin "$HEAD_SHA"
+
       # No GITLEAKS_LICENSE secret is required for OSS / public-repo usage.
       # If this repo becomes private, the action will require a license key.
       - name: Gitleaks

.github/workflows/publish.yml

@@ -257,7 +257,7 @@ jobs:
   # ── Phase 3: reusable CI gate ──────────────────────────────────────────────
   # Runs for both rc (when guard says go) and stable. No `secrets:` passed —
   # ci.yml and its entire reusable-workflow chain (ci-quality, ci-tests,
-  # ci-e2e, ci-scope-parity, ci-report) reference zero `secrets.*` values;
+  # ci-e2e, ci-report) reference zero `secrets.*` values;
   # passing any would be unused surface. GITHUB_TOKEN is implicit.
   ci:
     needs: [route, rc-guard]

.github/workflows/scorecard.yml

@@ -53,6 +53,6 @@ jobs:
           retention-days: 5
 
       - name: Upload to Security tab
-        uses: github/codeql-action/upload-sarif@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4.35.5
+        uses: github/codeql-action/upload-sarif@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4.36.0
         with:
           sarif_file: results.sarif

.github/workflows/trivy.yml

@@ -50,10 +50,10 @@ jobs:
           persist-credentials: false
 
       - name: Setup Buildx
-        uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0
+        uses: docker/setup-buildx-action@d7f5e7f509e45cec5c76c4d5afdd7de93d0b3df5 # v4.1.0
 
       - name: Build image (load locally for scan)
-        uses: docker/build-push-action@bcafcacb16a39f128d818304e6c9c0c18556b85f # v7.1.0
+        uses: docker/build-push-action@f9f3042f7e2789586610d6e8b85c8f03e5195baf # v7.2.0
         with:
           context: .
           file: ${{ matrix.image.dockerfile }}
@@ -76,7 +76,7 @@ jobs:
           exit-code: '0'
 
       - name: Upload to Security tab
-        uses: github/codeql-action/upload-sarif@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4.35.5
+        uses: github/codeql-action/upload-sarif@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4.36.0
         with:
           sarif_file: trivy-${{ matrix.image.name }}.sarif
           category: trivy-${{ matrix.image.name }}

.github/workflows/workflow-lint.yml

@@ -76,7 +76,7 @@ jobs:
         continue-on-error: true
 
       - name: Upload SARIF
-        uses: github/codeql-action/upload-sarif@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4.35.5
+        uses: github/codeql-action/upload-sarif@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4.36.0
         with:
           sarif_file: zizmor.sarif
           category: zizmor

.gitleaks.toml

@@ -0,0 +1,12 @@
+title = "GitNexus"
+
+[extend]
+useDefault = true
+
+# Fake embedding API keys in unit tests (current probe + historical placeholder).
+[allowlist]
+description = "fake embedding API keys in http-embedder unit tests"
+regexes = [
+  '''secret-key-12345''',
+  '''test-api-key-redaction-check''',
+]

AGENTS.md

@@ -39,8 +39,7 @@ Commands and gotchas live under **Repo reference** below and in **[CONTRIBUTING.
 ## Reference docs
 
 - **[ARCHITECTURE.md](ARCHITECTURE.md)**, **[CONTRIBUTING.md](CONTRIBUTING.md)**, **[GUARDRAILS.md](GUARDRAILS.md)**
-- **Call-resolution DAG (legacy path):** See ARCHITECTURE.md § Call-Resolution DAG. Typed 6-stage DAG inside the `parse` phase; language-specific behavior behind `inferImplicitReceiver` / `selectDispatch` hooks on `LanguageProvider`. Shared code in `gitnexus/src/core/ingestion/` must not name languages. Types: `gitnexus/src/core/ingestion/call-types.ts`.
-- **Scope-resolution pipeline (RFC #909 Ring 3):** See ARCHITECTURE.md § Scope-Resolution Pipeline. Replaces the legacy DAG for languages in `MIGRATED_LANGUAGES` (see `registry-primary-flag.ts`). A language plugs in by implementing `ScopeResolver` (`scope-resolution/contract/scope-resolver.ts`) and registering it in `SCOPE_RESOLVERS`. CI parity gate runs BOTH paths per migrated language on every PR.
+- **Call & inheritance resolution (RFC #909 Ring 3):** See ARCHITECTURE.md § Scope-Resolution Pipeline. All languages resolve calls and inheritance through the scope-resolution pipeline (`Registry.lookup`, `preEmitInheritanceEdges`, `emitHeritageEdges`, `buildMro` → `MethodDispatchIndex`). **Shared code in `gitnexus/src/core/ingestion/` must not name languages** — plug language behavior in via `LanguageProvider` / `ScopeResolver` hooks. A language plugs in by implementing `ScopeResolver` (`scope-resolution/contract/scope-resolver.ts`) and registering it in `SCOPE_RESOLVERS`. (The legacy call-resolution DAG + `@heritage` capture path were removed in RING4-1 #942.)
 - **Cursor:** `.cursor/index.mdc` (always-on); `.cursor/rules/*.mdc` (glob-scoped). Legacy `.cursorrules` deprecated.
 - **GitNexus:** skills in `.claude/skills/gitnexus/`; MCP rules in `gitnexus:start` block below.
 
@@ -81,18 +80,18 @@ This project is indexed by GitNexus as **GitNexus** (26675 symbols, 35395 relati
 
 ## Always Do
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
 - **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+- When exploring unfamiliar code, use `query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `context({name: "symbolName"})`.
 
 ## Never Do
 
-- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER edit a function, class, or method without first running `impact` on it.
 - NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
-- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+- NEVER rename symbols with find-and-replace — use `rename` which understands the call graph.
+- NEVER commit changes without running `detect_changes()` to check affected scope.
 
 ## Resources
 

ARCHITECTURE.md

@@ -15,7 +15,7 @@ Monorepo: **CLI/MCP** (`gitnexus/`) + **browser UI** (`gitnexus-web/`).
 
 ## End-to-end flow: index → graph → tools
 
-1. **Ingestion** — `analyze.ts` → `runFullAnalysis` (`run-analyze.ts`) → `runPipelineFromRepo` (`pipeline.ts`). DAG of 12 phases builds a `KnowledgeGraph` in memory, then loads into LadybugDB under `.gitnexus/`. Repo registered in `~/.gitnexus/registry.json` for MCP discovery.
+1. **Ingestion** — `analyze.ts` → `runFullAnalysis` (`run-analyze.ts`) → `runPipelineFromRepo` (`pipeline.ts`). DAG of 14 phases builds a `KnowledgeGraph` in memory, then loads into LadybugDB under `.gitnexus/`. Repo registered in `~/.gitnexus/registry.json` for MCP discovery.
 
 2. **Persistence** — `repo-manager.ts` (paths, registry, KuzuDB cleanup). `lbug-adapter.ts` (graph load, queries, embedding batches).
 
@@ -65,7 +65,7 @@ Monorepo: **CLI/MCP** (`gitnexus/`) + **browser UI** (`gitnexus-web/`).
 | Wiki generation | `src/core/wiki/` |
 | Language support | `src/core/ingestion/languages/` + `tree-sitter-queries.ts` + `gitnexus-shared/src/languages.ts` |
 | Import resolution | `src/core/ingestion/import-processor.ts` + `import-resolvers/configs/` + `model/resolution-context.ts` |
-| Call resolution/MRO | `src/core/ingestion/call-processor.ts` + `model/resolve.ts` |
+| Call resolution/inheritance/MRO | `src/core/ingestion/scope-resolution/` (pipeline, passes, graph-bridge) |
 | Type extraction | `src/core/ingestion/type-extractors/` |
 | Worker pool | `src/core/ingestion/workers/` |
 | Web UI | `gitnexus-web/src/` |
@@ -77,11 +77,11 @@ Monorepo: **CLI/MCP** (`gitnexus/`) + **browser UI** (`gitnexus-web/`).
 
 ## Pipeline Phase DAG
 
-12 phases defined in `gitnexus/src/core/ingestion/pipeline-phases/`, each with explicit `deps` and typed output.
+14 phases defined in `gitnexus/src/core/ingestion/pipeline-phases/`, each with explicit `deps` and typed output.
 
 ```
 scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
-  → crossFile → mro → communities → processes
+  → crossFile → scopeResolution → pruneLocalSymbols → mro → communities → processes
 ```
 
 | Phase | File | Deps | Output |
@@ -95,11 +95,13 @@ scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
 | `tools` | `tools.ts` | `parse` | Tool nodes + HANDLES_TOOL edges |
 | `orm` | `orm.ts` | `parse` | QUERIES edges (Prisma, Supabase) |
 | `crossFile` | `cross-file.ts` + `cross-file-impl.ts` | `parse`, `routes`, `tools`, `orm` | Cross-file type propagation in topological import order |
-| `mro` | `mro.ts` | `crossFile`, `structure` | METHOD_OVERRIDES + METHOD_IMPLEMENTS edges |
-| `communities` | `communities.ts` | `mro`, `structure` | Community nodes + MEMBER_OF edges (Leiden algorithm) |
-| `processes` | `processes.ts` | `communities`, `routes`, `tools`, `structure` | Process nodes + STEP_IN_PROCESS edges |
+| `scopeResolution` | `scope-resolution/pipeline/phase.ts` | `parse`, `crossFile`, `structure` | Binding/reference + inheritance edges; disposes BindingAccumulator |
+| `pruneLocalSymbols` | `prune-local-symbols.ts` | `scopeResolution` | Drops inert block-local `Const`/`Variable`/`Static` nodes (only a `File→DEFINES` edge) post-resolution |
+| `mro` | `mro.ts` | `crossFile`, `scopeResolution`, `pruneLocalSymbols`, `structure` | METHOD_OVERRIDES + METHOD_IMPLEMENTS edges |
+| `communities` | `communities.ts` | `mro`, `pruneLocalSymbols`, `structure` | Community nodes + MEMBER_OF edges (Leiden algorithm) |
+| `processes` | `processes.ts` | `communities`, `routes`, `tools`, `pruneLocalSymbols`, `structure` | Process nodes + STEP_IN_PROCESS edges |
 
-**Non-phase files in the same directory:** `parse-impl.ts`, `cross-file-impl.ts` (implementation), `wildcard-synthesis.ts` (whole-module import expansion), `orm-extraction.ts` (sequential ORM fallback), `types.ts`, `runner.ts`, `index.ts`.
+**Non-phase files in the same directory:** `parse-impl.ts`, `cross-file-impl.ts` (implementation), `wildcard-synthesis.ts` (whole-module import expansion), `types.ts`, `runner.ts`, `index.ts`.
 
 ### DAG runner
 
@@ -119,7 +121,8 @@ scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
 - **Single graph accumulator** — all phases mutate the same `KnowledgeGraph` in `ctx`; the graph is the primary output.
 - **Typed phase access** — `getPhaseOutput<T>(deps, 'name')` for type-safe upstream results.
 - **Binding accumulator lifecycle** — created in `parse`, disposed by `crossFile` (in `finally`). No other phase should take ownership.
-- **Skippable phases** — `skipGraphPhases` omits MRO/communities/processes (faster tests). `skipWorkers` forces sequential parsing.
+- **Skippable phases** — `skipGraphPhases` omits MRO/communities/processes (faster tests); `pruneLocalSymbols` still runs (it is graph cleanup, not analysis). `skipWorkers` is no longer a sequential escape hatch — it (like `--workers 0` / `GITNEXUS_WORKER_POOL_SIZE=0`) is rejected with an actionable error, since the worker pool is the sole parse path (§ Chunked parse-and-resolve).
+- **Local-symbol pruning** — `pruneLocalSymbols` removes inert block-local value symbols after scope resolution has consumed them. Opt out per-call with `PipelineOptions.keepLocalValueSymbols` or globally with the `GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS` env var.
 
 ### How to add a new phase
 
@@ -147,105 +150,18 @@ export const myPhase: PipelinePhase<MyPhaseOutput> = {
 
 ---
 
-## Call-Resolution DAG
+## Semantic model
 
-Typed 6-stage pipeline in `call-processor.ts` (inside the `parse` phase) that resolves method/function calls and emits CALLS edges. Language behavior plugs in at two `LanguageProvider` hook points (stages 3–4); shared code names no languages. Scope: call resolution only — import resolution, type extraction, heritage, and symbol-table population live in other phases.
+`SemanticModel` (`gitnexus/src/core/ingestion/model/semantic-model.ts`) is the authoritative store for every symbol-indexed lookup (by `nodeId`, `simpleName`, `qualifiedName`, or `filePath`). The scope-resolution pipeline reads from here: `findOwnedMember`, `pickOverload`, and `findExportedDefByName` all consult `model.methods` / `model.fields` / `model.symbols`.
 
-### Stages
-
-```
-extract-call ──▶ classify-form ──▶ infer-receiver ──▶ select-dispatch ──▶ resolve-target ──▶ emit-edge
-     (1)              (2)            (3)  [hook]       (4)  [hook]         (5)                 (6)
-```
-
-| Stage | Produces | Location |
-|-------|----------|----------|
-| **extract-call** | `ExtractedCallSite` (name, form, receiver, argCount) | `call-extractors/` (per-language); runs in worker |
-| **classify-form** | callForm (`free`/`member`/`constructor`) + arity | `call-analysis.ts` → `inferCallForm`; shared, runs in worker |
-| **infer-receiver** | `ReceiverEnriched` (receiver type finalized) | `call-processor.ts`; shared default chain, then `inferImplicitReceiver` hook |
-| **select-dispatch** | `DispatchDecision` (primary, fallback, ancestryView) | `selectDispatch` hook, falls back to shared default |
-| **resolve-target** | `TieredCandidates` | `model/resolve.ts` → `lookupMethodByOwnerWithMRO` (MRO walk) |
-| **emit-edge** | CALLS edge in graph | `call-processor.ts`; writes edge with confidence tier |
-
-### Provider hooks
-
-Both hooks are optional on `LanguageProvider`. Ruby is the only current implementer.
-
-**`inferImplicitReceiver`** — called after shared infer-receiver defaults. Returns `ImplicitReceiverOverride | null`.
-
-| | |
-|---|---|
-| Inputs | `calledName`, `callForm`, `receiverName`, `receiverTypeName`, `callNode` (AST), `filePath` |
-| Non-null fields | `callForm`, `receiverName`, `receiverTypeName` (required); `receiverSource: 'implicit-self'` (fixed); `hint?` (opaque, passed to `selectDispatch`) |
-| Null | Keep existing `ReceiverEnriched` state |
-
-**`selectDispatch`** — called after infer-receiver (including hook). Returns `DispatchDecision | null`; null uses shared default (constructor → `primary:'constructor'`; typed receiver → `primary:'owner-scoped'`; else → `primary:'free'`).
-
-| | |
-|---|---|
-| Inputs | `calledName`, `callForm`, `receiverName`, `receiverTypeName`, `receiverSource`, `hint` |
-| Non-null fields | `primary: 'owner-scoped' \| 'free' \| 'constructor'`; `fallback?: 'free-arity-narrowed'`; `ancestryView?: 'instance' \| 'singleton'`; `hint?` |
-
-**`DispatchDecision` field semantics:**
-- `primary: 'owner-scoped'` — MRO walk from receiver's type; used when receiver type is known.
-- `fallback: 'free-arity-narrowed'` — after owner-scoped miss, search free-call candidates by arity only (Ruby uses this for implicit-self calls that miss their owner's MRO).
-- `ancestryView: 'singleton'` — walk singleton/class ancestry instead of instance ancestry (Ruby `def self.foo` bodies, so `extend`-ed methods are found).
-
-### Adding language behavior
-
-1. **Implicit receivers** — implement `inferImplicitReceiver`: return null if call already has a receiver; otherwise use `findEnclosingClassInfo` (`ast-helpers.ts`) to find the enclosing context, return `ImplicitReceiverOverride` with `receiverSource: 'implicit-self'`, and optionally set `hint` for `selectDispatch`.
-2. **Custom dispatch** — implement `selectDispatch`: inspect `receiverSource` and `hint`, return `DispatchDecision` with `primary`, optional `fallback`, optional `ancestryView`; return null to keep shared defaults.
-3. **MRO strategy** — confirm `mroStrategy` is `'first-wins'`, `'c3'`, `'ruby-mixin'`, or `'none'`; consumed by `lookupMethodByOwnerWithMRO`.
-
-**Ruby example** (`languages/ruby.ts` + `utils/ruby-self-call.ts`): `inferImplicitReceiver` rewrites bare-identifier calls to `self.method` and sets `hint` to `'instance'`/`'singleton'`; `selectDispatch` uses hint for `ancestryView` and adds `fallback: 'free-arity-narrowed'` for implicit-self calls.
-
-### Code references
-
-| Module | Purpose |
-|--------|---------|
-| `core/ingestion/call-types.ts` | DAG types: `ReceiverEnriched`, `DispatchDecision`, `ImplicitReceiverOverride` |
-| `core/ingestion/language-provider.ts` | Hook signatures: `inferImplicitReceiver`, `selectDispatch` |
-| `core/ingestion/call-processor.ts` | `processCalls`: stages 3–6 |
-| `core/ingestion/model/resolve.ts` | `lookupMethodByOwnerWithMRO`: stage 5 MRO walk |
-| `core/ingestion/languages/ruby.ts` | Both hooks + `mroStrategy: 'ruby-mixin'` |
-| `core/ingestion/utils/ruby-self-call.ts` | Bare-call rewrite for `inferImplicitReceiver` |
-
-### Coexistence with the scope-resolution pipeline
-
-The Call-Resolution DAG is the **legacy path**. RFC #909 Ring 3 introduces a parallel **scope-resolution pipeline** (next section) that replaces stages 1–6 with a scope-indexed registry lookup. Both paths ship side-by-side and are gated per-language via `MIGRATED_LANGUAGES` + the `REGISTRY_PRIMARY_<LANG>` env var.
-
-- **Unmigrated language** → Call-Resolution DAG runs; scope-resolution phase is a no-op.
-- **Migrated language** (currently: Python, C#) → scope-resolution owns CALLS/ACCESSES/USES emission; the legacy DAG gates off for that language via `isRegistryPrimary(lang)` checks in `call-processor.ts` and `import-processor.ts`.
-- `import-processor` still populates `importMap` for migrated languages — heritage's `ctx.resolve` reads it to disambiguate parent classes. Only edge emission is gated.
-- CI runs BOTH paths for every migrated language on every PR (`.github/workflows/ci-scope-parity.yml`); both must pass.
-
-#### Same-graph guarantee
-
-Edges emitted by the scope-resolution pipeline and edges emitted by the legacy DAG are indistinguishable to downstream consumers (MCP tools, HTTP API, embeddings, group bridge):
-
-- **Node identity** — both paths use `generateId(...)` from `lib/utils.ts`, the same qualified-name keyspace, and the same node labels (`File`, `Folder`, `Class`, `Method`, `Function`, …). Overload disambiguation suffixes `parameterTypes` into the id consistently — see `scope-resolution/graph-bridge/ids.ts` and the legacy emitter in `call-processor.ts`.
-- **Edge vocabulary** — both paths emit the same reasons: `'import-resolved' | 'global' | 'local-call' | 'same-file' | 'interface-dispatch' | 'read' | 'write'`. Migrating a language must not change which reasons consumers see for previously-resolved edges.
-- **Confidence tier** — both paths attach a numeric `confidence` to each edge using the same scale.
-
-The CI parity workflow (`.github/workflows/ci-scope-parity.yml`) runs both paths against every migrated language's fixture corpus and fails on any divergence.
-
-#### Semantic-model source of truth
-
-Two independent invariants.
-
-**ParsedFile = the AST-level truth.** `ParsedFile` (`gitnexus-shared/src/scope-resolution/parsed-file.ts`) is the single per-file artifact both resolution paths consume. Scope-resolution passes MUST NOT build a parallel parse representation. If a per-language hook needs AST-level facts that `ParsedFile` doesn't expose, it should reuse the orchestrator's `treeCache` (`RunScopeResolutionInput.treeCache`) rather than re-invoking `parser.parse(...)` on its own — the C# `populateNamespaceSiblings` hook is the reference implementation of this pattern.
-
-**SemanticModel = the symbol-level truth.** `SemanticModel` (`gitnexus/src/core/ingestion/model/semantic-model.ts`) is the authoritative store for every symbol-indexed lookup (by `nodeId`, `simpleName`, `qualifiedName`, or `filePath`). Both paths read from here:
-
-- Legacy Call-Resolution DAG → `call-processor` Tier 1/2/3 via `model.symbols.lookupExactAll`, `model.methods.lookupMethodByName`, `model.types.lookupClassByName`, `lookupMethodByOwnerWithMRO`.
-- Scope-resolution pipeline → `findOwnedMember`, `pickOverload`, `findExportedDefByName` all consult `model.methods` / `model.fields` / `model.symbols`.
+`ParsedFile` (`gitnexus-shared/src/scope-resolution/parsed-file.ts`) is the single per-file artifact the scope-resolution pipeline consumes. Scope-resolution passes MUST NOT build a parallel parse representation. If a per-language hook needs AST-level facts that `ParsedFile` doesn't expose, it should reuse the orchestrator's `treeCache` (`RunScopeResolutionInput.treeCache`) rather than re-invoking `parser.parse(...)` on its own — the C# `populateNamespaceSiblings` hook is the reference implementation of this pattern.
 
 The scope-resolution pipeline additionally carries `WorkspaceResolutionIndex` for `Scope`-valued lookups (`classScopeByDefId`, `moduleScopeByFile`) that `SemanticModel` structurally cannot hold. No symbol-indexed duplicates exist outside `SemanticModel`.
 
 **Write / read phase contract.** The model is mutable during three ordered phases and read-only afterward:
 
 ```
- Phase 1: legacy parse     ──► symbolTable.add fans into types/methods/fields
+ Phase 1: parse            ──► symbolTable.add fans into types/methods/fields
  Phase 2: scope-resolution ──► reconcileOwnership() registers corrected ownerIds
  Phase 3: finalize         ──► model.attachScopeIndexes(bundle) — one-shot freeze
  ─────────────────────────── phase boundary ───────────────────────────
@@ -255,7 +171,7 @@ The scope-resolution pipeline additionally carries `WorkspaceResolutionIndex` fo
 
 `runScopeResolution` narrows `MutableSemanticModel` → `SemanticModel` at the phase boundary so downstream passes physically cannot mutate the model even accidentally.
 
-**Transitional: reconciliation pass.** `reconcileOwnership` (`scope-resolution/pipeline/reconcile-ownership.ts`) is a shim for languages whose legacy extractor doesn't resolve `enclosingClassId` at parse time (Python class-body methods are the canonical case). It walks `parsed.localDefs[i].ownerId` after `populateOwners` and registers any missed methods/fields into the model. Idempotent — safe to re-run, safe alongside languages whose legacy extractor already carries `ownerId` (C#).
+**Reconciliation pass.** `reconcileOwnership` (`scope-resolution/pipeline/reconcile-ownership.ts`) is a shim for languages whose parse-time extractor doesn't resolve `enclosingClassId` at parse time (Python class-body methods are the canonical case). It walks `parsed.localDefs[i].ownerId` after `populateOwners` and registers any missed methods/fields into the model. Idempotent — safe to re-run, safe alongside languages whose extractor already carries `ownerId` (C#).
 
 The architectural end state is for every language's parse-time extractor to emit the correct `ownerId` directly, making reconciliation a no-op (tracked as a follow-up refactor). The dev-mode validator `validateOwnershipParity` surfaces any drift via `onWarn` under `NODE_ENV !== 'production' && VALIDATE_SEMANTIC_MODEL !== '0'`.
 
@@ -265,7 +181,7 @@ References: `semantic-model.ts` file-head (full write/read contract); `contract/
 
 ## Scope-Resolution Pipeline (RFC #909 Ring 3)
 
-Language-agnostic registry-primary resolver. Replaces the Call-Resolution DAG for migrated languages. Adding a language is one interface implementation (`ScopeResolver`) plus two registrations — no changes to shared code, no new pipeline phase.
+Language-agnostic scope-resolution resolver. This is the resolution path for every language — it owns CALLS/ACCESSES/USES emission and inheritance edges. Adding a language is one interface implementation (`ScopeResolver`) plus one registration in the `SCOPE_RESOLVERS` map — no changes to shared code, no new pipeline phase. (RING4-1 #942 removed the legacy call-resolution DAG and the per-language `MIGRATED_LANGUAGES` flag, so `SCOPE_RESOLVERS` registration is all that's needed.)
 
 ### Pipeline stages
 
@@ -286,7 +202,7 @@ Language-agnostic registry-primary resolver. Replaces the Call-Resolution DAG fo
 ```
 
 Orchestrator: `runScopeResolution(input, provider)` in `scope-resolution/pipeline/run.ts`.
-Pipeline phase: `scopeResolutionPhase` in `scope-resolution/pipeline/phase.ts` — iterates `SCOPE_RESOLVERS ∩ MIGRATED_LANGUAGES`, reads per-file Trees from the parse phase's `scopeTreeCache`, disposes the cache at the end.
+Pipeline phase: `scopeResolutionPhase` in `scope-resolution/pipeline/phase.ts` — iterates the registered `SCOPE_RESOLVERS` over the worker-serialized `ParsedFile`s. (Per-language `emitScopeCaptures` hooks may reuse a cached Tree via the orchestrator's `treeCache`, but in worker-pool runs that cache is empty — Trees can't cross MessageChannels — so they consume the pre-extracted `ParsedFile` instead; § Performance notes.)
 
 ### `ScopeResolver` contract
 
@@ -312,7 +228,6 @@ Single interface a language implements to plug into the pipeline. Contract fully
 
 1. Implement `ScopeResolver` in `languages/<lang>/scope-resolver.ts`.
 2. Add entry to `SCOPE_RESOLVERS` in `scope-resolution/pipeline/registry.ts`.
-3. Add the language to `MIGRATED_LANGUAGES` in `registry-primary-flag.ts` when the shadow-harness corpus parity ≥ 99% fixtures / ≥ 98% corpus.
 
 CI auto-discovers the set via `tsx`. No workflow edit required.
 
@@ -328,7 +243,6 @@ CI auto-discovers the set via `tsx`. No workflow edit required.
 | `scope-resolution/graph-bridge/*.ts` | CLI-local translation from resolved references → `KnowledgeGraph` edges |
 | `scope-resolution/scope/*.ts` | Generic scope-chain walkers + namespace targets |
 | `scope-resolution/workspace-index.ts` | Build-once O(1) lookup index |
-| `registry-primary-flag.ts` | `MIGRATED_LANGUAGES` set + `isRegistryPrimary(lang)` |
 | `languages/python/index.ts` | Python `ScopeResolver` hooks + known-limitation docs |
 | `languages/python/captures.ts` | `emitPythonScopeCaptures` (honors cross-phase Tree cache) |
 | `languages/csharp/index.ts` | C# `ScopeResolver` hooks + known-limitation docs |
@@ -337,7 +251,7 @@ CI auto-discovers the set via `tsx`. No workflow edit required.
 
 ### Performance notes
 
-- **Cross-phase Tree cache**: parse phase writes Trees into `scopeTreeCache` (separate from the chunk-local `astCache`) ONLY for languages with `emitScopeCaptures`. Scope-resolution reads from it to skip the second parse. Cleared at end of the phase. Workers leave the cache empty — Trees can't cross MessageChannels; cache miss = fresh parse. `PROF_SCOPE_RESOLUTION=1` emits hit/miss counters and a worker-engaged warning.
+- **Cross-phase Tree cache**: the orchestrator's `treeCache` (`RunScopeResolutionInput.treeCache`) lets a scope-resolution per-language hook (`emitScopeCaptures`) reuse a tree instead of re-parsing. Workers leave it empty — Trees can't cross MessageChannels — so in normal (worker-pool) runs scope-resolution does NOT rely on it: workers serialize each file's `ParsedFile` (+ capture side-channel) and stream them in, so scope-resolution consumes the pre-extracted artifact rather than re-parsing on the main thread (§ Chunked parse-and-resolve). `PROF_SCOPE_RESOLUTION=1` emits hit/miss counters and a worker-engaged warning.
 - **Typed relationship iteration**: heritage + MRO walk only the EXTENDS / IMPLEMENTS / HAS_METHOD edges via `iterRelationshipsByType`, not the full relationship map.
 - **Workspace-resolution-index**: O(1) `findOwnedMember` / `findExportedDef` / `classScopeByDefId` built once per run.
 - **SCC-ordered cross-file return-type propagation** (PR #1050): `propagateImportedReturnTypes` walks `indexes.sccs` in reverse-topological order (leaves first), so multi-hop alias chains like `models.User → service.user → app.user` collapse to the terminal class in a single linear pass. Within each importer, the source module's `typeBindings` is chain-followed BEFORE mirroring (so we mirror terminal types, not intermediate refs), and the importer's own `typeBindings` is chain-followed AFTER mirroring (so local `const x = importedFn()` resolves before downstream importers run). Cyclic SCCs reach a partial fixpoint within a single pass without iterating to convergence — see the `ts-circular` cross-file-binding fixture which only asserts pipeline-no-throw. PROF output (`PROF_SCOPE_RESOLUTION=1`) splits `finalize` from `propagate` so quadratic regressions in the chain-follow surface independently.
@@ -351,7 +265,7 @@ CI auto-discovers the set via `tsx`. No workflow edit required.
 ```
  Unified Graph Schema (44 node types, 21 relationship types)
            ↑
- Unified Resolution (3-tier name lookup + MRO walk)
+ Scope-Resolution Pipeline (registry lookup + 3-tier import resolution + MRO)
            ↑
  Language Providers (import semantics, type config, export checker, MRO strategy)
            ↑
@@ -376,7 +290,7 @@ Each language implements `LanguageProvider` (`language-provider.ts`). Key fields
 
 ### Unified capture tags
 
-Per-language tree-sitter queries use different AST node names but produce the **same semantic capture tags**: `@definition.class`, `@definition.function`, `@call.name`, `@import.source`, `@heritage.extends`. Downstream extraction needs no language branching. Defined in `tree-sitter-queries.ts`.
+Per-language tree-sitter queries use different AST node names but produce the **same semantic capture tags**: `@definition.class`, `@definition.function`, `@call.name`, `@import.source`, `@reference.inherits`. Downstream extraction needs no language branching. Defined in `tree-sitter-queries.ts`.
 
 ### Import resolution
 
@@ -400,23 +314,26 @@ Unified 3-tier algorithm (`model/resolution-context.ts`), per-language `importSe
 ### Chunked parse-and-resolve
 
 `parse` processes files in ~20 MB byte-budget chunks to bound memory. Per chunk:
-1. Worker pool dispatches files (or sequential fallback via `skipWorkers`)
+1. Worker pool dispatches files (the sole parse path — there is no sequential fallback; `skipWorkers`, `--workers 0`, and `GITNEXUS_WORKER_POOL_SIZE=0` are rejected with an actionable error)
 2. Each worker: detect language → load grammar → run queries → return unified `ParseWorkerResult`
 3. Synthesize wildcard bindings (`wildcard-synthesis.ts`)
-4. Resolve imports and heritage
+4. Resolve imports
 5. Collect `BindingAccumulator` entries for cross-file propagation
 
+Inheritance edges are emitted later, by the scope-resolution phase (`preEmitInheritanceEdges` + `emitHeritageEdges`), not during `parse`.
+
 Workers: `workers/worker-pool.ts`, `workers/parse-worker.ts`.
 
-### Heritage and MRO
+**Worker-serialized ParsedFiles (#2038).** To index very large repos (e.g. the Linux kernel) without OOM, the worker pool is the *sole* parse path and workers serialize each file's `ParsedFile` (plus its capture side-channel) in parallel, streaming them to scope-resolution through a disk-backed store. Scope-resolution consumes the pre-extracted artifact instead of re-parsing every file on the main thread — tree-sitter's native input buffers are not GC-reclaimable, so the former main-thread re-parse leaked native memory until the process died. Pool creation is lazy / cache-miss-gated, so a warm all-cache-hit run replays cached worker output without spawning a worker (hence `usedWorkerPool` can be false even when the repo has parseable files).
 
-All languages emit unified `ExtractedHeritage` (child, parent, `EXTENDS`/`IMPLEMENTS`). MRO phase walks the heritage graph using per-language strategy:
+### Inheritance and MRO
+
+Inheritance is captured by the `@reference.inherits` tag and emitted by the scope-resolution phase: `preEmitInheritanceEdges` resolves each base in scope, then `emitHeritageEdges` writes the `EXTENDS`/`IMPLEMENTS` edges. The phase then computes method resolution order via each `ScopeResolver`'s `buildMro` hook, feeding a `MethodDispatchIndex` used for owner-scoped lookups. Per-language strategy:
 - **`first-wins`** — Java, C#, C++, TS, Ruby, Go
 - **`c3`** — Python (C3 linearization)
+- **`ruby-mixin`** — Ruby (mixin-aware linearization)
 - **`none`** — single-inheritance languages
 
-Unified walk: `lookupMethodByOwnerWithMRO()` in `model/resolve.ts`.
-
 ---
 
 ## Full analysis flow

CLAUDE.md

@@ -35,7 +35,7 @@ If always-on instructions grow, load deep conventions via conditional reads (e.g
 ## Reference Documentation
 
 - **This repository:** [AGENTS.md](AGENTS.md) (Cursor + monorepo notes), [ARCHITECTURE.md](ARCHITECTURE.md), [CONTRIBUTING.md](CONTRIBUTING.md), [GUARDRAILS.md](GUARDRAILS.md).
-- **Call-resolution DAG:** See ARCHITECTURE.md § Call-Resolution DAG. Shared pipeline code in `gitnexus/src/core/ingestion/` must not name languages — use `LanguageProvider` hooks instead (see AGENTS.md).
+- **Call & inheritance resolution:** See ARCHITECTURE.md § Scope-Resolution Pipeline. Shared pipeline code in `gitnexus/src/core/ingestion/` must not name languages — use `LanguageProvider` / `ScopeResolver` hooks instead (see AGENTS.md). (The legacy call-resolution DAG was removed in #942.)
 - **GitNexus:** `.claude/skills/gitnexus/`; MCP and indexed-repo rules live only in [AGENTS.md](AGENTS.md) (`gitnexus:start` … `gitnexus:end`). See **GitNexus rules** below.
 
 ## Changelog
@@ -62,18 +62,18 @@ This project is indexed by GitNexus as **GitNexus** (26675 symbols, 35395 relati
 
 ## Always Do
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
 - **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+- When exploring unfamiliar code, use `query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `context({name: "symbolName"})`.
 
 ## Never Do
 
-- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER edit a function, class, or method without first running `impact` on it.
 - NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
-- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+- NEVER rename symbols with find-and-replace — use `rename` which understands the call graph.
+- NEVER commit changes without running `detect_changes()` to check affected scope.
 
 ## Resources
 

CONTRIBUTING.md

@@ -13,6 +13,8 @@ This project uses the [PolyForm Noncommercial License 1.0.0](https://polyformpro
 
 ## Development setup
 
+**Prerequisites:** Node.js — `gitnexus/` requires `>=22.0.0` and `gitnexus-web/` requires `^20.19.0 || >=22.12.0` (enforced via the `engines` field in each package). Use `nvm install` to match the local version.
+
 1. Clone the repository.
 2. **CLI / MCP package:** `cd gitnexus && npm install && npm run build`
 3. **Web UI (if needed):** `cd gitnexus-web && npm install`

README.md

@@ -22,6 +22,9 @@
   <a href="https://securityscorecards.dev/viewer/?uri=github.com/abhigyanpatwari/GitNexus">
     <img src="https://api.securityscorecards.dev/projects/github.com/abhigyanpatwari/GitNexus/badge" alt="OpenSSF Scorecard"/>
   </a>
+  <a href="https://github.com/abhigyanpatwari/GitNexus/actions/workflows/ci.yml">
+    <img src="https://github.com/abhigyanpatwari/GitNexus/actions/workflows/ci.yml/badge.svg" alt="CI Workflows"/>
+  </a>
 
   <p><strong>Enterprise (SaaS & Self-hosted)</strong> - <a href="https://akonlabs.com">akonlabs.com</a></p>
 
@@ -226,12 +229,14 @@ gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS
 gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
 gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
 gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
+gitnexus analyze --skip-skills     # Skip installing .claude/skills/gitnexus/ skill files
+gitnexus analyze --default-branch develop  # Branch used in the generated regression-compare example (base_ref)
 gitnexus analyze --skip-git        # Index folders that are not Git repositories
 gitnexus analyze --embeddings [limit]  # Enable embedding generation (slower, better search)
 gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
 gitnexus analyze --worker-timeout 60  # Increase worker idle timeout for slow parses
 gitnexus analyze --wal-checkpoint-threshold 67108864  # 64 MiB. Control LadybugDB WAL auto-checkpoint threshold (default: 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)
-gitnexus analyze --workers <n>        # Parse worker pool size (default: cores-1, capped at 16; 0 = sequential)
+gitnexus analyze --workers <n>        # Parse worker pool size (>=1; default: cores-1, capped at 16, auto-sized to the repo). 0 is rejected — there is no sequential mode.
 gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
 gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
 gitnexus list                    # List all indexed repositories
@@ -273,13 +278,43 @@ gitnexus analyze --embeddings 100000
 
 If embeddings are skipped on a large repository, the indexed graph likely exceeds the default safety cap. Re-run with `gitnexus analyze --embeddings 0` to remove the cap, or `gitnexus analyze --embeddings <n>` to choose a higher limit while still keeping memory bounded.
 
+#### Project config (`.gitnexusrc`)
+
+Commit a `.gitnexusrc` JSON file at the repo root to preconfigure recurring `analyze` options per project, instead of re-passing the same flags every run. It is read from the resolved repo root (not `.gitnexus/`, which is gitignored index storage). **CLI flags always override `.gitnexusrc`.**
+
+```jsonc
+{
+  // Default branch used in the generated regression-compare example (base_ref).
+  // Use this so a project on `develop`/`master` doesn't get "main" rewritten
+  // over its fix on every analyze. (Alias: "branch".)
+  "defaultBranch": "develop",
+  "skipContextFiles": true, // alias of skipAgentsMd: keep your own AGENTS.md/CLAUDE.md
+  "skipSkills": true, // don't install .claude/skills/gitnexus/
+  "embeddings": true, // generate embeddings by default
+  "workerTimeout": 60
+}
+```
+
+A nested `analyze` block is also accepted (and overrides flat keys for the same option):
+
+```json
+{ "analyze": { "defaultBranch": "develop", "skipSkills": true } }
+```
+
+Notes:
+
+- The default branch is resolved as: `--default-branch` > `.gitnexusrc` `defaultBranch`/`branch` > auto-detected `origin/HEAD` > `main`.
+- `skipContextFiles` / `skipAiContext` are aliases for `skipAgentsMd` — they skip the `AGENTS.md` / `CLAUDE.md` block only. They do **not** imply `skipSkills`. `indexOnly` is the stronger option that skips all file injection.
+- Supported keys: `defaultBranch` (`branch`), `skipAgentsMd` (`skipContextFiles`, `skipAiContext`), `skipSkills`, `indexOnly`, `stats`/`noStats`, `embeddings`, `dropEmbeddings`, `name`, `allowDuplicateName`, `maxFileSize`, `workerTimeout`, `walCheckpointThreshold`, `workers`, `embeddingThreads`, `embeddingBatchSize`, `embeddingSubBatchSize`, `embeddingDevice`.
+- The file is JSON only. Unknown keys and invalid values fail fast with an actionable error before analysis starts.
+
 #### Environment variables
 
 Most `analyze` knobs are also CLI flags (`--workers`, `--worker-timeout`, `--max-file-size`, `--verbose`). Use the env-var form when you'd otherwise repeat the same flag every run, or when invoking GitNexus from a long-running host (MCP server, eval-server, CI shell) that already manages its own environment. CLI flags take precedence over env vars; env vars take precedence over built-in defaults.
 
 | Variable                               | Default                   | Effect                                                                                                                                                     | Tune when…                                                                                                                                  |
 | -------------------------------------- | ------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------- |
-| `GITNEXUS_WORKER_POOL_SIZE`            | `cores - 1`, capped at 16 | Parse worker pool size. `0` disables the pool (sequential fallback). Equivalent to `--workers <n>`.                                                        | Constrained containers (cgroup CPU limits), CI runners with explicit quotas, or debugging a worker-only crash via `0`.                      |
+| `GITNEXUS_WORKER_POOL_SIZE`            | `cores - 1`, capped at 16 | Parse worker pool size (must be ≥ 1). Equivalent to `--workers <n>`. The worker pool is the sole parse path — there is no sequential parser, so `0` is rejected with an actionable error (the pool self-heals via quarantine + respawn). | Constrained containers (cgroup CPU limits) or CI runners with explicit quotas. To narrow down a worker crash set `1` for a single-worker pool — not `0`. |
 | `GITNEXUS_PARSE_CHUNK_CONCURRENCY`     | `2`                       | Number of chunks whose file contents may be read into memory in parallel while the pool dispatches the current chunk. Worker dispatch itself stays serial. | Repos large enough to chunk (multi-MB total source) where disk I/O is a measurable fraction of analyze wall-clock.                          |
 | `GITNEXUS_VERBOSE`                     | unset                     | When `1`, enables verbose ingestion logs (skipped-file warnings, per-chunk throughput, parse-cache stats). Equivalent to `--verbose`.                      | Debugging an analyze that "completed" but seems to have missed files; tuning `--workers` / chunk concurrency against observable throughput. |
 | `GITNEXUS_PROFILE_DEFERRED`            | unset                     | When `1`, emits `[deferred-profile]` timing/progress logs for the post-chunk deferred resolution band (imports → heritage → buildHeritageMap → legacy call resolution). Implied by `GITNEXUS_VERBOSE`. | Diagnosing analyze stalls in "Resolving calls (all chunks)" on large Java/Kotlin repos (issue #1741) without the full verbose ingestion noise. |

TESTING.md

@@ -4,11 +4,11 @@ How we structure tests and which commands to run locally and in CI.
 
 ## Packages
 
-| Package        | Path           | Runner   | Notes                          |
-| -------------- | -------------- | -------- | ------------------------------ |
-| CLI + MCP core | `gitnexus/`    | Vitest   | Primary test surface in CI     |
-| Web UI         | `gitnexus-web/`| Vitest   | Unit/component tests           |
-| Web UI E2E     | `gitnexus-web/`| Playwright | Run when changing UI flows   |
+| Package        | Path            | Runner     | Notes                      |
+| -------------- | --------------- | ---------- | -------------------------- |
+| CLI + MCP core | `gitnexus/`     | Vitest     | Primary test surface in CI |
+| Web UI         | `gitnexus-web/` | Vitest     | Unit/component tests       |
+| Web UI E2E     | `gitnexus-web/` | Playwright | Run when changing UI flows |
 
 ## Test lanes
 
@@ -16,25 +16,25 @@ How we structure tests and which commands to run locally and in CI.
 
 From `gitnexus/`:
 
-| Command                  | What it runs                                         | When to use                     |
-| ------------------------ | ---------------------------------------------------- | ------------------------------- |
-| `npm test`               | Full suite (all 3 vitest projects)                   | Before opening a PR             |
-| `npm run test:unit`      | Unit tests only (`test/unit/`)                       | Tight development loop          |
-| `npm run test:integration` | Integration tests (`test/integration/`)            | After changing pipelines, DB, workers |
-| `npm run test:coverage`  | Full suite + v8 coverage with thresholds             | Checking coverage impact        |
-| `npm run test:parity`    | Scope-resolution parity for all migrated languages   | After changing resolver or scope code |
-| `npm run test:cross-platform` | Platform-sensitive subset only                  | Debugging a Windows/macOS issue |
-| `npm run test:watch`     | Vitest in watch mode                                 | Active development              |
+| Command                       | What it runs                                       | When to use                           |
+| ----------------------------- | -------------------------------------------------- | ------------------------------------- |
+| `npm test`                    | Full suite (all 3 vitest projects)                 | Before opening a PR                   |
+| `npm run test:unit`           | Unit tests only (`test/unit/`)                     | Tight development loop                |
+| `npm run test:integration`    | Integration tests (`test/integration/`)            | After changing pipelines, DB, workers |
+| `npm run test:coverage`       | Full suite + v8 coverage with thresholds           | Checking coverage impact              |
+| `npm run test:parity`         | Scope-resolution parity for all migrated languages | After changing resolver or scope code |
+| `npm run test:cross-platform` | Platform-sensitive subset only                     | Debugging a Windows/macOS issue       |
+| `npm run test:watch`          | Vitest in watch mode                               | Active development                    |
 
 ### `gitnexus-web/` commands
 
 From `gitnexus-web/`:
 
-| Command               | What it runs                      | When to use                    |
-| ---------------------- | --------------------------------- | ------------------------------ |
-| `npm test`             | Unit/component tests (vitest)     | After changing web code        |
-| `npm run test:coverage`| Unit tests + coverage             | Checking coverage impact       |
-| `npm run test:e2e`     | Playwright browser tests          | After changing UI flows (requires `gitnexus serve` + `npm run dev`) |
+| Command                 | What it runs                  | When to use                                                         |
+| ----------------------- | ----------------------------- | ------------------------------------------------------------------- |
+| `npm test`              | Unit/component tests (vitest) | After changing web code                                             |
+| `npm run test:coverage` | Unit tests + coverage         | Checking coverage impact                                            |
+| `npm run test:e2e`      | Playwright browser tests      | After changing UI flows (requires `gitnexus serve` + `npm run dev`) |
 
 ### Before opening a PR
 
@@ -59,11 +59,11 @@ Skip with `git commit --no-verify` (use sparingly).
 
 `gitnexus/vitest.config.ts` defines three projects for safety isolation:
 
-| Project    | Files                         | Parallelism | Purpose                                       |
-| ---------- | ----------------------------- | ----------- | ---------------------------------------------- |
-| `lbug-db`  | Native LadybugDB integration tests (explicit list) | Sequential  | Prevents file-lock conflicts from native mmap addon |
-| `cli-e2e`  | `skills-e2e.test.ts`          | Sequential  | CLI process spawning requires serial execution |
-| `default`  | Everything else               | Parallel    | Fast execution for pure logic and parser tests |
+| Project   | Files                                              | Parallelism | Purpose                                             |
+| --------- | -------------------------------------------------- | ----------- | --------------------------------------------------- |
+| `lbug-db` | Native LadybugDB integration tests (explicit list) | Sequential  | Prevents file-lock conflicts from native mmap addon |
+| `cli-e2e` | `skills-e2e.test.ts`                               | Sequential  | CLI process spawning requires serial execution      |
+| `default` | Everything else                                    | Parallel    | Fast execution for pure logic and parser tests      |
 
 When adding a new test that uses native LadybugDB (`@ladybugdb/core`), add it to the `lbug-db` project's explicit include list and the `default` project's exclude list.
 
@@ -74,21 +74,11 @@ When adding a new test that uses native LadybugDB (`@ladybugdb/core`), add it to
 - **Resolver / parity** — Language-specific call-resolution tests in `test/integration/resolvers/`.
 - **E2E (web)** — Critical user paths only; prefer `data-testid` attributes for stable selectors. Tests run against real backend (`gitnexus serve`) and Vite dev server.
 
-## Scope-resolution parity
+## Scope-resolution tests
 
-Migrated languages (listed in `MIGRATED_LANGUAGES` in `src/core/ingestion/registry-primary-flag.ts`) are tested in both legacy and registry-primary modes on every PR.
+Every language resolves calls and inheritance through the scope-resolution pipeline — the legacy call-resolution DAG and the per-language `REGISTRY_PRIMARY_<LANG>` flag were removed in RING4-1 (#942). Each language's resolver test lives at `test/integration/resolvers/<slug>.test.ts` and runs once, on the single scope-resolution path, as part of the normal `tests` job (`vitest test/**/*.test.ts`).
 
-For each migrated language, CI runs the resolver test file twice:
-1. `REGISTRY_PRIMARY_<LANG>=0` — legacy DAG path
-2. `REGISTRY_PRIMARY_<LANG>=1` — registry-primary path
-
-Both must pass. Known legacy gaps are listed in `LEGACY_RESOLVER_PARITY_EXPECTED_FAILURES` in `test/integration/resolvers/helpers.ts` and are automatically skipped in legacy mode.
-
-Adding a language to `MIGRATED_LANGUAGES` automatically enrolls it in parity — no workflow or config edit needed. The test file must exist at `test/integration/resolvers/<slug>.test.ts`.
-
-Run parity locally: `cd gitnexus && npm run test:parity`
-
-Run for a single language: `cd gitnexus && npx tsx scripts/run-parity.ts --language python`
+Adding a language: register its `ScopeResolver` in `scope-resolution/pipeline/registry.ts` (`SCOPE_RESOLVERS`) and add the resolver test file — no workflow or config edit needed.
 
 ## Cross-platform testing
 
@@ -120,12 +110,12 @@ To check the cross-platform list is up to date, run `npm run test:cross-platform
 
 GitHub Actions (`.github/workflows/ci.yml`) orchestrate:
 
-| Workflow              | Jobs                           | Purpose                                         |
-| --------------------- | ------------------------------ | ------------------------------------------------ |
-| `ci-quality.yml`      | format, lint, typecheck, typecheck-web, workflow-convention | Code quality gates |
+| Workflow              | Jobs                                                              | Purpose                                                               |
+| --------------------- | ----------------------------------------------------------------- | --------------------------------------------------------------------- |
+| `ci-quality.yml`      | format, lint, typecheck, typecheck-web, workflow-convention       | Code quality gates                                                    |
 | `ci-tests.yml`        | ubuntu/coverage, cross-platform (Win/Mac), packaged-install-smoke | Full suite + coverage on Ubuntu; platform-sensitive subset on Win/Mac |
-| `ci-scope-parity.yml` | discover, parity               | Scope-resolution parity for all migrated languages |
-| `ci-e2e.yml`          | e2e (chromium)                 | Playwright E2E, gated on `gitnexus-web/**` changes |
+| `ci-scope-parity.yml` | discover, parity                                                  | Scope-resolution parity for all migrated languages                    |
+| `ci-e2e.yml`          | e2e (chromium)                                                    | Playwright E2E, gated on `gitnexus-web/**` changes                    |
 
 The `CI Gate` job in `ci.yml` is the single required check for branch protection. It requires quality, tests, e2e, and scope-parity to all pass.
 

eval/uv.lock

@@ -21,7 +21,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.4"
+version = "3.14.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -30,95 +30,111 @@ dependencies = [
     { name = "frozenlist" },
     { name = "multidict" },
     { name = "propcache" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
     { name = "yarl" },
 ]
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+    { url = "https://files.pythonhosted.org/packages/9c/ae/3839726cd49150a53ed340cc24ce5ba09d4c2117020ef9d45542bec5eb2f/aiohttp-3.14.0-cp314-cp314t-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:49a33ded29b0b2fa7a367a02cf0fb89af602bb87542a16177ec8ce1c9c51d12a", size = 1665437, upload-time = "2026-06-01T19:40:35.01Z" },
+    { url = "https://files.pythonhosted.org/packages/35/1e/c237923232c7da7f0392ea25d89fc5e60c0e93f685f4ebca8e7bcdd5271c/aiohttp-3.14.0-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:2cc736a9c9fc2bc4dd71fd404815741b6573df27c3f985948ec4076989ac57de", size = 1834090, upload-time = "2026-06-01T19:40:37.733Z" },
+    { url = "https://files.pythonhosted.org/packages/98/02/a5a7a2524f92d3911761b405a7c067c751891942144adc13e2ad79611e39/aiohttp-3.14.0-cp314-cp314t-musllinux_1_2_armv7l.whl", hash = "sha256:b4141a3e5342ee3053a9cab54d25b64ed28289c1041e4c54b3d99839314d90ce", size = 1816907, upload-time = "2026-06-01T19:40:40.46Z" },
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+    { url = "https://files.pythonhosted.org/packages/c9/8e/140e715a0a4bbc211979ea30ec8396ad2ed5bf90ab87d8058fc4668b1923/aiohttp-3.14.0-cp314-cp314t-musllinux_1_2_riscv64.whl", hash = "sha256:667b881d083ccae3900ea5a241e17e5007ca78844c53ed389bb63d48f729d9c7", size = 1659497, upload-time = "2026-06-01T19:40:46.265Z" },
+    { url = "https://files.pythonhosted.org/packages/10/c7/7ba5de8af9650b9767b063c675427b8685f43fa7ce563673a7bc3af60f08/aiohttp-3.14.0-cp314-cp314t-musllinux_1_2_s390x.whl", hash = "sha256:b584dfe615d151e9b8f0a8ecb3aee6147f2927ec5b95ba25fe621f5377510928", size = 1870829, upload-time = "2026-06-01T19:40:49.583Z" },
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+    { url = "https://files.pythonhosted.org/packages/39/98/31b9ad9fbc01f0075ee7221002df5fd2d10b647f451ca5f30edc802d9dd6/aiohttp-3.14.0-cp314-cp314t-win32.whl", hash = "sha256:a8d93334d4961c9d566b1f046c81dee475b7c21eb730728d38237bfa70d1c8e6", size = 490597, upload-time = "2026-06-01T19:40:54.937Z" },
+    { url = "https://files.pythonhosted.org/packages/59/1f/299b21441c8de42ff70fddc7cfe65e92f810abcf740739a09b56f7835364/aiohttp-3.14.0-cp314-cp314t-win_amd64.whl", hash = "sha256:2d2ffe9b614f50f069068b3b52e73414e4107fc10b7efc939a76acff9251fdd2", size = 525789, upload-time = "2026-06-01T19:40:57.306Z" },
+    { url = "https://files.pythonhosted.org/packages/70/11/7f83fcba9ee05d4c54d61b3f8104da0d43a59adac44dd28effc0c9a10422/aiohttp-3.14.0-cp314-cp314t-win_arm64.whl", hash = "sha256:7a3fc4358e65826c515350f199c210de747cf669998211b1ee6c2e46de364b24", size = 467399, upload-time = "2026-06-01T19:40:59.993Z" },
 ]
 
 [[package]]
@@ -926,7 +942,7 @@ wheels = [
 
 [[package]]
 name = "litellm"
-version = "1.83.14"
+version = "1.87.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohttp" },
@@ -942,9 +958,9 @@ dependencies = [
     { name = "tiktoken" },
     { name = "tokenizers" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/8d/7c/c095649380adc96c8630273c1768c2ad1e74aa2ee1dd8dd05d218a60569f/litellm-1.83.14.tar.gz", hash = "sha256:24aef9b47cdc424c833e32f3727f411741c690832cd1fe4405e0077144fe09c9", size = 14836599, upload-time = "2026-04-26T03:16:10.176Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/77/0d/ccdf682ccfd7f18bf0e179c39d85616b8f8ef05a798588285310412db13d/litellm-1.87.0.tar.gz", hash = "sha256:cafc1882cb0cbab8374c41180af86e4a067796e4524e15f59e99f6e689cd1bd8", size = 15453755, upload-time = "2026-06-02T03:53:29.076Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/7f/5c/1b5691575420135e90578543b2bf219497caa33cfd0af64cb38f30288450/litellm-1.83.14-py3-none-any.whl", hash = "sha256:92b11ba2a32cf80707ddf388d18526696c7999a21b418c5e3b6eda1243d2cfdb", size = 16457054, upload-time = "2026-04-26T03:16:05.72Z" },
+    { url = "https://files.pythonhosted.org/packages/98/20/88a372fa7e50fc2c33458c6eef94a79afcf7bdfa43610079531b82b484a3/litellm-1.87.0-py3-none-any.whl", hash = "sha256:fbbba7e47ae29b55f878fe1acc80effb92761bc168f6236bd81a0cb6e147d855", size = 17103948, upload-time = "2026-06-02T03:53:25.677Z" },
 ]
 
 [[package]]

gitnexus-claude-plugin/hooks/resolve-analyze-cmd.cjs

@@ -27,6 +27,8 @@
  */
 
 const { execFileSync } = require('child_process');
+const fs = require('fs');
+const path = require('path');
 
 const NPX_REF = 'gitnexus@latest';
 
@@ -34,46 +36,72 @@ const NPX_REF = 'gitnexus@latest';
 const PNPM_ALLOW_BUILD_BASE = ['@ladybugdb/core', 'gitnexus', 'tree-sitter'];
 const PNPM_ALLOW_BUILD_EMBEDDINGS = ['onnxruntime-node'];
 
-// Probe timeout, kept under Claude Code's 10s hook budget. In a linked worktree
-// the stale-index hook first runs `git rev-parse --git-common-dir` (~2s) and
-// `git rev-parse HEAD` (~3s); the pnpm path then adds up to four 1s probes
-// (which gitnexus, npm --version, which pnpm, pnpm --version), so the worst case
-// is ~9s — within budget but tight. A healthy `which`/`where`/`--version`
-// returns in well under a second, so the realistic cost is far lower.
+// Version-probe timeout, kept under Claude Code's 10s hook budget. PATH presence
+// detection is now spawn-free (resolveOnPath scans PATH directly), so the only
+// subprocesses left are the version probes: in a linked worktree the stale-index
+// hook first runs `git rev-parse --git-common-dir` (~2s) and `git rev-parse HEAD`
+// (~3s); the pnpm path then adds up to two 1s `--version` probes (npm, pnpm), so
+// the worst case is ~7s — within budget. A healthy `--version` returns in well
+// under a second, so the realistic cost is far lower.
 const PROBE_TIMEOUT_MS = 1000;
 
 /**
- * Pick the best match from `where`/`which` output. A global `gitnexus` may be a
- * `.cmd`/`.bat` (npm), a `.exe`, or an extensionless shim (Volta, scoop), so on
- * Windows we prefer a recognized executable extension but accept any hit — the
- * emitted hint is `gitnexus analyze` regardless of which shim resolves it. Pure
- * and exported so the shim-matching can be unit-tested without spawning.
+ * Absolute path to `command` on PATH, or null — a pure-Node, spawn-free lookup
+ * that mirrors how a shell resolves a bare command name: each PATH dir × the
+ * platform's executable extensions (PATHEXT on Windows; the bare name + X_OK on
+ * POSIX). This replaces the former `where`/`which` subprocess (#1938 "Option A"):
+ * it is byte-for-byte identical on every OS, with no dependency on the probe
+ * binary being reachable (a sanitized PATH that drops System32 / `/usr/bin` no
+ * longer defeats detection), no shell-spawn surface (CVE-2024-27980), and no
+ * spawn timeout to tune. On Windows it matches PATHEXT extensions ONLY — exactly
+ * what `where`/cmd.exe resolve — so neither an un-spawnable `.ps1`-only shim (not
+ * in default PATHEXT) nor a bare extensionless file (which the shell cannot launch
+ * as `command`) is a false positive. `preferExecExt` returns a recognized
+ * `.cmd`/`.bat`/`.exe` shim ahead of an exotic PATHEXT hit (e.g. `.COM`) when both
+ * match, matching what a user would actually launch. Pure (platform/env injectable)
+ * so it is unit-testable without touching the host PATH.
  */
-function pickPathMatch(output, { isWin, gitnexusWrapper } = {}) {
-  const lines = output
-    .split('\n')
-    .map((l) => l.trim())
-    .filter(Boolean);
-  if (isWin && gitnexusWrapper) {
-    return lines.find((l) => /\.(cmd|bat|exe)$/i.test(l)) || lines[0] || null;
-  }
-  return lines[0] || null;
-}
-
-/** Absolute path to `command` on PATH, or null. `gitnexusWrapper` enables the Windows shim match. */
-function resolveOnPath(command, gitnexusWrapper = false) {
-  const isWin = process.platform === 'win32';
-  try {
-    const output = execFileSync(isWin ? 'where' : 'which', [command], {
-      encoding: 'utf-8',
-      timeout: PROBE_TIMEOUT_MS,
-      stdio: ['ignore', 'pipe', 'ignore'],
-      windowsHide: true,
-    });
-    return pickPathMatch(output, { isWin, gitnexusWrapper });
-  } catch {
-    return null;
+function resolveOnPath(
+  command,
+  preferExecExt = false,
+  { platform = process.platform, env = process.env } = {},
+) {
+  const pathValue = env.PATH || env.Path || env.path || '';
+  if (!pathValue) return null;
+  const isWin = platform === 'win32';
+  const exts = isWin
+    ? (env.PATHEXT || '.COM;.EXE;.BAT;.CMD')
+        .split(';')
+        .map((e) => e.trim())
+        .filter(Boolean)
+        .map((e) => (e.startsWith('.') ? e : `.${e}`))
+    : [''];
+  let weakHit = null;
+  // Split on the host's PATH delimiter. `platform` is injected only to choose the
+  // extension/exec-bit rules; the PATH string is always host-format, so it must
+  // split on the host delimiter (`path.delimiter`) — in production `platform` IS
+  // the host, so they coincide. (Deriving the delimiter from an injected platform
+  // would split a Windows drive-letter path `C:\…` at its colon under a POSIX
+  // injection.)
+  for (const dir of pathValue.split(path.delimiter).filter(Boolean)) {
+    for (const ext of exts) {
+      const candidate = path.join(dir, `${command}${ext}`);
+      try {
+        if (!fs.statSync(candidate).isFile()) continue;
+        if (!isWin) fs.accessSync(candidate, fs.constants.X_OK);
+        // Prefer a runnable .cmd/.bat/.exe shim; remember an exotic PATHEXT hit
+        // (e.g. .COM) only as a last resort if nothing better turns up.
+        if (isWin && preferExecExt && !/\.(cmd|bat|exe)$/i.test(ext)) {
+          weakHit = weakHit || candidate;
+          continue;
+        }
+        return candidate;
+      } catch {
+        /* not a runnable file here — try the next candidate */
+      }
+    }
   }
+  return weakHit;
 }
 
 // One spawn of `<command> --version` → { major, minor } (each null when
@@ -193,12 +221,12 @@ function formatPnpmDlxCommand(gitnexusArgs, options = {}, deps = {}) {
 function formatAnalyzeCommand(options = {}, deps = {}) {
   const suffix = options.embeddings ? ' --embeddings' : '';
   // Keep the stale-index hook budget tight by querying each tool at most once.
-  // A memoized PATH probe is shared with resolveInvocationMode (so `gitnexus`
-  // isn't probed twice), and pnpm's version is captured by a single
-  // `pnpm --version` that proves both presence (for mode resolution) and
-  // version (for the allow-build gate) — replacing the former `which pnpm` +
-  // `pnpm --version` double spawn. Injected deps (tests) and forced/global
-  // modes skip the pnpm probe.
+  // The memoized `probe` is a spawn-free PATH scan (resolveOnPath) shared with
+  // resolveInvocationMode, so `gitnexus` is scanned only once and no subprocess
+  // is spawned for presence. pnpm's *version* is still captured by a single
+  // `pnpm --version` (the allow-build gate needs the number), which also proves
+  // presence; the memoized scan only re-checks pnpm when that version is
+  // unreadable. Injected deps (tests) and forced/global modes skip the pnpm probe.
   const cache = new Map();
   const probe = (command, gitnexusWrapper) => {
     const key = `${command}:${gitnexusWrapper ? 1 : 0}`;
@@ -256,7 +284,7 @@ module.exports = {
   formatPnpmDlxCommand,
   resolveInvocationMode,
   buildRunnerArgv,
-  pickPathMatch,
+  resolveOnPath,
   getNpmMajorVersion,
   NPX_REF,
   PNPM_ALLOW_BUILD_BASE,

gitnexus-claude-plugin/skills/gitnexus-debugging/SKILL.md

@@ -16,10 +16,10 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 ## Workflow
 
 ```
-1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
-2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
+1. query({query: "<error or symptom>"})            → Find related execution flows
+2. context({name: "<suspect>"})                    → See callers/callees/processes
 3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
-4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
+4. cypher({query: "MATCH path..."})                 → Custom traces if needed
 ```
 
 > If "Index is stale" → run `node .gitnexus/run.cjs analyze` in terminal.
@@ -28,11 +28,11 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ```
 - [ ] Understand the symptom (error message, unexpected behavior)
-- [ ] gitnexus_query for error text or related code
+- [ ] query for error text or related code
 - [ ] Identify the suspect function from returned processes
-- [ ] gitnexus_context to see callers and callees
+- [ ] context to see callers and callees
 - [ ] Trace execution flow via process resource if applicable
-- [ ] gitnexus_cypher for custom call chain traces if needed
+- [ ] cypher for custom call chain traces if needed
 - [ ] Read source files to confirm root cause
 ```
 
@@ -40,7 +40,7 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 | Symptom              | GitNexus Approach                                          |
 | -------------------- | ---------------------------------------------------------- |
-| Error message        | `gitnexus_query` for error text → `context` on throw sites |
+| Error message        | `query` for error text → `context` on throw sites |
 | Wrong return value   | `context` on the function → trace callees for data flow    |
 | Intermittent failure | `context` → look for external calls, async deps            |
 | Performance issue    | `context` → find symbols with many callers (hot paths)     |
@@ -48,24 +48,24 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ## Tools
 
-**gitnexus_query** — find code related to error:
+**query** — find code related to error:
 
 ```
-gitnexus_query({query: "payment validation error"})
+query({query: "payment validation error"})
 → Processes: CheckoutFlow, ErrorHandling
 → Symbols: validatePayment, handlePaymentError, PaymentException
 ```
 
-**gitnexus_context** — full context for a suspect:
+**context** — full context for a suspect:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates (external API!)
 → Processes: CheckoutFlow (step 3/7)
 ```
 
-**gitnexus_cypher** — custom call chain traces:
+**cypher** — custom call chain traces:
 
 ```cypher
 MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
@@ -75,11 +75,11 @@ RETURN [n IN nodes(path) | n.name] AS chain
 ## Example: "Payment endpoint returns 500 intermittently"
 
 ```
-1. gitnexus_query({query: "payment error handling"})
+1. query({query: "payment error handling"})
    → Processes: CheckoutFlow, ErrorHandling
    → Symbols: validatePayment, handlePaymentError
 
-2. gitnexus_context({name: "validatePayment"})
+2. context({name: "validatePayment"})
    → Outgoing calls: verifyCard, fetchRates (external API!)
 
 3. READ gitnexus://repo/my-app/process/CheckoutFlow

gitnexus-claude-plugin/skills/gitnexus-exploring/SKILL.md

@@ -18,8 +18,8 @@ description: "Use when the user asks how code works, wants to understand archite
 ```
 1. READ gitnexus://repos                          → Discover indexed repos
 2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
-3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
-4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
+3. query({query: "<what you want to understand>"})  → Find related execution flows
+4. context({name: "<symbol>"})            → Deep dive on specific symbol
 5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
 ```
 
@@ -29,9 +29,9 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ```
 - [ ] READ gitnexus://repo/{name}/context
-- [ ] gitnexus_query for the concept you want to understand
+- [ ] query for the concept you want to understand
 - [ ] Review returned processes (execution flows)
-- [ ] gitnexus_context on key symbols for callers/callees
+- [ ] context on key symbols for callers/callees
 - [ ] READ process resource for full execution traces
 - [ ] Read source files for implementation details
 ```
@@ -47,18 +47,18 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ## Tools
 
-**gitnexus_query** — find execution flows related to a concept:
+**query** — find execution flows related to a concept:
 
 ```
-gitnexus_query({query: "payment processing"})
+query({query: "payment processing"})
 → Processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Symbols grouped by flow with file locations
 ```
 
-**gitnexus_context** — 360-degree view of a symbol:
+**context** — 360-degree view of a symbol:
 
 ```
-gitnexus_context({name: "validateUser"})
+context({name: "validateUser"})
 → Incoming calls: loginHandler, apiMiddleware
 → Outgoing calls: checkToken, getUserById
 → Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
@@ -68,10 +68,10 @@ gitnexus_context({name: "validateUser"})
 
 ```
 1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
-2. gitnexus_query({query: "payment processing"})
+2. query({query: "payment processing"})
    → CheckoutFlow: processPayment → validateCard → chargeStripe
    → RefundFlow: initiateRefund → calculateRefund → processRefund
-3. gitnexus_context({name: "processPayment"})
+3. context({name: "processPayment"})
    → Incoming: checkoutHandler, webhookHandler
    → Outgoing: validateCard, chargeStripe, saveTransaction
 4. Read src/payments/processor.ts for implementation details

gitnexus-claude-plugin/skills/gitnexus-impact-analysis/SKILL.md

@@ -17,9 +17,9 @@ description: "Use when the user wants to know what will break if they change som
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
+1. impact({target: "X", direction: "upstream"})  → What depends on this
 2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
-3. gitnexus_detect_changes()                               → Map current git changes to affected flows
+3. detect_changes()                               → Map current git changes to affected flows
 4. Assess risk and report to user
 ```
 
@@ -28,11 +28,11 @@ description: "Use when the user wants to know what will break if they change som
 ## Checklist
 
 ```
-- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
+- [ ] impact({target, direction: "upstream"}) to find dependents
 - [ ] Review d=1 items first (these WILL BREAK)
 - [ ] Check high-confidence (>0.8) dependencies
 - [ ] READ processes to check affected execution flows
-- [ ] gitnexus_detect_changes() for pre-commit check
+- [ ] detect_changes() for pre-commit check
 - [ ] Assess risk level and report to user
 ```
 
@@ -55,10 +55,10 @@ description: "Use when the user wants to know what will break if they change som
 
 ## Tools
 
-**gitnexus_impact** — the primary tool for symbol blast radius:
+**impact** — the primary tool for symbol blast radius:
 
 ```
-gitnexus_impact({
+impact({
   target: "validateUser",
   direction: "upstream",
   minConfidence: 0.8,
@@ -73,10 +73,10 @@ gitnexus_impact({
   - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_detect_changes** — git-diff based impact analysis:
+**detect_changes** — git-diff based impact analysis:
 
 ```
-gitnexus_detect_changes({scope: "staged"})
+detect_changes({scope: "staged"})
 
 → Changed: 5 symbols in 3 files
 → Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
@@ -86,7 +86,7 @@ gitnexus_detect_changes({scope: "staged"})
 ## Example: "What breaks if I change validateUser?"
 
 ```
-1. gitnexus_impact({target: "validateUser", direction: "upstream"})
+1. impact({target: "validateUser", direction: "upstream"})
    → d=1: loginHandler, apiMiddleware (WILL BREAK)
    → d=2: authRouter, sessionManager (LIKELY AFFECTED)
 

gitnexus-claude-plugin/skills/gitnexus-pr-review/SKILL.md

@@ -18,10 +18,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 1. gh pr diff <number>                                    → Get the raw diff
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+2. detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
 3. For each changed symbol:
-   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
-4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+   impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. context({name: "<key symbol>"})               → Understand callers/callees
 5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
 6. Summarize findings with risk assessment
 ```
@@ -32,10 +32,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 - [ ] Fetch PR diff (gh pr diff or git diff base...head)
-- [ ] gitnexus_detect_changes to map changes to affected execution flows
-- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] detect_changes to map changes to affected execution flows
+- [ ] impact on each non-trivial changed symbol
 - [ ] Review d=1 items (WILL BREAK) — are callers updated?
-- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] context on key changed symbols to understand full picture
 - [ ] Check if affected processes have test coverage
 - [ ] Assess overall risk level
 - [ ] Write review summary with findings
@@ -63,20 +63,20 @@ description: "Use when the user wants to review a pull request, understand what
 
 ## Tools
 
-**gitnexus_detect_changes** — map PR diff to affected execution flows:
+**detect_changes** — map PR diff to affected execution flows:
 
 ```
-gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+detect_changes({scope: "compare", base_ref: "main"})
 
 → Changed: 8 symbols in 4 files
 → Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Risk: MEDIUM
 ```
 
-**gitnexus_impact** — blast radius per changed symbol:
+**impact** — blast radius per changed symbol:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream"})
+impact({target: "validatePayment", direction: "upstream"})
 
 → d=1 (WILL BREAK):
   - processCheckout (src/checkout.ts:42) [CALLS, 100%]
@@ -86,20 +86,20 @@ gitnexus_impact({target: "validatePayment", direction: "upstream"})
   - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_impact with tests** — check test coverage:
+**impact with tests** — check test coverage:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+impact({target: "validatePayment", direction: "upstream", includeTests: true})
 
 → Tests that cover this symbol:
   - validatePayment.test.ts [direct]
   - checkout.integration.test.ts [via processCheckout]
 ```
 
-**gitnexus_context** — understand a changed symbol's role:
+**context** — understand a changed symbol's role:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates
@@ -112,20 +112,20 @@ gitnexus_context({name: "validatePayment"})
 1. gh pr diff 42 > /tmp/pr42.diff
    → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
 
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+2. detect_changes({scope: "compare", base_ref: "main"})
    → Changed symbols: validatePayment, PaymentInput, formatAmount
    → Affected processes: CheckoutFlow, RefundFlow
    → Risk: MEDIUM
 
-3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+3. impact({target: "validatePayment", direction: "upstream"})
    → d=1: processCheckout, webhookHandler (WILL BREAK)
    → webhookHandler is NOT in the PR diff — potential breakage!
 
-4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+4. impact({target: "PaymentInput", direction: "upstream"})
    → d=1: validatePayment (in PR), createPayment (NOT in PR)
    → createPayment uses the old PaymentInput shape — breaking change!
 
-5. gitnexus_context({name: "formatAmount"})
+5. context({name: "formatAmount"})
    → Called by 12 functions — but change is backwards-compatible (added optional param)
 
 6. Review summary:

gitnexus-claude-plugin/skills/gitnexus-refactoring/SKILL.md

@@ -16,9 +16,9 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
-2. gitnexus_query({query: "X"})                            → Find execution flows involving X
-3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
+1. impact({target: "X", direction: "upstream"})  → Map all dependents
+2. query({query: "X"})                            → Find execution flows involving X
+3. context({name: "X"})                           → See all incoming/outgoing refs
 4. Plan update order: interfaces → implementations → callers → tests
 ```
 
@@ -29,65 +29,65 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ### Rename Symbol
 
 ```
-- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
+- [ ] rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
 - [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
-- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
-- [ ] gitnexus_detect_changes() — verify only expected files changed
+- [ ] If satisfied: rename({..., dry_run: false}) — apply edits
+- [ ] detect_changes() — verify only expected files changed
 - [ ] Run tests for affected processes
 ```
 
 ### Extract Module
 
 ```
-- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
-- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
+- [ ] context({name: target}) — see all incoming/outgoing refs
+- [ ] impact({target, direction: "upstream"}) — find all external callers
 - [ ] Define new module interface
 - [ ] Extract code, update imports
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ### Split Function/Service
 
 ```
-- [ ] gitnexus_context({name: target}) — understand all callees
+- [ ] context({name: target}) — understand all callees
 - [ ] Group callees by responsibility
-- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
+- [ ] impact({target, direction: "upstream"}) — map callers to update
 - [ ] Create new functions/services
 - [ ] Update callers
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ## Tools
 
-**gitnexus_rename** — automated multi-file rename:
+**rename** — automated multi-file rename:
 
 ```
-gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
 → 12 edits across 8 files
 → 10 graph edits (high confidence), 2 ast_search edits (review)
 → Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
 ```
 
-**gitnexus_impact** — map all dependents first:
+**impact** — map all dependents first:
 
 ```
-gitnexus_impact({target: "validateUser", direction: "upstream"})
+impact({target: "validateUser", direction: "upstream"})
 → d=1: loginHandler, apiMiddleware, testUtils
 → Affected Processes: LoginFlow, TokenRefresh
 ```
 
-**gitnexus_detect_changes** — verify your changes after refactoring:
+**detect_changes** — verify your changes after refactoring:
 
 ```
-gitnexus_detect_changes({scope: "all"})
+detect_changes({scope: "all"})
 → Changed: 8 files, 12 symbols
 → Affected processes: LoginFlow, TokenRefresh
 → Risk: MEDIUM
 ```
 
-**gitnexus_cypher** — custom reference queries:
+**cypher** — custom reference queries:
 
 ```cypher
 MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
@@ -98,24 +98,24 @@ RETURN caller.name, caller.filePath ORDER BY caller.filePath
 
 | Risk Factor         | Mitigation                                |
 | ------------------- | ----------------------------------------- |
-| Many callers (>5)   | Use gitnexus_rename for automated updates |
+| Many callers (>5)   | Use rename for automated updates |
 | Cross-area refs     | Use detect_changes after to verify scope  |
-| String/dynamic refs | gitnexus_query to find them               |
+| String/dynamic refs | query to find them               |
 | External/public API | Version and deprecate properly            |
 
 ## Example: Rename `validateUser` to `authenticateUser`
 
 ```
-1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+1. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
    → 12 edits: 10 graph (safe), 2 ast_search (review)
    → Files: validator.ts, login.ts, middleware.ts, config.json...
 
 2. Review ast_search edits (config.json: dynamic reference!)
 
-3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
+3. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
    → Applied 12 edits across 8 files
 
-4. gitnexus_detect_changes({scope: "all"})
+4. detect_changes({scope: "all"})
    → Affected: LoginFlow, TokenRefresh
    → Risk: MEDIUM — run tests for these flows
 ```

gitnexus-cursor-integration/skills/gitnexus-debugging/SKILL.md

@@ -15,10 +15,10 @@ description: Trace bugs through call chains using knowledge graph
 ## Workflow
 
 ```
-1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
-2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
+1. query({query: "<error or symptom>"})            → Find related execution flows
+2. context({name: "<suspect>"})                    → See callers/callees/processes
 3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
-4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
+4. cypher({query: "MATCH path..."})                 → Custom traces if needed
 ```
 
 > If "Index is stale" → run `node .gitnexus/run.cjs analyze` in terminal.
@@ -27,11 +27,11 @@ description: Trace bugs through call chains using knowledge graph
 
 ```
 - [ ] Understand the symptom (error message, unexpected behavior)
-- [ ] gitnexus_query for error text or related code
+- [ ] query for error text or related code
 - [ ] Identify the suspect function from returned processes
-- [ ] gitnexus_context to see callers and callees
+- [ ] context to see callers and callees
 - [ ] Trace execution flow via process resource if applicable
-- [ ] gitnexus_cypher for custom call chain traces if needed
+- [ ] cypher for custom call chain traces if needed
 - [ ] Read source files to confirm root cause
 ```
 
@@ -39,7 +39,7 @@ description: Trace bugs through call chains using knowledge graph
 
 | Symptom | GitNexus Approach |
 |---------|-------------------|
-| Error message | `gitnexus_query` for error text → `context` on throw sites |
+| Error message | `query` for error text → `context` on throw sites |
 | Wrong return value | `context` on the function → trace callees for data flow |
 | Intermittent failure | `context` → look for external calls, async deps |
 | Performance issue | `context` → find symbols with many callers (hot paths) |
@@ -47,22 +47,22 @@ description: Trace bugs through call chains using knowledge graph
 
 ## Tools
 
-**gitnexus_query** — find code related to error:
+**query** — find code related to error:
 ```
-gitnexus_query({query: "payment validation error"})
+query({query: "payment validation error"})
 → Processes: CheckoutFlow, ErrorHandling
 → Symbols: validatePayment, handlePaymentError, PaymentException
 ```
 
-**gitnexus_context** — full context for a suspect:
+**context** — full context for a suspect:
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates (external API!)
 → Processes: CheckoutFlow (step 3/7)
 ```
 
-**gitnexus_cypher** — custom call chain traces:
+**cypher** — custom call chain traces:
 ```cypher
 MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
 RETURN [n IN nodes(path) | n.name] AS chain
@@ -71,11 +71,11 @@ RETURN [n IN nodes(path) | n.name] AS chain
 ## Example: "Payment endpoint returns 500 intermittently"
 
 ```
-1. gitnexus_query({query: "payment error handling"})
+1. query({query: "payment error handling"})
    → Processes: CheckoutFlow, ErrorHandling
    → Symbols: validatePayment, handlePaymentError
 
-2. gitnexus_context({name: "validatePayment"})
+2. context({name: "validatePayment"})
    → Outgoing calls: verifyCard, fetchRates (external API!)
 
 3. READ gitnexus://repo/my-app/process/CheckoutFlow

gitnexus-cursor-integration/skills/gitnexus-exploring/SKILL.md

@@ -17,8 +17,8 @@ description: Navigate unfamiliar code using GitNexus knowledge graph
 ```
 1. READ gitnexus://repos                          → Discover indexed repos
 2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
-3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
-4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
+3. query({query: "<what you want to understand>"})  → Find related execution flows
+4. context({name: "<symbol>"})            → Deep dive on specific symbol
 5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
 ```
 
@@ -28,9 +28,9 @@ description: Navigate unfamiliar code using GitNexus knowledge graph
 
 ```
 - [ ] READ gitnexus://repo/{name}/context
-- [ ] gitnexus_query for the concept you want to understand
+- [ ] query for the concept you want to understand
 - [ ] Review returned processes (execution flows)
-- [ ] gitnexus_context on key symbols for callers/callees
+- [ ] context on key symbols for callers/callees
 - [ ] READ process resource for full execution traces
 - [ ] Read source files for implementation details
 ```
@@ -46,16 +46,16 @@ description: Navigate unfamiliar code using GitNexus knowledge graph
 
 ## Tools
 
-**gitnexus_query** — find execution flows related to a concept:
+**query** — find execution flows related to a concept:
 ```
-gitnexus_query({query: "payment processing"})
+query({query: "payment processing"})
 → Processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Symbols grouped by flow with file locations
 ```
 
-**gitnexus_context** — 360-degree view of a symbol:
+**context** — 360-degree view of a symbol:
 ```
-gitnexus_context({name: "validateUser"})
+context({name: "validateUser"})
 → Incoming calls: loginHandler, apiMiddleware
 → Outgoing calls: checkToken, getUserById
 → Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
@@ -65,10 +65,10 @@ gitnexus_context({name: "validateUser"})
 
 ```
 1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
-2. gitnexus_query({query: "payment processing"})
+2. query({query: "payment processing"})
    → CheckoutFlow: processPayment → validateCard → chargeStripe
    → RefundFlow: initiateRefund → calculateRefund → processRefund
-3. gitnexus_context({name: "processPayment"})
+3. context({name: "processPayment"})
    → Incoming: checkoutHandler, webhookHandler
    → Outgoing: validateCard, chargeStripe, saveTransaction
 4. Read src/payments/processor.ts for implementation details

gitnexus-cursor-integration/skills/gitnexus-impact-analysis/SKILL.md

@@ -16,9 +16,9 @@ description: Analyze blast radius before making code changes
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
+1. impact({target: "X", direction: "upstream"})  → What depends on this
 2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
-3. gitnexus_detect_changes()                               → Map current git changes to affected flows
+3. detect_changes()                               → Map current git changes to affected flows
 4. Assess risk and report to user
 ```
 
@@ -27,11 +27,11 @@ description: Analyze blast radius before making code changes
 ## Checklist
 
 ```
-- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
+- [ ] impact({target, direction: "upstream"}) to find dependents
 - [ ] Review d=1 items first (these WILL BREAK)
 - [ ] Check high-confidence (>0.8) dependencies
 - [ ] READ processes to check affected execution flows
-- [ ] gitnexus_detect_changes() for pre-commit check
+- [ ] detect_changes() for pre-commit check
 - [ ] Assess risk level and report to user
 ```
 
@@ -54,9 +54,9 @@ description: Analyze blast radius before making code changes
 
 ## Tools
 
-**gitnexus_impact** — the primary tool for symbol blast radius:
+**impact** — the primary tool for symbol blast radius:
 ```
-gitnexus_impact({
+impact({
   target: "validateUser",
   direction: "upstream",
   minConfidence: 0.8,
@@ -71,9 +71,9 @@ gitnexus_impact({
   - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_detect_changes** — git-diff based impact analysis:
+**detect_changes** — git-diff based impact analysis:
 ```
-gitnexus_detect_changes({scope: "staged"})
+detect_changes({scope: "staged"})
 
 → Changed: 5 symbols in 3 files
 → Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
@@ -83,7 +83,7 @@ gitnexus_detect_changes({scope: "staged"})
 ## Example: "What breaks if I change validateUser?"
 
 ```
-1. gitnexus_impact({target: "validateUser", direction: "upstream"})
+1. impact({target: "validateUser", direction: "upstream"})
    → d=1: loginHandler, apiMiddleware (WILL BREAK)
    → d=2: authRouter, sessionManager (LIKELY AFFECTED)
 

gitnexus-cursor-integration/skills/gitnexus-pr-review/SKILL.md

@@ -18,10 +18,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 1. gh pr diff <number>                                    → Get the raw diff
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+2. detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
 3. For each changed symbol:
-   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
-4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+   impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. context({name: "<key symbol>"})               → Understand callers/callees
 5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
 6. Summarize findings with risk assessment
 ```
@@ -32,10 +32,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 - [ ] Fetch PR diff (gh pr diff or git diff base...head)
-- [ ] gitnexus_detect_changes to map changes to affected execution flows
-- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] detect_changes to map changes to affected execution flows
+- [ ] impact on each non-trivial changed symbol
 - [ ] Review d=1 items (WILL BREAK) — are callers updated?
-- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] context on key changed symbols to understand full picture
 - [ ] Check if affected processes have test coverage
 - [ ] Assess overall risk level
 - [ ] Write review summary with findings
@@ -63,20 +63,20 @@ description: "Use when the user wants to review a pull request, understand what
 
 ## Tools
 
-**gitnexus_detect_changes** — map PR diff to affected execution flows:
+**detect_changes** — map PR diff to affected execution flows:
 
 ```
-gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+detect_changes({scope: "compare", base_ref: "main"})
 
 → Changed: 8 symbols in 4 files
 → Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Risk: MEDIUM
 ```
 
-**gitnexus_impact** — blast radius per changed symbol:
+**impact** — blast radius per changed symbol:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream"})
+impact({target: "validatePayment", direction: "upstream"})
 
 → d=1 (WILL BREAK):
   - processCheckout (src/checkout.ts:42) [CALLS, 100%]
@@ -86,20 +86,20 @@ gitnexus_impact({target: "validatePayment", direction: "upstream"})
   - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_impact with tests** — check test coverage:
+**impact with tests** — check test coverage:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+impact({target: "validatePayment", direction: "upstream", includeTests: true})
 
 → Tests that cover this symbol:
   - validatePayment.test.ts [direct]
   - checkout.integration.test.ts [via processCheckout]
 ```
 
-**gitnexus_context** — understand a changed symbol's role:
+**context** — understand a changed symbol's role:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates
@@ -112,20 +112,20 @@ gitnexus_context({name: "validatePayment"})
 1. gh pr diff 42 > /tmp/pr42.diff
    → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
 
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+2. detect_changes({scope: "compare", base_ref: "main"})
    → Changed symbols: validatePayment, PaymentInput, formatAmount
    → Affected processes: CheckoutFlow, RefundFlow
    → Risk: MEDIUM
 
-3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+3. impact({target: "validatePayment", direction: "upstream"})
    → d=1: processCheckout, webhookHandler (WILL BREAK)
    → webhookHandler is NOT in the PR diff — potential breakage!
 
-4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+4. impact({target: "PaymentInput", direction: "upstream"})
    → d=1: validatePayment (in PR), createPayment (NOT in PR)
    → createPayment uses the old PaymentInput shape — breaking change!
 
-5. gitnexus_context({name: "formatAmount"})
+5. context({name: "formatAmount"})
    → Called by 12 functions — but change is backwards-compatible (added optional param)
 
 6. Review summary:

gitnexus-cursor-integration/skills/gitnexus-refactoring/SKILL.md

@@ -15,9 +15,9 @@ description: Plan safe refactors using blast radius and dependency mapping
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
-2. gitnexus_query({query: "X"})                            → Find execution flows involving X
-3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
+1. impact({target: "X", direction: "upstream"})  → Map all dependents
+2. query({query: "X"})                            → Find execution flows involving X
+3. context({name: "X"})                           → See all incoming/outgoing refs
 4. Plan update order: interfaces → implementations → callers → tests
 ```
 
@@ -27,60 +27,60 @@ description: Plan safe refactors using blast radius and dependency mapping
 
 ### Rename Symbol
 ```
-- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
+- [ ] rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
 - [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
-- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
-- [ ] gitnexus_detect_changes() — verify only expected files changed
+- [ ] If satisfied: rename({..., dry_run: false}) — apply edits
+- [ ] detect_changes() — verify only expected files changed
 - [ ] Run tests for affected processes
 ```
 
 ### Extract Module
 ```
-- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
-- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
+- [ ] context({name: target}) — see all incoming/outgoing refs
+- [ ] impact({target, direction: "upstream"}) — find all external callers
 - [ ] Define new module interface
 - [ ] Extract code, update imports
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ### Split Function/Service
 ```
-- [ ] gitnexus_context({name: target}) — understand all callees
+- [ ] context({name: target}) — understand all callees
 - [ ] Group callees by responsibility
-- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
+- [ ] impact({target, direction: "upstream"}) — map callers to update
 - [ ] Create new functions/services
 - [ ] Update callers
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ## Tools
 
-**gitnexus_rename** — automated multi-file rename:
+**rename** — automated multi-file rename:
 ```
-gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
 → 12 edits across 8 files
 → 10 graph edits (high confidence), 2 ast_search edits (review)
 → Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
 ```
 
-**gitnexus_impact** — map all dependents first:
+**impact** — map all dependents first:
 ```
-gitnexus_impact({target: "validateUser", direction: "upstream"})
+impact({target: "validateUser", direction: "upstream"})
 → d=1: loginHandler, apiMiddleware, testUtils
 → Affected Processes: LoginFlow, TokenRefresh
 ```
 
-**gitnexus_detect_changes** — verify your changes after refactoring:
+**detect_changes** — verify your changes after refactoring:
 ```
-gitnexus_detect_changes({scope: "all"})
+detect_changes({scope: "all"})
 → Changed: 8 files, 12 symbols
 → Affected processes: LoginFlow, TokenRefresh
 → Risk: MEDIUM
 ```
 
-**gitnexus_cypher** — custom reference queries:
+**cypher** — custom reference queries:
 ```cypher
 MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
 RETURN caller.name, caller.filePath ORDER BY caller.filePath
@@ -90,24 +90,24 @@ RETURN caller.name, caller.filePath ORDER BY caller.filePath
 
 | Risk Factor | Mitigation |
 |-------------|------------|
-| Many callers (>5) | Use gitnexus_rename for automated updates |
+| Many callers (>5) | Use rename for automated updates |
 | Cross-area refs | Use detect_changes after to verify scope |
-| String/dynamic refs | gitnexus_query to find them |
+| String/dynamic refs | query to find them |
 | External/public API | Version and deprecate properly |
 
 ## Example: Rename `validateUser` to `authenticateUser`
 
 ```
-1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+1. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
    → 12 edits: 10 graph (safe), 2 ast_search (review)
    → Files: validator.ts, login.ts, middleware.ts, config.json...
 
 2. Review ast_search edits (config.json: dynamic reference!)
 
-3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
+3. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
    → Applied 12 edits across 8 files
 
-4. gitnexus_detect_changes({scope: "all"})
+4. detect_changes({scope: "all"})
    → Affected: LoginFlow, TokenRefresh
    → Risk: MEDIUM — run tests for these flows
 ```

gitnexus-shared/src/graph/types.ts

@@ -115,7 +115,23 @@ export type RelationshipType =
   | 'HANDLES_TOOL'
   | 'ENTRY_POINT_OF'
   | 'WRAPS'
-  | 'QUERIES';
+  | 'QUERIES'
+  /** Vue component event system: a handler function in a parent component is
+   *  bound to an event emitted by a child component (`@event="handlerFn"`).
+   *  Source = handler Function/Method node in the parent.
+   *  Target = the child component's File node.
+   *  `reason` encodes the event name: `vue-event: @<eventName>`.
+   *  Complements `EMITS_EVENT`; together they enable Cypher queries that
+   *  trace which handlers receive which component's emitted events. */
+  | 'BINDS_EVENT_HANDLER'
+  /** Vue component event system: a component calls `emit('eventName', ...)`
+   *  or `this.$emit('eventName', ...)`, advertising that it can emit that event.
+   *  Source = the component's own File node (self-referential annotation).
+   *  Target = the same File node.
+   *  `reason` encodes the event name: `vue-emit: <eventName>`.
+   *  Complements `BINDS_EVENT_HANDLER`; a Cypher query joining on the
+   *  component File node reveals all (emitter, handler) pairs. */
+  | 'EMITS_EVENT';
 
 export interface GraphNode {
   id: string;

gitnexus-shared/src/index.ts

@@ -116,6 +116,8 @@ export type {
   FieldRegistry,
   FieldLookupOptions,
 } from './scope-resolution/registries/field-registry.js';
+export { buildMacroRegistry } from './scope-resolution/registries/macro-registry.js';
+export type { MacroRegistry } from './scope-resolution/registries/macro-registry.js';
 export { lookupCore } from './scope-resolution/registries/lookup-core.js';
 export type { CoreLookupParams } from './scope-resolution/registries/lookup-core.js';
 export { lookupQualified } from './scope-resolution/registries/lookup-qualified.js';
@@ -127,7 +129,12 @@ export {
   CONFIDENCE_EPSILON,
 } from './scope-resolution/registries/tie-breaks.js';
 export type { TieBreakKey } from './scope-resolution/registries/tie-breaks.js';
-export { CLASS_KINDS, METHOD_KINDS, FIELD_KINDS } from './scope-resolution/registries/context.js';
+export {
+  CLASS_KINDS,
+  METHOD_KINDS,
+  FIELD_KINDS,
+  MACRO_KINDS,
+} from './scope-resolution/registries/context.js';
 export type {
   RegistryContext,
   RegistryProviders,
@@ -176,13 +183,3 @@ export {
   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 {
-  ShadowAgreement,
-  ShadowCallsite,
-  ShadowDiff,
-} from './scope-resolution/shadow/diff.js';
-export { aggregateDiffs } from './scope-resolution/shadow/aggregate.js';
-export type { LanguageParityRow, ShadowParityReport } from './scope-resolution/shadow/aggregate.js';

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

@@ -8,8 +8,7 @@
  *
  * Part of RFC #909 Ring 2 SHARED — #913.
  *
- * Consumed by: #915 (SCC finalize link pass), #923 (shadow harness when
- * resolving callsite file → enclosing module).
+ * Consumed by: #915 (SCC finalize link pass).
  */
 
 import type { ScopeId } from './types.js';

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

@@ -74,4 +74,28 @@ export interface ParsedFile {
    */
   readonly localDefs: readonly SymbolDefinition[];
   readonly referenceSites: readonly ReferenceSite[];
+  /**
+   * Opaque, language-private serialization of capture-time side-channel
+   * state that a provider's `emitScopeCaptures` populates into module-level
+   * maps as a SIDE EFFECT (not onto the scopes/defs of this `ParsedFile`).
+   *
+   * Such state is computed inside the parse worker (where `emitScopeCaptures`
+   * runs) and would otherwise be lost across the worker→main MessageChannel
+   * and the disk store, because scope-resolution reuses the serialized
+   * `ParsedFile` and SKIPS re-extraction on the main thread (#1983 — the
+   * whole point is to avoid a main-thread tree-sitter re-parse). Carrying the
+   * data here lets the main thread repopulate those maps WITHOUT re-parsing.
+   *
+   * Shared / ingestion code treats this as opaque (`unknown`) per AGENTS.md
+   * (no language names in shared code). The producing language fills it via
+   * the `LanguageProvider.collectCaptureSideChannel` hook (worker side) and
+   * consumes it via the `ScopeResolver.applyCaptureSideChannel` hook
+   * (main-thread resolution side). It MUST be plain JSON-serializable data
+   * (objects / arrays / primitives) so it round-trips through the disk-backed
+   * `parsedfile-store` (JSON.stringify + interning reviver).
+   *
+   * Optional: providers whose `emitScopeCaptures` is pure (no module-level
+   * side effects — the contract default) leave this undefined.
+   */
+  readonly captureSideChannel?: unknown;
 }

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

@@ -37,7 +37,12 @@ export type ReferenceKind =
   | 'write'
   | 'type-reference'
   | 'inherits'
-  | 'import-use';
+  | 'import-use'
+  // A macro invocation (`log!(...)` / `vec![...]`). Resolved against
+  // `Macro`-labeled definitions ONLY (see `MacroRegistry`) so a macro
+  // never aliases a same-named free function — macros and functions are
+  // disjoint namespaces. Emitted as a `USES` edge, not `CALLS`.
+  | 'macro';
 
 /**
  * How a call site binds its target. Informs `Registry.lookup` Step 2

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

@@ -162,3 +162,10 @@ export const FIELD_KINDS: readonly NodeLabel[] = Object.freeze([
   'Const',
   'Static',
 ]);
+
+// Macros occupy a namespace disjoint from functions/methods: a `log!`
+// invocation must resolve ONLY to a `macro_rules! log` definition, never
+// to a same-named `fn log`. `MACRO_KINDS` is therefore a singleton
+// (`['Macro']`) and is NOT merged into METHOD_KINDS — keeping the two
+// keyspaces separate is what prevents the cross-namespace false-edge.
+export const MACRO_KINDS: readonly NodeLabel[] = Object.freeze(['Macro']);

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

@@ -57,8 +57,7 @@ export interface RawSignals {
  *
  * Emission order mirrors the `EvidenceWeights` layout: where-found →
  * type-binding → corroborators → arity → degraded. Stable order makes
- * the per-signal contributions easy to reason about in tests and in the
- * shadow-mode parity dashboard.
+ * the per-signal contributions easy to reason about in tests.
  */
 export function composeEvidence(signals: RawSignals): readonly ResolutionEvidence[] {
   const out: ResolutionEvidence[] = [];
@@ -141,7 +140,7 @@ export function composeEvidence(signals: RawSignals): readonly ResolutionEvidenc
 
 /**
  * Sum evidence weights and clamp to `[0, 1]`. Separate from `composeEvidence`
- * so tests and the parity dashboard can inspect the raw evidence list.
+ * so tests can inspect the raw evidence list.
  */
 export function confidenceFromEvidence(evidence: readonly ResolutionEvidence[]): number {
   let sum = 0;

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

@@ -0,0 +1,43 @@
+/**
+ * `MacroRegistry` — scope-aware lookup for macro definitions
+ * (`macro_rules!` in Rust; `#define` in C/C++) referenced from a macro
+ * invocation site.
+ *
+ * Thin wrapper over `lookupCore`, specialized for the macro namespace:
+ *
+ *   - `acceptedKinds` = `MACRO_KINDS` (`['Macro']` only). Crucially this
+ *     does NOT include `Function`/`Method`, so a `log!(…)` invocation can
+ *     never resolve to a same-named free function `fn log` — macros and
+ *     functions are disjoint namespaces (the false-`CALLS`-edge class the
+ *     #1934 review flagged).
+ *   - `useReceiverTypeBinding` is **false** — a macro invocation has no
+ *     receiver; resolution is name-through-the-lexical-chain + the global
+ *     qualified fallback, exactly like `ClassRegistry`.
+ *   - Arity is not applied — macros are variadic by nature.
+ */
+
+import type { Resolution, ScopeId } from '../types.js';
+import { lookupCore, type CoreLookupParams } from './lookup-core.js';
+import { MACRO_KINDS, type RegistryContext } from './context.js';
+
+export interface MacroRegistry {
+  /**
+   * Look up a macro definition by simple or scoped name anchored at
+   * `scope`. Returns a confidence-ranked `Resolution[]`; consume `[0]`
+   * for the best answer.
+   */
+  lookup(name: string, scope: ScopeId): readonly Resolution[];
+}
+
+export function buildMacroRegistry(ctx: RegistryContext): MacroRegistry {
+  const params: CoreLookupParams = {
+    acceptedKinds: MACRO_KINDS,
+    useReceiverTypeBinding: false,
+    ownerScopedContributor: null,
+  };
+  return {
+    lookup(name: string, scope: ScopeId) {
+      return lookupCore(name, scope, params, ctx);
+    },
+  };
+}

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

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

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

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

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

@@ -59,4 +59,13 @@ export interface SymbolDefinition {
   isExplicit?: boolean;
   /** Links Method/Constructor/Property to owning Class/Struct/Trait nodeId */
   ownerId?: string;
+  /** #1982/#1993: bridge-held enclosing-namespace path (e.g. `NS1`, `Outer.Inner`)
+   *  tagged during the C++ resolution phase. Lets the graph bridge retry a
+   *  namespace-prefixed node-lookup key and lets the qualified-base resolver
+   *  break same-tail cross-namespace inheritance ties. A deliberate sidecar,
+   *  separate from `qualifiedName`: it does NOT participate in graph node
+   *  identity (node keys derive from filePath/type/qualifiedName) and leaves the
+   *  qualifiedName-keyed resolution index untouched. Absent for the common case
+   *  (non-namespace-nested defs and all non-C++ languages). */
+  namespacePrefix?: string;
 }

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

@@ -439,7 +439,7 @@ export interface Reference {
   readonly toDef: DefId;
   /** Location of the reference in source. */
   readonly atRange: Range;
-  readonly kind: 'call' | 'read' | 'write' | 'type-reference' | 'inherits' | 'import-use';
+  readonly kind: 'call' | 'read' | 'write' | 'type-reference' | 'inherits' | 'import-use' | 'macro';
   readonly confidence: number;
   readonly evidence: readonly ResolutionEvidence[];
 }

gitnexus-web/package-lock.json

@@ -18,7 +18,7 @@
         "@tailwindcss/vite": "^4.3.0",
         "axios": "^1.16.1",
         "d3": "^7.9.0",
-        "dompurify": "^3.4.3",
+        "dompurify": "^3.4.7",
         "gitnexus-shared": "file:../gitnexus-shared",
         "graphology": "^0.26.0",
         "graphology-indices": "^0.17.0",
@@ -26,11 +26,11 @@
         "graphology-layout-forceatlas2": "^0.10.1",
         "graphology-layout-noverlap": "^0.4.2",
         "graphology-utils": "^2.3.0",
-        "i18next": "^26.2.0",
+        "i18next": "^26.3.0",
         "i18next-browser-languagedetector": "^8.2.1",
-        "langchain": "^1.3.5",
+        "langchain": "^1.4.2",
         "lru-cache": "^11.2.4",
-        "lucide-react": "^1.14.0",
+        "lucide-react": "^1.16.0",
         "mermaid": "^11.15.0",
         "mnemonist": "^0.39.0",
         "pandemonium": "^2.4.0",
@@ -57,7 +57,7 @@
         "@types/react": "^19.2.14",
         "@types/react-dom": "^19.2.3",
         "@types/react-syntax-highlighter": "^15.5.13",
-        "@vercel/node": "^5.8.2",
+        "@vercel/node": "^5.8.8",
         "@vitejs/plugin-react": "^5.1.4",
         "@vitest/coverage-v8": "^4.1.5",
         "jsdom": "^29.1.1",
@@ -1357,16 +1357,13 @@
       }
     },
     "node_modules/@langchain/core": {
-      "version": "1.1.45",
-      "resolved": "https://registry.npmjs.org/@langchain/core/-/core-1.1.45.tgz",
-      "integrity": "sha512-Y/wvuglLTMKJahkl4QD9dBIdF/z/CxZJWdTfHJF/q2jtlJtoFf6Mb5JpGxZfsi3mBY6NSG941FSLTcqhCKrhBA==",
+      "version": "1.1.48",
+      "resolved": "https://registry.npmjs.org/@langchain/core/-/core-1.1.48.tgz",
+      "integrity": "sha512-fQU6Guyb1pwc2fEplmA8FPbKfOMAofjnyJzExevro0FxEiuGHE18Ov/ZHmT9trWCDTZRI9eW1VIc6aChxV8pAQ==",
       "license": "MIT",
       "dependencies": {
         "@cfworker/json-schema": "^4.0.2",
         "@standard-schema/spec": "^1.1.0",
-        "ansi-styles": "^5.0.0",
-        "camelcase": "6",
-        "decamelize": "1.2.0",
         "js-tiktoken": "^1.0.12",
         "langsmith": ">=0.5.0 <1.0.0",
         "mustache": "^4.2.0",
@@ -1965,9 +1962,9 @@
       "license": "MIT"
     },
     "node_modules/@rollup/pluginutils": {
-      "version": "5.3.0",
-      "resolved": "https://registry.npmjs.org/@rollup/pluginutils/-/pluginutils-5.3.0.tgz",
-      "integrity": "sha512-5EdhGZtnu3V88ces7s53hhfK5KSASnJZv8Lulpc04cWO3REESroJXg73DFsOmgbU2BhwV0E20bu2IDZb3VKW4Q==",
+      "version": "5.4.0",
+      "resolved": "https://registry.npmjs.org/@rollup/pluginutils/-/pluginutils-5.4.0.tgz",
+      "integrity": "sha512-MfPp06CjRLfXQ3wY0R8vJDYBy/MvVcc9OulEfR0B8Iv9ko+GCNaRZ+EpJYFl27LhKsZK0o420sYCRHCjfCgeUg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -2430,9 +2427,9 @@
       "license": "MIT"
     },
     "node_modules/@ts-morph/common/node_modules/brace-expansion": {
-      "version": "1.1.14",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.14.tgz",
-      "integrity": "sha512-MWPGfDxnyzKU7rNOW9SP/c50vi3xrmrua/+6hfPbCS2ABNWfx24vPidzvC7krjU/RTo235sV776ymlsMtGKj8g==",
+      "version": "1.1.15",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.15.tgz",
+      "integrity": "sha512-EwOCDEex4quD37XhqM3omwtMoJjr//isUZz1JopUNWms+4Z2ViyM/k1YIRePpoVNnQhENnxtFjLaxNHrT7xIUg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -2933,9 +2930,9 @@
       }
     },
     "node_modules/@vercel/build-utils": {
-      "version": "13.25.0",
-      "resolved": "https://registry.npmjs.org/@vercel/build-utils/-/build-utils-13.25.0.tgz",
-      "integrity": "sha512-p2wqxi2I95T+g/+uP+Dc/uq2PApW7F9RbE/Vvwp28JY8SoCGHNUs2pxigttgaNDNF6IlUEMOTz+eJvsXToV/1w==",
+      "version": "13.26.4",
+      "resolved": "https://registry.npmjs.org/@vercel/build-utils/-/build-utils-13.26.4.tgz",
+      "integrity": "sha512-0g3ZxtZUJZbt4y0Vu4pkHtu1UN58FbVF9cqGT8T6jHp0EHdLGFj5TVCiME8ALeK4tjPImSmxnKZvvB5yb2hqEw==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -2959,9 +2956,9 @@
       "license": "Apache-2.0"
     },
     "node_modules/@vercel/nft": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/@vercel/nft/-/nft-1.5.0.tgz",
-      "integrity": "sha512-IWTDeIoWhQ7ZtRO/JRKH+jhmeQvZYhtGPmzw/QGDY+wDCQqfm25P9yIdoAFagu4fWsK4IwZXDFIjrmp5rRm/sA==",
+      "version": "1.10.0",
+      "resolved": "https://registry.npmjs.org/@vercel/nft/-/nft-1.10.0.tgz",
+      "integrity": "sha512-iLOW4fcsgkipfOh2Bw3wB38YDfxTlxr7+j4uFeui2OswkNT28jIitS/aMce7tS0mef1YPQ8zLIDYr3a0aahNrA==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -2986,9 +2983,9 @@
       }
     },
     "node_modules/@vercel/node": {
-      "version": "5.8.2",
-      "resolved": "https://registry.npmjs.org/@vercel/node/-/node-5.8.2.tgz",
-      "integrity": "sha512-Wt6KBr0LoIhUuzeH7E8S+1HRlS6oSA+98FJH/59wY2tYoxsHXbx5uiNkSBqBsM0nIwlJWR3B86tm9q9Xi22XdQ==",
+      "version": "5.8.8",
+      "resolved": "https://registry.npmjs.org/@vercel/node/-/node-5.8.8.tgz",
+      "integrity": "sha512-+uRT9evnGWUE6klrJJED4fCvlSxNShbIc/UY4FeUzt2sdcy5a5b1IoYlo94RJd7tAY9Jg2lR2cVfGfsnWH81ZA==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -2996,10 +2993,10 @@
         "@edge-runtime/primitives": "4.1.0",
         "@edge-runtime/vm": "3.2.0",
         "@types/node": "20.11.0",
-        "@vercel/build-utils": "13.25.0",
+        "@vercel/build-utils": "13.26.4",
         "@vercel/error-utils": "2.1.0",
-        "@vercel/nft": "1.5.0",
-        "@vercel/static-config": "3.3.0",
+        "@vercel/nft": "1.10.0",
+        "@vercel/static-config": "3.4.0",
         "async-listen": "3.0.0",
         "cjs-module-lexer": "1.2.3",
         "edge-runtime": "2.5.9",
@@ -3060,9 +3057,9 @@
       }
     },
     "node_modules/@vercel/static-config": {
-      "version": "3.3.0",
-      "resolved": "https://registry.npmjs.org/@vercel/static-config/-/static-config-3.3.0.tgz",
-      "integrity": "sha512-GpS3tPwUeDJCkrKbMNtS2XLRFgfxTlN7YNUL+Bo23+fGolrDw6Oq79R3yvxTYgqRaJMGSEqC7iMw6mj6I5loxg==",
+      "version": "3.4.0",
+      "resolved": "https://registry.npmjs.org/@vercel/static-config/-/static-config-3.4.0.tgz",
+      "integrity": "sha512-wCq90CMUB//ggnFh77NQO1xaLFsS4LigQIqKrH6ohnr9Br/KI1FhlErx62WfCOuueWaW+LVsbLOqNXIUjK8t6A==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -3331,7 +3328,9 @@
       "version": "5.2.0",
       "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-5.2.0.tgz",
       "integrity": "sha512-Cxwpt2SfTzTtXcfOlzGEee8O+c+MmUgGrNiBcXnuWxuFJHe6a5Hz7qwhwe5OgaSYI0IJvkLqWX1ASG+cJOkEiA==",
+      "dev": true,
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=10"
       },
@@ -3598,18 +3597,6 @@
         "node": ">= 0.4"
       }
     },
-    "node_modules/camelcase": {
-      "version": "6.3.0",
-      "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-6.3.0.tgz",
-      "integrity": "sha512-Gmy6FhYlCY7uOElZUSbxo2UCDH8owEk996gkbrpsgGtrJLM3J7jGxl9Ic7Qwwj4ivOE5AWZWRMecDdF7hqGjFA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
     "node_modules/caniuse-lite": {
       "version": "1.0.30001764",
       "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001764.tgz",
@@ -4396,15 +4383,6 @@
         }
       }
     },
-    "node_modules/decamelize": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/decamelize/-/decamelize-1.2.0.tgz",
-      "integrity": "sha512-z2S+W9X73hAUUki+N+9Za2lBlun89zigOyGrsax+KUQ6wKW4ZoWpEYBkGhQjwAjjDCkWxhY0VKEhk8wzY7F5cA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/decimal.js": {
       "version": "10.6.0",
       "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
@@ -4483,9 +4461,9 @@
       "peer": true
     },
     "node_modules/dompurify": {
-      "version": "3.4.3",
-      "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.4.3.tgz",
-      "integrity": "sha512-VVwJidIJcp1hpg2OMXML3ZVRPYSZiq4aX7qBh83BSIpOaRDqI+qxhXjjIWnpzkOXhmp0L81lnoME1mnCc9H48A==",
+      "version": "3.4.7",
+      "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.4.7.tgz",
+      "integrity": "sha512-2jBxDJY4RR06tQNy4w5FlFH7kfxsQZlufd0sbv+chfHCxeJwrFw2baUDsSwvBISD4K4RDbd0PTfy3uNXsR6siA==",
       "license": "(MPL-2.0 OR Apache-2.0)",
       "optionalDependencies": {
         "@types/trusted-types": "^2.0.7"
@@ -5029,22 +5007,6 @@
         "node": ">= 6"
       }
     },
-    "node_modules/glob/node_modules/minimatch": {
-      "version": "10.2.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz",
-      "integrity": "sha512-MULkVLfKGYDFYejP07QOurDLLQpcjk7Fw+7jXS2R2czRQzR56yHRveU5NDJEOviH+hETZKSkIk5c+T23GjFUMg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "brace-expansion": "^5.0.5"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
     "node_modules/gopd": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.2.0.tgz",
@@ -5334,9 +5296,9 @@
       }
     },
     "node_modules/i18next": {
-      "version": "26.2.0",
-      "resolved": "https://registry.npmjs.org/i18next/-/i18next-26.2.0.tgz",
-      "integrity": "sha512-zwBHldHdTmwN7r6UNc7lC6GWNN+YYg3DrRSeHR5PRRBf5QnJZcYHrQc0uaU26qZeYxR7iFZD+Y315dPnKP47wA==",
+      "version": "26.3.0",
+      "resolved": "https://registry.npmjs.org/i18next/-/i18next-26.3.0.tgz",
+      "integrity": "sha512-gHSgGpUXVmuqE2El1W61DmxeyeTlFfZgdJRWMo9jScAn5pu7TuTuiccb1zh3E2J9hEBVGJ23+96x0ieBhfuIHA==",
       "funding": [
         {
           "type": "individual",
@@ -5790,12 +5752,12 @@
       "integrity": "sha512-Ls993zuzfayK269Svk9hzpeGUKob/sIgZzyHYdjQoAdQetRKpOLj+k/QQQ/6Qi0Yz65mlROrfd+Ev+1+7dz9Kw=="
     },
     "node_modules/langchain": {
-      "version": "1.3.5",
-      "resolved": "https://registry.npmjs.org/langchain/-/langchain-1.3.5.tgz",
-      "integrity": "sha512-QSB8TEo6G1tWupgNt1Osm8ylLLoOMq1lLw5NeijnIwRPI5BqdBjUn4/U8usbjEJJcQnbXSK2qTKgTx7zvblnBw==",
+      "version": "1.4.2",
+      "resolved": "https://registry.npmjs.org/langchain/-/langchain-1.4.2.tgz",
+      "integrity": "sha512-SLGipy0r4nqQD0aiUOBYLMeGFfB/QiYnMndfZ8sGN89vXDCIXbYqcE7G/4QDDX3nZsM7/emQpoScmlxEX6sDnQ==",
       "license": "MIT",
       "dependencies": {
-        "@langchain/langgraph": "^1.2.9",
+        "@langchain/langgraph": "^1.3.2",
         "@langchain/langgraph-checkpoint": "^1.0.1",
         "langsmith": ">=0.5.0 <1.0.0",
         "zod": "^3.25.76 || ^4"
@@ -5804,7 +5766,7 @@
         "node": ">=20"
       },
       "peerDependencies": {
-        "@langchain/core": "^1.1.42"
+        "@langchain/core": "^1.1.48"
       }
     },
     "node_modules/langsmith": {
@@ -6142,9 +6104,9 @@
       }
     },
     "node_modules/lucide-react": {
-      "version": "1.14.0",
-      "resolved": "https://registry.npmjs.org/lucide-react/-/lucide-react-1.14.0.tgz",
-      "integrity": "sha512-+1mdWcfSJVUsaTIjN9zoezmUhfXo5l0vP7ekBMPo3jcS/aIkxHnXqAPsByszMZx/Y8oQBRJxJx5xg+RH3urzxA==",
+      "version": "1.16.0",
+      "resolved": "https://registry.npmjs.org/lucide-react/-/lucide-react-1.16.0.tgz",
+      "integrity": "sha512-dYwyPzb4MEKpGUmNYk3WKWPnMrHs3FKM+q94kAnJrcDIqqn1hq2xY8scaS2ovsOCM5D51ey2gaRG3PBb1vgoYQ==",
       "license": "ISC",
       "peerDependencies": {
         "react": "^16.5.1 || ^17.0.0 || ^18.0.0 || ^19.0.0"
@@ -8350,9 +8312,9 @@
       }
     },
     "node_modules/tar": {
-      "version": "7.5.15",
-      "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.15.tgz",
-      "integrity": "sha512-dzGK0boVlC4W5QFuQN1EFSl3bIDYsk7Tj40U6eIBnK2k/8ml7TZ5agbI5j5+qnoVcAA+rNtBml8SEiLxZpNqRQ==",
+      "version": "7.5.16",
+      "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.16.tgz",
+      "integrity": "sha512-56adEpPMouktRlBLXiaYFFzZ/3+JXa8P9n7WbR+ibIjtviN55mEaOkiysCnPnWm+7kkui1Dn8J9l+g6zV8731w==",
       "dev": true,
       "license": "BlueOak-1.0.0",
       "dependencies": {

gitnexus-web/package.json

@@ -28,7 +28,7 @@
     "@tailwindcss/vite": "^4.3.0",
     "axios": "^1.16.1",
     "d3": "^7.9.0",
-    "dompurify": "^3.4.3",
+    "dompurify": "^3.4.7",
     "gitnexus-shared": "file:../gitnexus-shared",
     "graphology": "^0.26.0",
     "graphology-indices": "^0.17.0",
@@ -36,11 +36,11 @@
     "graphology-layout-forceatlas2": "^0.10.1",
     "graphology-layout-noverlap": "^0.4.2",
     "graphology-utils": "^2.3.0",
-    "i18next": "^26.2.0",
+    "i18next": "^26.3.0",
     "i18next-browser-languagedetector": "^8.2.1",
-    "langchain": "^1.3.5",
+    "langchain": "^1.4.2",
     "lru-cache": "^11.2.4",
-    "lucide-react": "^1.14.0",
+    "lucide-react": "^1.16.0",
     "mermaid": "^11.15.0",
     "mnemonist": "^0.39.0",
     "pandemonium": "^2.4.0",
@@ -67,7 +67,7 @@
     "@types/react": "^19.2.14",
     "@types/react-dom": "^19.2.3",
     "@types/react-syntax-highlighter": "^15.5.13",
-    "@vercel/node": "^5.8.2",
+    "@vercel/node": "^5.8.8",
     "@vitejs/plugin-react": "^5.1.4",
     "@vitest/coverage-v8": "^4.1.5",
     "jsdom": "^29.1.1",

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

@@ -65,66 +65,90 @@ export const BASE_SYSTEM_PROMPT = `You are Nexus, a Code Analysis Agent with acc
 
 ## ⚠️ MANDATORY: GROUNDING
 Every factual claim MUST include a citation.
-- File refs: [[src/auth.ts:45-60]] (line range with hyphen)
+- File refs: [[src/auth.ts:45-60]] (repo-relative path, line range with hyphen)
+- Symbol refs: [[Function:validateUser]] or [[Class:AuthService]]
+- Do NOT wrap citations in backticks or code blocks — keep them as plain text
 - NO citation = NO claim. Say "I didn't find evidence" instead of guessing.
 
-## ⚠️ MANDATORY: VALIDATION
-Every output MUST be validated.
-- Use cypher to validate the results and confirm completeness of context before final output.
-- NO validation = NO claim. Say "I didn't find evidence" instead of guessing.
-- Do not blindly trust readme or single source of truth. Always validate and cross-reference. Never be lazy.
+## 🧠 CORE PROTOCOL (Iterative Loop)
+You are an investigator, not a one-shot query engine. For each question:
+1. **Plan** — Briefly state what you are looking for and why.
+2. **Execute** — Run tools to gather evidence.
+3. **Analyze & pivot** — Did the output fully answer the question?
+   - Yes → proceed to grounding.
+   - Revealed new files/functions → loop back and investigate them immediately.
+   - Tool failed → fix the input and retry. Never stop after one error.
+4. **Trace** — Use cypher, explore, or impact to follow graph connections.
+5. **Read** — Use read to verify logic. Do not guess behavior from names alone.
+6. **Validate** — Cross-check findings with cypher before final output. README/docs are summaries, not proof.
+7. **Ground** — Cite every finding with [[path:START-END]] or [[Type:Name]].
 
-## 🧠 CORE PROTOCOL
-You are an investigator. For each question:
-1. **Search** → Use cypher, search or grep to find relevant code
-2. **Read** → Use read to see the actual source
-3. **Trace** → Use cypher to follow connections in the graph
-4. **Cite** → Ground every finding with [[file:line]] or [[Type:Name]]
-5. **Validate** → Use cypher to validate the results and confirm completeness of context before final output. ( MUST DO )
+Before EVERY tool call, briefly state what you are doing and why. Keep narration to one line per step.
 
-## 🛠️ TOOLS
-- **\`search\`** — Hybrid search. Results grouped by process with cluster context.
-- **\`cypher\`** — Cypher queries against the graph. Use \`{{QUERY_VECTOR}}\` for vector search.
-- **\`grep\`** — Regex search. Best for exact strings, TODOs, error codes.
-- **\`read\`** — Read file content. Always use after search/grep to see full code.
-- **\`explore\`** — Deep dive on a symbol, cluster, or process. Shows membership, participation, connections.
+## BE DIRECT
+- No pleasantries. No "Great question!" or "I'd be happy to help."
+- Don't repeat advice already given in this conversation.
+- Match response length to query complexity.
+- Don't pad with generic "let me know if you need more" — users will ask.
+
+## 🛠️ TOOLS (exact names — use these only)
+- **\`search\`** — Hybrid keyword + semantic search. Results grouped by process with cluster context. Start here for discovery.
+- **\`cypher\`** — Cypher queries against the graph. Use \`{{QUERY_VECTOR}}\` placeholder for vector search.
+- **\`grep\`** — Regex search across files. Best for exact strings, TODOs, error codes.
+- **\`read\`** — Read file content. Always use after search/grep to see full source.
+- **\`explore\`** — Deep dive on a symbol, cluster, or process.
 - **\`overview\`** — Codebase map showing all clusters and processes.
 - **\`impact\`** — Impact analysis. Shows affected processes, clusters, and risk level.
 
+**Tool strategy:**
+- Discovery → \`search\` or \`overview\`
+- Structure → \`cypher\`, \`explore\`, or \`impact\`
+- Verification → \`read\` (required before concluding)
+- Exact patterns → \`grep\`
+
 ## 📊 GRAPH SCHEMA
-Nodes: File, Folder, Function, Class, Interface, Method, Community, Process
-Relations: \`CodeRelation\` with \`type\` property: CONTAINS, DEFINES, IMPORTS, CALLS, EXTENDS, IMPLEMENTS, MEMBER_OF, STEP_IN_PROCESS
+Typed node labels: File, Folder, Function, Class, Interface, Method, CodeElement, Community, Process
+Single relation table: \`CodeRelation\` with \`type\` property: CONTAINS, DEFINES, IMPORTS, CALLS, EXTENDS, IMPLEMENTS, MEMBER_OF, STEP_IN_PROCESS
 
-## 📐 GRAPH SEMANTICS (Important!)
-**Edge Types:**
-- \`CALLS\`: Method invocation OR constructor injection. If A receives B as parameter and uses it, A→B is CALLS. This is intentional simplification.
-- \`IMPORTS\`: File-level import/include statement.
-- \`EXTENDS/IMPLEMENTS\`: Class inheritance.
-
-**Process Nodes:**
-- Process labels use format: "EntryPoint → Terminal" (e.g., "onCreate → showToast")
-- These are heuristic names from tracing execution flow, NOT application-defined names
-- Entry points are detected via export status, naming patterns, and framework conventions
+✅ \`MATCH (f:Function) RETURN f.name LIMIT 10\`
+✅ \`MATCH (a)-[r:CodeRelation {type: 'CALLS'}]->(b:Function) RETURN a.name, b.name\`
+❌ \`MATCH ()-[:CALLS]->()\` — WRONG, no such relationship label
 
 Cypher examples:
-- \`MATCH (f:Function) RETURN f.name LIMIT 10\`
-- \`MATCH (f:File)-[:CodeRelation {type: 'IMPORTS'}]->(g:File) RETURN f.name, g.name\`
+- Find callers: \`MATCH (caller:Function)-[:CodeRelation {type: 'CALLS'}]->(fn:Function {name: 'validate'}) RETURN caller.name, caller.filePath\`
+- File imports: \`MATCH (f:File)-[:CodeRelation {type: 'IMPORTS'}]->(g:File) RETURN f.name, g.name\`
+- Semantic search: include \`{{QUERY_VECTOR}}\` in cypher and provide a \`query\` parameter
 
-## 📝CRITICAL RULES
-- **impact output is trusted.** Do NOT re-validate with cypher. Optionally run the suggested grep commands for dynamic patterns.
+## 📐 GRAPH SEMANTICS
+- \`CALLS\`: Method invocation or constructor injection (intentional simplification).
+- \`IMPORTS\`: File-level import/include.
+- \`EXTENDS/IMPLEMENTS\`: Class inheritance.
+- Process labels use format "EntryPoint → Terminal" (heuristic, not app-defined names).
+
+## 🎯 VISUAL GROUNDING (not a tool)
+The user sees a knowledge graph alongside this chat. Citations automatically highlight nodes in the graph UI.
+- Include [[path:START-END]] and [[Type:Name]] refs as you discover relevant code — the UI highlights them for the user.
+- Prefer 2-6 high-signal references over large dumps.
+- There is NO \`highlight_in_graph\` tool. Ground with citations; the UI handles visualization.
+
+## 📝 CRITICAL RULES
+- **impact output is trusted.** Do NOT re-validate with cypher. Optionally run suggested grep for dynamic patterns.
 - **Cite or retract.** Never state something you can't ground.
-- **Read before concluding.** Don't guess from names alone.
-- **Retry on failure.** If a tool fails, fix the input and try again.
-- **Cyfer tool validation** prefer using cyfer tool in anything that requires graph connections.
-- **OUTPUT STYLE** Prefer using tables and mermaid diagrams instead of long explanations.
-- ALWAYS USE MERMAID FOR VISUALIZATION AND STRUCTURING THE OUTPUT.
+- **Iterative depth.** If Function A calls Function B, read Function B. Trace logic to the source.
+- **Prefer cypher** for anything requiring graph connections.
+
+## ERROR RECOVERY
+If a tool call fails (Cypher syntax, file not found, invalid regex), do NOT stop.
+- Read the error, fix the input, and retry at least once.
+- For Cypher errors, verify typed node labels and \`CodeRelation {type: '...'}\` filters match the GRAPH SCHEMA section above.
+- If search returns nothing, try grep or a different query before concluding.
 
 ## 🎯 OUTPUT STYLE
-Think like a senior architect. Be concise—no fluff, short, precise and to the point.
+Think like a senior architect. Be concise — no fluff.
 - Use tables for comparisons/rankings
-- Use mermaid diagrams for flows/dependencies
+- Use mermaid diagrams for flows, architecture, and dependencies
 - Surface deep insights: patterns, coupling, design decisions
-- End with **TL;DR** (short summary of the response, summing up the response and the most critical parts)
+- End with **TL;DR**
 
 ## MERMAID RULES
 When generating diagrams:
@@ -132,6 +156,7 @@ When generating diagrams:
 - Wrap labels with spaces in quotes: A["My Label"]
 - Use simple IDs: A, B, C or auth, db, api
 - Flowchart: graph TD or graph LR (not flowchart)
+- Keep diagrams focused — 5-10 nodes max
 - Always test mentally: would this parse?
 
 BAD:  A[User's Data] --> B(Process & Save)

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

@@ -16,6 +16,20 @@ import { z } from 'zod';
 import { NODE_TABLES, REL_TYPES } from 'gitnexus-shared';
 import type { EnrichedSearchResult, GrepResult } from '../../services/backend-client';
 
+/**
+ * Tool names registered by createGraphRAGTools — kept in sync with each tool's `name`
+ * field (enforced by agent-prompt.test.ts) and with BASE_SYSTEM_PROMPT in agent.ts.
+ */
+export const GRAPH_RAG_TOOL_NAMES = [
+  'search',
+  'cypher',
+  'grep',
+  'read',
+  'overview',
+  'explore',
+  'impact',
+] as const;
+
 const validLabel = (label: string): boolean => (NODE_TABLES as readonly string[]).includes(label);
 
 const validRelType = (t: string): boolean => (REL_TYPES as readonly string[]).includes(t);

gitnexus-web/test/unit/agent-prompt.test.ts

@@ -0,0 +1,82 @@
+import { describe, expect, it } from 'vitest';
+import { BASE_SYSTEM_PROMPT } from '../../src/core/llm/agent';
+import {
+  createGraphRAGTools,
+  GRAPH_RAG_TOOL_NAMES,
+  type GraphRAGBackend,
+} from '../../src/core/llm/tools';
+import { NODE_REF_REGEX } from '../../src/lib/grounding-patterns';
+
+/** Legacy or phantom tool names that must not appear in the system prompt. */
+const FORBIDDEN_TOOL_NAMES = [
+  'hybrid_search',
+  'semantic_search',
+  'semantic_search_with_context',
+  'execute_cypher',
+  'execute_vector_cypher',
+  'grep_code',
+  'read_file',
+  'get_graph_schema',
+  'get_code_content',
+  'get_codebase_stats',
+] as const;
+
+/**
+ * No-op backend. createGraphRAGTools only captures these methods inside each tool's
+ * async execute closure — it never invokes them at construction time — so empty
+ * implementations are enough to build the tools and read their registered names.
+ */
+const stubBackend: GraphRAGBackend = {
+  executeQuery: async () => [],
+  search: async () => [],
+  grep: async () => [],
+  readFile: async () => '',
+};
+
+describe('BASE_SYSTEM_PROMPT tool parity', () => {
+  it('documents every registered Graph RAG tool by exact name', () => {
+    for (const name of GRAPH_RAG_TOOL_NAMES) {
+      expect(BASE_SYSTEM_PROMPT).toContain(`\`${name}\``);
+    }
+  });
+
+  it('keeps GRAPH_RAG_TOOL_NAMES in sync with the tools createGraphRAGTools registers', () => {
+    const registered = createGraphRAGTools(stubBackend).map((t) => t.name);
+    expect(registered.sort()).toEqual([...GRAPH_RAG_TOOL_NAMES].sort());
+  });
+
+  it('does not reference legacy or non-existent tool names', () => {
+    for (const name of FORBIDDEN_TOOL_NAMES) {
+      // Word-boundary match catches both backticked and bare-prose mentions.
+      expect(BASE_SYSTEM_PROMPT).not.toMatch(new RegExp(`\\b${name}\\b`));
+    }
+  });
+
+  it('uses explicit file citation format expected by the UI parser', () => {
+    expect(BASE_SYSTEM_PROMPT).toMatch(/\[\[src\/[^\]]+:\d+-\d+\]\]/);
+    expect(BASE_SYSTEM_PROMPT).not.toContain('[[file:line]]');
+  });
+
+  it('documents a parser-recognized symbol citation format', () => {
+    // Use the UI parser's own allowlist (NODE_REF_REGEX) so this tracks the parser
+    // instead of forking its label list. NODE_REF_REGEX is /g; use a non-global copy
+    // so the match is stateless.
+    expect(BASE_SYSTEM_PROMPT).toMatch(new RegExp(NODE_REF_REGEX.source));
+  });
+
+  it('documents typed node labels, not polymorphic CodeNode', () => {
+    expect(BASE_SYSTEM_PROMPT).toContain('MATCH (f:Function)');
+    expect(BASE_SYSTEM_PROMPT).not.toContain('CodeNode');
+    expect(BASE_SYSTEM_PROMPT).not.toContain('INHERITS');
+  });
+
+  it('clarifies highlight_in_graph is not a callable tool', () => {
+    // Reword-proof, registry-level guarantee: the load-bearing fact is that
+    // highlight_in_graph is not a registered tool, regardless of prompt phrasing.
+    expect(GRAPH_RAG_TOOL_NAMES).not.toContain('highlight_in_graph');
+    // The prompt still addresses it explicitly...
+    expect(BASE_SYSTEM_PROMPT).toContain('highlight_in_graph');
+    // ...and must never instruct the model to call it (guards an affirmative reword).
+    expect(BASE_SYSTEM_PROMPT).not.toMatch(/\b(?:use|call|invoke)\s+`?highlight_in_graph/i);
+  });
+});

gitnexus/CHANGELOG.md

@@ -4,6 +4,71 @@ All notable changes to GitNexus will be documented in this file.
 
 ## [Unreleased]
 
+## [1.6.6] - 2026-06-08
+
+### Added
+
+- **Scope-resolution (RFC #909) migrations completed across the language matrix** — Rust (#1639), JavaScript (#1640), Ruby (#1831), Swift (#937, #1948), Vue SFC (#940, #1950), Dart (#939, #1970), COBOL (#941, #1835, #1842), and Kotlin (#1727, #1746, #1782) now run on the registry-primary path; Java reached 100% scope-resolution parity and joined `MIGRATED_LANGUAGES` (#1805); per-language progress reporting added to the scope-resolution phase (#1813)
+- **HTTP route & consumer contract extraction (group mode)** — Spring interface routes attributed to controllers (#1743); named/positional Java Spring route args (#1834); Kotlin Spring HTTP route, consumer, and WebClient long-form extraction (#1849, #1855, #1884); Java HTTP consumer contracts (#1872); OpenFeign `@RequestLine` consumer contracts incl. plain interfaces without `@FeignClient` (#1904, #1917); FastAPI `include_router(prefix=...)` cross-file routes (#1877); indirect call patterns via FastAPI `Depends()` and frontend HTTP consumers (#1852); gRPC consumer FQN derivation from Java imports for client-jar consumers (#1889)
+- **C++ overload & template resolution** — operator-call resolution (#1754), template partial ordering (#1885), user-defined conversion ranking (#1829), nullptr/ellipsis pointer conversion ranks (#1708), SFINAE filter (#1623), expanded `type_traits` constraint registry (#1648), structured resolver-suppression outcomes (#1785), function-type ADL entities (#1822), and a parameter-type class sidecar (#1642)
+- **Go enhancements** — structural interface implementation inference (#1966) and a `builtInNames` set for the Go language provider (#1886)
+- **Self-healing worker pool** — automatic worker replacement plus deferred-resolution observability and verbose progress logging (#1741, #1773, #1947)
+- **`.gitnexusrc` config file and `gitnexus analyze --default-branch`** (#243, #1996)
+- **CLI / MCP impact ergonomics** — `--uid/--file/--kind` disambiguation flags (#1907, #1914), `limit/offset/summaryOnly` pagination on the impact tool (#1818), and a per-symbol `processes` field on `byDepth` items (#1867)
+- **`gitnexus analyze --repair-fts`** — enforces FTS verification with hardened repair safeguards (#1720)
+- **Web viewer** — Tree View and Circles View (#1799), GitLab repository URLs (#1565), `GITNEXUS_BACKEND_URL` env var for Docker deployments (#1286), and web + CLI internationalization (#1748)
+- **Wiki** — local Claude/Codex providers (#1769), an opencode local provider (#2039), and `gitnexus wiki --lang <lang>` for multilanguage wiki generation (#1613)
+- **`detect-changes` git-worktree support** (#1654)
+- **DeepSeek V4 API support** (#1594)
+- **Devcontainer for the Claude / Codex / Cursor CLIs** (#1875) and antigravity integration setup + hook adapter (#1730)
+- **Object-literal methods linked to exported bindings** (#1718)
+- **`eval-server --host`** for a user-configured bind IP (#1667)
+- **PR reviewer swarm agents** (#1851)
+- **tree-sitter node-type/field validation gate** — validates against the grammar and removes dead literal handling (#1937)
+
+### Fixed
+
+- **Parsing-layer coverage gaps closed across the language matrix** (umbrella #1919) — remaining open gaps (#2072) plus Java F35/F38/F41 (#1928, #2045), PHP F53/F54/F55 (#1931, #1989), COBOL F17–F23 (#1925, #1959), Rust F66/F68/F71/F72 (#1934, #1974), Python F57/F58/F61 (#1932, #1964), JS/TS F44/F83/F85/F86/F87 (#1929, #1968), and Ruby F62 (#1933, #1972)
+- **Fully-qualified nested-type identity for C++ and Ruby** — distinct nodes for union-, anonymous-namespace-, and same-tail-nested types (#1978, #1981, #2004, #2005); cross-namespace same-tail inheritance bases resolved (#1993, #2005); Ruby same-tail nested mixin modules qualified with `IMPLEMENTS` routed by scope (#1991, #2006); shared codec for `__heritage__`/`__property__` markers (#1994, #2007); graph nodes materialized for scoped class/module/impl declarations (#1975, #1977); generic Rust inherent-impl methods owned through the mod-qualified `Impl` node (#1992, #2003)
+- **C# resolution & memory** — global-namespace `typeBindings` O(files²) OOM eliminated (#1871, #1954) and namespace-siblings OOM with worker-path re-parse removed (#1905); qualified/alias constructor names, `:base`/`:this` initializers, and generic type-arg stripping (#2046); primary-base receiver type normalization (#2036); spurious `IMPORTS` edges from ungated `using` resolution stopped (#1881, #1908)
+- **C++ dependent-base and member lookup** — resolution across nested/inline namespaces (#1634, #1814), base-specifier qualifier threading (#1815, #1819), call-site types threaded into qualified member lookup (#1632, #1810), variadic pack dependent lookup (#1909), uninitialized multi-declarators (#1965), and typedef-enum / anonymous-struct declarations (#1941)
+- **Kotlin type resolution** — smart-cast refinement for `when/is` and `if/is` (#1758, #1774), overload target-id by parameter types (#1761, #1777), cross-file iterable return propagation (#1759, #1775), method-chain fixpoint receiver types (#1760, #1776), virtual dispatch via constructor type override (#1762, #1778), interface default-method dispatch via implements-split MRO (#1763, #1779), and default-parameter arity detection (#2034)
+- **Go declarations** — multi-name declaration capture (#2032), fixed-array parameter binding normalization (#1988), and generic composite-literal constructor inference F33 (#1976)
+- **Rust / PHP / Vue / Java parsing** — Rust `struct_expression` name pattern split (#2051); PHP import decomposition, namespace-less `.phtml` module scopes, and Blade-template exclusion (#1801, #1790, #1989); Vue JSDoc, dual-script merge, and lang plumbing F89/F90/F92 (#1936, #2050); Java inherited `RequestMapping` prefix deduplication (#2057) and same-module type resolution for duplicate FQNs (#1712)
+- **TypeScript** — HOC pattern false positives fixed with `export default` HOC support (#1943) and suffix-index reuse in the scope resolver (#1840)
+- **Inheritance on the worker path** — all languages' inheritance migrated to scope-resolution in worker mode (#1951, #1956); centralized heritage supertype matching (#1921, #1922, #1940); `File->Member` `DEFINES` edges skipped for class members (#1949); phantom `Function` defs for array-method callbacks no longer emitted (#1906)
+- **MCP** — sibling-clone repo-ID collisions prevented and generated MCP tool names corrected (#2067); orphan processes avoided by handling stdin close/end and the startup race (#2049); duplicate-name repo resolution disambiguated for worktrees (#1753); Windows setup fallback when global `gitnexus` resolves to a non-spawnable shim (#1694)
+- **Worker pool** — resilient zero-copy ingestion worker pool prevents analyze hangs on TS-root-scale loads (#1693); cache-hit native workers no longer abort (#1751, #1833); worker-pool docs drift corrected and worker-side stack surfaced on crash (#2068, #2070)
+- **LadybugDB** — FTS loaded in the Windows read pool (#2040) and probed-then-loaded on Windows (#1690, #1692); non-ASCII KuzuDB paths resolved on Windows (#1811, #1817); WAL corruption detected in schema init with recovery surfaced (#1647, #1650); WAL checkpoint-threshold control (#1772); init lock skipped for read-only opens (#1783, #1784); `serve` kept stable when sidecars are missing (#1747)
+- **Server / API** — `gitnexus serve` startup restored under Express 5 (#1749); `/api/graph`, `/api/search`, `/api/grep` opened read-only (#1686); native read-only enforcement and prepared statements for Cypher query paths (#1655); `eval-server` localhost binding left to the OS (#1722)
+- **Embeddings** — local ONNX runtime guarded on macOS Intel before the transformers.js import (#1987)
+- **Web agent** — Nexus AI agent system prompt aligned with registered tools (#1984) and the agent stopped cleanly on user Stop (#1820)
+- **Group / contracts** — HTTP graph and source contracts unioned (#1709); `httpx` `AsyncClient` alias imports detected (#1687); Node gRPC `loadPackageDefinition` gate no longer matches every member call (#1916); manifest/workspace extraction moved before `closeLbug` (#1802, #1807)
+- **Hooks / install** — `gitnexus` resolved on `PATH` via a pure-Node, all-OS scan (#1938, #1980); offline-first extension installs (#1161); actionable error and docs for the `pnpm dlx`/`pnpx` native-load crash (#307, #1967); `onnxruntime-common` declared as a runtime dependency (#2074); vendored grammars materialized to fix Windows EPERM (#1728, #1729)
+- **CLI** — missing LadybugDB native binary detected at startup with actionable guidance (#835, #1837); `--no-stats` applied to the keep-marker stats line (#1706, #1765); skipped large-file paths surfaced by default (#1659, #1661); build.js skipped when running outside the monorepo (#1795, #1816); auto-heap raised to 16 GB with tightened cross-platform OOM guidance for UE5-scale repos (#1652)
+- **Wiki** — hidden 60s default timeout removed with timeout/retry flag validation and surfaced timeout errors (#1651); budget-aware grouping to prevent context overflow on large repos (#627, #1832)
+- **`detect-changes`** — `resolveWorktreeCwd` guarded against overriding a separately-indexed worktree (#1691)
+- **Windows reliability** — `windowsHide:true` passed to every `child_process` spawn-family call (#1794)
+
+### Changed
+
+- **Legacy resolution deletion (Ring 4)** — removed the legacy call-resolution DAG + heritage processor (RING4-1, #942, #2023), the legacy resolution-context + tiered-lookup plumbing (RING4-2, #943, #2033), and the shadow-mode parity harness (RING4-3, #944, #2071)
+- **CONTRIBUTING** — clarified local development setup (#2024)
+- **Tests / CI** — cli-e2e made read-only and eval-server tests hardened under load (#2000, #1786, #1838, #1688); parity shards consolidated and the cross-platform matrix narrowed (#1798); devcontainer smoke build hardened against Docker Hub flakes (#1969); gitleaks stabilized (#2027)
+
+### Performance
+
+- **Linux-kernel-scale analysis overhaul** — worker-pool parse, finalize O(n²), and the scope-resolution memory wall (#1983, #2038)
+- **Scope-capture linearized across all languages (O(n²)→O(n))** plus Python import-resolution linearization (#1918), the Go-specific re-walk fix (#1848, #1915), and owner-keyed lookup for Step 2 member resolution (#1657)
+- **C++ ADL candidates indexed once instead of per-site rescans** (#1990)
+- **Inert local value symbols pruned** during ingestion (#2065)
+
+### Chore / Dependencies
+
+- `@ladybugdb/core` bump in /gitnexus (#2056)
+- Routine dependency bumps across /gitnexus, /gitnexus-web, /eval, and GitHub Actions — incl. `hono`, `vitest`, `@vitest/coverage-v8`, `tsx`, `lru-cache`, `express`/`@types/express`, `express-rate-limit`, `qs`, `node-addon-api`, `brace-expansion`, `langchain`, `i18next`, `dompurify`, `lucide-react`, `axios`, `zod`, `@langchain/langgraph`, `@vercel/node`, `langsmith`, `aiohttp`, `idna`, and the `docker/*` / `github/codeql-action` / `release-drafter` / `dependency-review-action` actions (#2056, #2044, #2043, #2042, #2016, #2015, #2013, #2012, #2011, #2010, #2009, #2008, #2018, #2019, #2017, #2020, #1986, #1911, #1864, #1863, #1861, #1860, #1866, #1844, #1845, #1826, #1825, #1824, #1791, #1789, #1768, #1767, #1739, #1740, #1738, #1736, #1735, #1734, #1731, #1713, #1698, #1697, #1696, #1689, #1604, #1552, #1464, #872)
+- **Security** — `@vercel/node` upgraded in /gitnexus-web with transitive advisories remediated (#1705)
+
 ## [1.6.5] - 2026-05-16
 
 ### Added

gitnexus/README.md

@@ -400,7 +400,7 @@ Values above **32768 KB (32 MB)** are clamped to the tree-sitter parser ceiling;
 
 ### Analyze reports a worker timeout
 
-Worker parse timeouts are recoverable. GitNexus retries stalled worker jobs with backoff, splits large jobs to isolate slow files, and falls back to the sequential parser when needed. If a large repository needs more time per worker job, use either:
+Worker parse timeouts are recoverable. GitNexus retries stalled worker jobs with backoff, splits large jobs to isolate slow files, and quarantines a file that repeatedly crashes its worker (respawning the slot so the pool keeps going). If a large repository needs more time per worker job, use either:
 
 ```bash
 # CLI flag, in seconds
@@ -423,6 +423,16 @@ Three env vars expose the pool's resilience layers (respawn budget, cumulative-t
 | `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`     | `5 × subBatchTimeoutMs` | Total retry wall-time budget per job before quarantining. Bounds exponentially-growing retry waits.                   |
 | `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD` | `max(3, poolSize)`      | Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, dispatches require a fresh pool. |
 
+### Graph cleanup tuning
+
+After scope resolution, analyze prunes inert block-local value symbols (a function-local `const`/`let`/`var` that ends up with only its structural `File→DEFINES` edge) to keep the graph focused on cross-symbol relationships. Module/file-scope symbols, class members, and any local with a real edge are always kept.
+
+| Variable                             | Default | Effect                                                                                                  |
+| ------------------------------------ | ------- | ------------------------------------------------------------------------------------------------------- |
+| `GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS`  | unset   | Set to `1`/`true` to keep inert block-local value symbols instead of pruning them.                      |
+
+Programmatic callers can pass `keepLocalValueSymbols: true` in `PipelineOptions` instead of setting the env var.
+
 ## Privacy
 
 - All processing happens locally on your machine

gitnexus/bench/parse-throughput.md

@@ -70,10 +70,17 @@ this doc, run it under instrumentation:
 ```bash
 # From the gitnexus/ subdir:
 cd gitnexus
-# Single-threaded baseline (sequential fallback):
-npx vitest run test/integration/parse-impl-large-fixture.test.ts --reporter=verbose
+# The worker pool is the sole parse path, so every run needs the dist worker
+# (`npm run build`) and a pool size pinned via GITNEXUS_WORKER_POOL_SIZE.
 
-# Worker-pool path (requires built dist/ — pre-built by `npm run build`):
+# Single-worker-pool baseline (closest analog to the old single-threaded run —
+# sequential parsing was removed, so a 1-worker pool is the floor):
+npm run build && \
+  GITNEXUS_WORKER_POOL_SIZE=1 \
+  GITNEXUS_VERBOSE=1 \
+  npx vitest run test/integration/parse-impl-large-fixture.test.ts --reporter=verbose
+
+# Multi-worker path:
 npm run build && \
   GITNEXUS_WORKER_POOL_SIZE=4 \
   GITNEXUS_PARSE_CHUNK_CONCURRENCY=2 \
@@ -97,22 +104,26 @@ node --inspect=0 \
 ## Latest measurement
 
 > _No measurement data has been collected yet — this file is the
-> methodology + harness scaffold. The single recorded data point is the
-> U6 wall-clock smoke baseline below; the worker-pool rows are
-> placeholders for future bench-pass output._
+> methodology + harness scaffold. The U6 smoke test confirms the
+> worker-pool path stays well within its wall-clock budget, but every
+> throughput/heap cell below is a `_TBD_` placeholder for a future
+> bench-pass._
 
 The U6 integration test (`gitnexus/test/integration/parse-impl-large-fixture.test.ts`)
-was observed completing the synthetic fixture in **~6 seconds** under
-the sequential path (`skipWorkers: true`) on the development machine,
-well under the 30 s `Promise.race` wall-clock budget. That number is a
-smoke baseline only — recorded here for reference, not as a regression
-target.
+runs the worker pool — the sole parse path now that sequential parsing
+has been removed (disabling the pool on a repo with parseable files
+raises a hard `WorkerPoolDisabledError`). It completes the synthetic
+fixture well within the 30 s `Promise.race` wall-clock budget on the
+development machine, but no worker-pool throughput/heap numbers have been
+captured yet, so the rows below are all `_TBD_`. (An earlier ~6 s figure
+recorded here was measured on the now-removed sequential path; it has
+been dropped rather than relabelled as a worker-pool baseline, since the
+two paths are not comparable.)
 
-| Path                                       | files/s | wall-clock           | peak heap | chunks | quarantined |
-| ------------------------------------------ | ------- | -------------------- | --------- | ------ | ----------- |
-| Sequential (`skipWorkers: true`, U6 smoke) | _TBD_   | ~6 s _(observation)_ | _TBD_     | 17     | 0           |
-| Worker pool, `--workers 4`, concurrency 2  | _TBD_   | _TBD_                | _TBD_     | _TBD_  | 0           |
-| Worker pool, `--workers 1`, concurrency 1  | _TBD_   | _TBD_                | _TBD_     | _TBD_  | 0           |
+| Path                                                                      | files/s | wall-clock | peak heap | chunks | quarantined |
+| ------------------------------------------------------------------------- | ------- | ---------- | --------- | ------ | ----------- |
+| Worker pool, `--workers 1` (`GITNEXUS_WORKER_POOL_SIZE=1`), concurrency 1 | _TBD_   | _TBD_      | _TBD_     | _TBD_  | 0           |
+| Worker pool, `--workers 4`, concurrency 2                                 | _TBD_   | _TBD_      | _TBD_     | _TBD_  | 0           |
 
 **Hardware:** _TBD — record OS, CPU, RAM, Node version, gitnexus SHA at
 the time of the bench-pass that populates the table above._

gitnexus/bench/python-scope/baseline-fingerprint.txt

@@ -1 +1 @@
-06687dff942d531c4d453b5906a8666c90db4867eb43ed18304aa59a8a93ef9d
+c03f87cd8cd1ee716dea93cceb27109ee5b4584bc9fe426eea3f18fd6f9854cc

gitnexus/bench/scope-capture/baselines.json

@@ -1,9 +1,9 @@
 {
   "_comment": "Per-language baselines for bench/scope-capture/measure.mjs --check. fingerprint = order-independent sha256 over the lang-resolution/<lang>-* fixture corpus + a 20-entity synthetic source (correctness gate; re-baseline intentionally on a legitimate capture change). scaling_budget = max allowed (t800/t250)/(800/250); ~1.0 is linear, ~3.2 is quadratic. The synthetic source is now HERITAGE-BEARING for every language (each Entity extends/implements/embeds/uses-trait/conforms-to a shared base) so the #1951 @reference.inherits synth is gated at scale, not just the base capture loop. All languages thread the tree-sitter captured node instead of re-deriving it with findNodeAtRange(tree.rootNode,...) per match, so all are linear (go #1915, python #1918, ruby/php/rust/csharp #1951, java #1956).",
   "go": {
-    "fingerprint": "a909c197b07921f974de1a8a47cc997b9580153db2d400ef13d205b6c1de5865",
+    "fingerprint": "09ecd94911b830f52fa8807560abcbd79f163d02a2072870c1a59297e9a326e1",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1966: Go structural interface implementation detection changes capture output (method_elem, return-type, pointer receiver raw form, struct_type/interface_type containers)."
+    "_rebaselined": "#1976: F33 generic composite literal constructor inference adds generic_type captures in composite_literal patterns; fingerprint drift expected."
   },
   "cobol": {
     "fingerprint": "68ee0e95eb9f86f2d92ca35f730f4c2d4d83abc1b5241ae767ff3437780ec8d1",
@@ -11,71 +11,76 @@
     "_note": "Updated for F17-F23 fixes (P2: TIMES guard, ADD GIVING, SQL AS alias). See PR #1959."
   },
   "c": {
-    "fingerprint": "0de009bdbfe095f530fa87eb32bce6ab83092c904f26b3c8fe8d8ab587cf6dc9",
+    "fingerprint": "12a196b2d6249c8d86a931b12ecebc2a0cdf8d6f47683acdd0d8e9d8bc7657f5",
     "scaling_budget": 1.5,
-    "_added": "#1956: c added to the scope-capture bench (was UNBENCHED). C has no inheritance \u2014 flat scale source. Adding it exposed + fixed a pre-existing O(n^2) findNodeAtRange root-walk in c/captures.ts (threaded c.node, byte-identical over c-* fixtures); scaling 3.475 -> 0.96."
+    "_added": "#1956: c added to the scope-capture bench (was UNBENCHED). C has no inheritance — flat scale source. Adding it exposed + fixed a pre-existing O(n^2) findNodeAtRange root-walk in c/captures.ts (threaded c.node, byte-identical over c-* fixtures); scaling 3.475 -> 0.96.",
+    "_note": "#1983: + c-static-linkage-worker fixture (caller.c/lib.c/lib.h/local.c — worker-path static-linkage side-channel test). Pure fixture-corpus drift: no c/captures.ts or query change branch-vs-main, existing fixtures' captures byte-identical (c-captures.test.ts 45/45), scaling stays linear (~0.97). The baseline was missed when the fixture landed; regenerated here. fingerprint 0de009b->39f3a83.",
+    "_rebaselined": "#1919 open-language coverage: new lang-resolution fixtures + intended capture additions (F5/F9 c-cpp, F26/F28/F29 dart, F47/F48/F49/F51/F52 kotlin, F75/F79 swift). Fingerprint-only drift; scaling_ratio ~1.0 (linear, no perf regression)."
   },
   "cpp": {
-    "fingerprint": "2f517381e8b03db221d13f65d5e485d021c17a2f7fa684446e09f33d78c3adb9",
+    "fingerprint": "fd3d3768cdebbb4767d7cf18b8d2df19d61de969c816d7f4d6b599f947811356",
     "scaling_budget": 1.5,
     "_added": "#1956: cpp added to the scope-capture bench (was UNBENCHED). Heritage-bearing scale source (: public Base, public Mixin) drives emitCppInheritanceCaptures at scale. Adding it exposed + fixed a pre-existing O(n^2) findNodeAtRange root-walk in cpp/captures.ts (~12 sites, threaded c.node, byte-identical over 263 cpp-* fixtures); scaling 2.30 -> 1.12.",
-    "_rebaselined": "#1965 / #1923 F4: uninitialized non-leading multi-declarators now emit @declaration.variable captures; cpp-adl-inner-callable-outer-noncallable data::Pair a, b adds the legitimate fixture drift. Linear (~1.06).",
-    "_note": "#1975: + cpp-out-of-line-class fixture (out-of-line struct Outer::Inner / Other::Inner). Pure fixture-corpus drift — the fix is the legacy structure-query qualified_identifier arm, NOT the cpp scope-extractor; existing fixtures' captures byte-identical. fixture_count 263->265. #1982: cpp-nested-tail-collision gains qualified heritage (struct DerivedA : Outer::Inner, struct DerivedB : Other::Inner) AND emitCppInheritanceCaptures now emits an ADDITIVE @reference.qualified-name capture on QUALIFIED bases (drives the qualified-first inheritance resolver). Purely additive — existing captures unchanged; same fixture file, no new fixture."
+    "_rebaselined": "#1919 open-language coverage: new lang-resolution fixtures + intended capture additions (F5/F9 c-cpp, F26/F28/F29 dart, F47/F48/F49/F51/F52 kotlin, F75/F79 swift). Fingerprint-only drift; scaling_ratio ~1.0 (linear, no perf regression).",
+    "_note": "#1975: + cpp-out-of-line-class fixture, fixture_count 263->265. #1990: + cpp-adl-ns-plus-hidden-friend-same-name fixture (ADL hidden-friend + namespace-callable merge parity test). Pure fixture-corpus drift — no scope-extractor change; existing fixtures' captures byte-identical. fixture_count 265->267. #1995: + cpp-union-nested-tail-collision and cpp-anon-ns-tail-collision fixtures — pure fixture-corpus drift; fixture_count 270->272, fingerprint 538e8be->d63ded6. #1993: + cpp-cross-namespace-same-tail fixture — pure fixture-corpus drift; fixture_count 272->273, fingerprint d63ded6->6d6207ae."
   },
   "csharp": {
-    "_rebaselined": "#1956 synth-widening: + csharp-qualified-base fixture; the synth now walks record_declaration + struct_declaration base_lists and handles alias_qualified_name (matching the #1940 legacy leg), so record/struct heritage now emits. csharp-record-base gains a record inherits capture. (record->record SAME-namespace EXTENDS is a separate registry resolution gap, tracked as follow-up.) Linear (~1.00). (Earlier #1956: heritage-bearing scale source.)",
-    "fingerprint": "68ef32c126d5c6de5d8184c6ad0a6104043036daf9805947db8b21741b883f43",
-    "scaling_budget": 1.5
+    "_rebaselined": "#1956 synth-widening: + csharp-qualified-base fixture; the synth now walks record_declaration + struct_declaration base_lists and handles alias_qualified_name (matching the #1940 legacy leg), so record/struct heritage now emits. csharp-record-base gains a record inherits capture. (record->record SAME-namespace EXTENDS is a separate registry resolution gap, tracked as follow-up.) Linear (~1.00). (Earlier #1956: heritage-bearing scale source.) | #942: scope-resolution-only cleanup reworded fixture comments; capture byte-positions shift, capture LOGIC unchanged. | #1924 F16: record primary-constructor base bindings now exclude constructor arguments; capture fingerprint changes, scaling remains linear. | #2036 review follow-up: csharp-record-base now exercises primary-constructor base dispatch end to end; +2 capture groups, scaling remains linear.",
+    "fingerprint": "2bb5bc8c19cb8eb08c9590545ad8a1968a7152951f7e12746e2d7901d542fed9",
+    "scaling_budget": 1.5,
+    "_note": "#2046: F35 qualified-constructor captures now emit @reference.qualified-name + a simple-name @reference.name on `new Ns.Foo()`/`new A.B.Foo()`; namespace_declaration/file_scoped_namespace_declaration now emit @declaration.namespace name captures (feeding the non-destructive namespacePrefix sidecar for `new B.Foo()` same-tail disambiguation). + csharp-interface-only-base and csharp-namespace-qualified-ctor fixtures. Pure capture-additive + fixture-corpus drift; scaling stays linear (~1.11)."
   },
   "rust": {
-    "fingerprint": "30224e2590064745548bc1d623811ae5d37227618854788695442a0acf1898fb",
+    "fingerprint": "ac610bbe97666bf285923479dd7b43a2fe4c5354aae8df1bcbafdc04fb220f82",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1956 tri-review U1: rust-qualified-trait fixture (scoped + generic-of-scoped impl trait paths); bareTypeIdentifier now resolves scoped_type_identifier bases by their name: tail (additive, no existing-fixture drift); linear (~1.04).",
-    "_note": "#1975: + rust-scoped-impl fixture (impl a::Inner / b::Inner inherent scoped impls). Pure fixture-corpus drift — the fix is the legacy @definition.impl scoped arm + findEnclosingClassInfo inherent-impl scoped target, NOT the rust scope-extractor; existing fixtures' captures byte-identical. fixture_count 120->121."
+    "_rebaselined": "#1956 tri-review U1: rust-qualified-trait fixture (scoped + generic-of-scoped impl trait paths); bareTypeIdentifier now resolves scoped_type_identifier bases by their name: tail (additive, no existing-fixture drift); linear (~1.04). #1975: + rust-scoped-impl fixture (impl a::Inner / b::Inner inherent scoped impls) — legacy @definition.impl scoped arm + findEnclosingClassInfo inherent-impl scoped target; rust scope-extractor captures byte-identical. | #942: scope-resolution-only cleanup reworded fixture comments; capture byte-positions shift, capture LOGIC unchanged.",
+    "_note": "PR #1934: F66/F68 let-binding pattern narrowing; F71 union (Struct-labeled, now materialized via legacy @definition.struct + resolvable); F72 macro FULLY WIRED — @declaration.macro/@reference.macro + MacroRegistry → USES edges to Macro nodes (never a same-named fn). + rust-macro / rust-union fixtures and merged with origin/main #1975 rust-scoped-impl; fingerprint re-baselined (scaling ~0.99, fixture_count 126). #1992: + rust-nested-tail-collision-generic and rust-generic-impl-same-method-name (F3) fixtures — pure fixture-corpus drift, no scope-extractor change; fixture_count 127->129, fingerprint 56ffc1c0->b00aea0f."
   },
   "php": {
-    "fingerprint": "f9c8eaf6d1084f9b95a9fb97ccce5e618a24d936c85fb8af4b96c73a560f7a7f",
+    "fingerprint": "bc2c27c5ba26d5aea61142a2a99fb772222f5b969205260eb7a71b4c0bd73cdb",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1956: heritage-bearing scale source (class extends Base + use trait); both forms gated at scale; linear (~1.04)."
+    "_rebaselined": "#1956: heritage-bearing scale source (class extends Base + use trait); both forms gated at scale; linear (~1.04).",
+    "_note": "PR #1931: F53 import multi-clause, F54 enum_case, F55 anonymous_class — fixture count 138→140, fingerprint drift expected."
   },
   "ruby": {
-    "fingerprint": "011c0533318ff61d99267d501866af8a616b1c212050628339064d8c149aafbf",
+    "fingerprint": "b5ea93bb3d0469c3821a8c70f5d5991c6f326e41097c119ad691154301dcc753",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1956 synth-widening: + ruby-qualified-base fixture; synth now reduces a scope_resolution superclass (class C < Mod::Super) to its trailing constant (matching the #1940 legacy leg), at parity. Linear (~1.03). (Earlier #1956: heritage-bearing scale source.)",
-    "_note": "F62: + scope_resolution class/module declaration captures — fixture count 78→81, fingerprint drift expected. #1975: + ruby-tail-collision fixture (Foo::Bar vs Baz::Bar stay distinct nodes) — pure fixture-corpus drift, scope-extractor captures unchanged; 81→82. #1978: + ruby-nested-tail-collision (same-tail Inner under Outer/Other modules + Shapes.Circle attr_accessor) — pure fixture-corpus drift, scope-extractor captures unchanged; 82→83. #1982: that fixture gains same-tail include + attr_accessor, AND emitRubyScopeCaptures now emits the FULL qualified owner in __heritage__/__property__ markers (buildEnclosingQualifiedName) — a CODE change LOCALIZED to nested owners: the golden shows ONLY this fixture drifts (+10 capture groups), all other ruby fixtures byte-identical, and 142/142 resolver tests pass. fixture_count 83 (same file)."
+    "_rebaselined": "#1956 synth-widening: + ruby-qualified-base fixture; synth now reduces a scope_resolution superclass (class C < Mod::Super) to its trailing constant (matching the #1940 legacy leg), at parity. Linear (~1.03). (Earlier #1956: heritage-bearing scale source.) | #942: scope-resolution-only cleanup reworded fixture comments; capture byte-positions shift, capture LOGIC unchanged.",
+    "_note": "F62: + scope_resolution class/module declaration captures — fixture count 78→81, fingerprint drift expected. #1975: + ruby-tail-collision fixture (Foo::Bar vs Baz::Bar stay distinct nodes) — pure fixture-corpus drift, scope-extractor captures unchanged; 81→82. #1991: + ruby-nested-mixin-tail-collision fixture (85→86). Recomputed on the #942 merge (fixture-comment rewording shifts capture byte-positions, capture LOGIC unchanged): bf6b13a -> b5ea93bb."
   },
   "swift": {
-    "fingerprint": "53325c6345161c5a495f997297af5a24fb718fd3e6647040160f8ab2a2c8e4c0",
+    "fingerprint": "180ac68e780bdf6f9089d53f51cbb9a66aed3e7774631cc3fcbaae5020213998",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1956: swift-qualified-base fixture + heritage-bearing scale source (class: Base, Serviceable \u2014 extends + protocol conformance); linear (~1.03)."
+    "_rebaselined": "#1919 open-language coverage: new lang-resolution fixtures + intended capture additions (F5/F9 c-cpp, F26/F28/F29 dart, F47/F48/F49/F51/F52 kotlin, F75/F79 swift). Fingerprint-only drift; scaling_ratio ~1.0 (linear, no perf regression)."
   },
   "dart": {
-    "fingerprint": "a9e882b537765e8fd0ddfcd33b38b253dd86fc5ddffa6e4bf5a85ed8ee615eaa",
+    "fingerprint": "94bf2c26e1ba96f4211634aa572c0a989b503e717e75dfc5df04f66c417de80f",
     "scaling_budget": 1.5,
     "_added": "#939: dart added to the scope-capture bench with the registry-primary migration. Heritage-bearing scale source (Entity extends Base implements Marker) gates the @reference.inherits synth + the postfix-chain reference walk at scale. emitDartScopeCaptures threads tree-sitter captured nodes (no findNodeAtRange root-walk), so it is linear (~1.0).",
-    "_rebaselined": "#1970 review + tri-review follow-ups: constructor-call retag, cascade calls, built-in suppression, enum scope, #1926 F24/F25, named-ctor dedup (crash fix), container-name binding suppression; heritage file-affinity resolution. Fixtures: member-call-contexts, constructor-body, named-constructor-body, heritage-name-collision, construct-cascade."
+    "_rebaselined": "#1919 review CF3 fix: extended kotlin-local-property-owner (init/accessor destructuring) + new dart-accessor-owner fixture (getter/setter ownership). Fingerprint-only corpus drift; scaling ~1.0."
   },
   "java": {
-    "fingerprint": "b63f9be458f7ece854e7b007159d7bf65b4b66a86e83a6c0656fc93ebd5d83da",
+    "fingerprint": "9b29cafe32873b4902bda311bd089ffc04efe08f13557b966d29544be514080a",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1956 synth-widening: + java-iface-extends fixture; synthesizeJavaInheritanceReferences now ALSO walks interface_declaration extends_interfaces (interface IA extends IB, IC<T>), matching the #1940 legacy leg. (Earlier U2+review: java-qualified-base fixture covers 2- AND 3-segment qualified bases guarding the legacy end-anchor; synth tail-resolves scoped bases.) Linear (~1.03). (Earliest: java added to bench, exposed+fixed the O(n^2) findNodeAtRange root-walk; 3.09 -> ~0.99.)"
+    "_rebaselined": "#1956 synth-widening: + java-iface-extends fixture; synthesizeJavaInheritanceReferences now ALSO walks interface_declaration extends_interfaces (interface IA extends IB, IC<T>), matching the #1940 legacy leg. (Earlier U2+review: java-qualified-base fixture covers 2- AND 3-segment qualified bases guarding the legacy end-anchor; synth tail-resolves scoped bases.) Linear (~1.03). (Earliest: java added to bench, exposed+fixed the O(n^2) findNodeAtRange root-walk; 3.09 -> ~0.99.) | #942: scope-resolution-only cleanup reworded fixture comments; capture byte-positions shift, capture LOGIC unchanged.",
+    "_note": "#1928 / #2045: F35 adds qualified + qualified-generic constructor query captures (`new pkg.Foo()`, `new a.b.Foo()`, `new pkg.Box<T>()`); F38 synthesizes `@reference.call.constructor` on `super(...)`/`this(...)` explicit_constructor_invocation nodes; F41 generic-aware stripQualifier in interpret (type-binding normalization). + java-qualified-constructor and java-explicit-constructor fixtures. Pure capture-additive + fixture-corpus drift; scaling stays linear (~1.06)."
   },
   "typescript": {
     "fingerprint": "3f44a4a6892698df2d145c8ff2812c3b318807648983c88aca28fbd694f172f9",
     "scaling_budget": 1.5,
-    "_rebaselined": "#1962: F44 (class scope@), F85 (enum member declarations), F87 (optional_parameter type annotations) add new captures \u2014 fingerprint drift expected.",
-    "_note": "#1968: F44, F85, F87 \u2014 fingerprint drift expected."
+    "_rebaselined": "#1962: F44 (class scope@), F85 (enum member declarations), F87 (optional_parameter type annotations) add new captures — fingerprint drift expected.",
+    "_note": "#1968: F44, F85, F87 — fingerprint drift expected."
   },
   "javascript": {
-    "fingerprint": "a8ddfb15620ae55e50651fc21ab14c4a1f874d9b19e208cc6cbf0a8daac8ec5b",
+    "fingerprint": "d72f03c6c502235d2d4b74d66baa5c7d361f040d7a1b72e84acad61210d05ae8",
     "scaling_budget": 1.5,
     "_added": "#1951: bench coverage added (was ungated); scale source heritage-bearing (extends Base); js/kotlin O(n^2) findNodeAtRange-per-match fixed to threaded captured node, now linear.",
-    "_rebaselined": "#1956 synth-widening: + javascript-qualified-base fixture; synthesizeJsInheritanceReferences now handles a member_expression base (class S extends ns.Base -> Base), matching the #1940 legacy leg + the TS terminalTsTypeNameNode property_identifier case, at parity. Linear (~1.05)."
+    "_rebaselined": "#1956 synth-widening: + javascript-qualified-base fixture; synthesizeJsInheritanceReferences now handles a member_expression base (class S extends ns.Base -> Base), matching the #1940 legacy leg + the TS terminalTsTypeNameNode property_identifier case, at parity. Linear (~1.05). | #942: scope-resolution-only cleanup reworded fixture comments; capture byte-positions shift, capture LOGIC unchanged."
   },
   "kotlin": {
-    "fingerprint": "5121a11855cd9cc44a357ae3ff50953de80cdd743f00e8924c31503b132bcd84",
+    "fingerprint": "90aa832978d9744e50058e77a04748390a7e34e36b309f6c1d178eb07280b7ea",
     "scaling_budget": 1.5,
     "_added": "#1951: bench coverage added (was ungated); scale source heritage-bearing (: Base()); js/kotlin O(n^2) findNodeAtRange-per-match fixed to threaded captured node, now linear.",
-    "_rebaselined": "#1956 synth-widening: + kotlin-qualified-base fixture; synthesizeKotlinInheritanceReferences now handles the explicit_delegation form (class F : Iface by d -> Iface), matching the #1940 legacy leg, at parity. Linear (~0.87)."
+    "_rebaselined": "#1919 review CF3 fix: extended kotlin-local-property-owner (init/accessor destructuring) + new dart-accessor-owner fixture (getter/setter ownership). Fingerprint-only corpus drift; scaling ~1.0."
   }
 }

gitnexus/hooks/claude/resolve-analyze-cmd.cjs

@@ -27,6 +27,8 @@
  */
 
 const { execFileSync } = require('child_process');
+const fs = require('fs');
+const path = require('path');
 
 const NPX_REF = 'gitnexus@latest';
 
@@ -34,46 +36,72 @@ const NPX_REF = 'gitnexus@latest';
 const PNPM_ALLOW_BUILD_BASE = ['@ladybugdb/core', 'gitnexus', 'tree-sitter'];
 const PNPM_ALLOW_BUILD_EMBEDDINGS = ['onnxruntime-node'];
 
-// Probe timeout, kept under Claude Code's 10s hook budget. In a linked worktree
-// the stale-index hook first runs `git rev-parse --git-common-dir` (~2s) and
-// `git rev-parse HEAD` (~3s); the pnpm path then adds up to four 1s probes
-// (which gitnexus, npm --version, which pnpm, pnpm --version), so the worst case
-// is ~9s — within budget but tight. A healthy `which`/`where`/`--version`
-// returns in well under a second, so the realistic cost is far lower.
+// Version-probe timeout, kept under Claude Code's 10s hook budget. PATH presence
+// detection is now spawn-free (resolveOnPath scans PATH directly), so the only
+// subprocesses left are the version probes: in a linked worktree the stale-index
+// hook first runs `git rev-parse --git-common-dir` (~2s) and `git rev-parse HEAD`
+// (~3s); the pnpm path then adds up to two 1s `--version` probes (npm, pnpm), so
+// the worst case is ~7s — within budget. A healthy `--version` returns in well
+// under a second, so the realistic cost is far lower.
 const PROBE_TIMEOUT_MS = 1000;
 
 /**
- * Pick the best match from `where`/`which` output. A global `gitnexus` may be a
- * `.cmd`/`.bat` (npm), a `.exe`, or an extensionless shim (Volta, scoop), so on
- * Windows we prefer a recognized executable extension but accept any hit — the
- * emitted hint is `gitnexus analyze` regardless of which shim resolves it. Pure
- * and exported so the shim-matching can be unit-tested without spawning.
+ * Absolute path to `command` on PATH, or null — a pure-Node, spawn-free lookup
+ * that mirrors how a shell resolves a bare command name: each PATH dir × the
+ * platform's executable extensions (PATHEXT on Windows; the bare name + X_OK on
+ * POSIX). This replaces the former `where`/`which` subprocess (#1938 "Option A"):
+ * it is byte-for-byte identical on every OS, with no dependency on the probe
+ * binary being reachable (a sanitized PATH that drops System32 / `/usr/bin` no
+ * longer defeats detection), no shell-spawn surface (CVE-2024-27980), and no
+ * spawn timeout to tune. On Windows it matches PATHEXT extensions ONLY — exactly
+ * what `where`/cmd.exe resolve — so neither an un-spawnable `.ps1`-only shim (not
+ * in default PATHEXT) nor a bare extensionless file (which the shell cannot launch
+ * as `command`) is a false positive. `preferExecExt` returns a recognized
+ * `.cmd`/`.bat`/`.exe` shim ahead of an exotic PATHEXT hit (e.g. `.COM`) when both
+ * match, matching what a user would actually launch. Pure (platform/env injectable)
+ * so it is unit-testable without touching the host PATH.
  */
-function pickPathMatch(output, { isWin, gitnexusWrapper } = {}) {
-  const lines = output
-    .split('\n')
-    .map((l) => l.trim())
-    .filter(Boolean);
-  if (isWin && gitnexusWrapper) {
-    return lines.find((l) => /\.(cmd|bat|exe)$/i.test(l)) || lines[0] || null;
-  }
-  return lines[0] || null;
-}
-
-/** Absolute path to `command` on PATH, or null. `gitnexusWrapper` enables the Windows shim match. */
-function resolveOnPath(command, gitnexusWrapper = false) {
-  const isWin = process.platform === 'win32';
-  try {
-    const output = execFileSync(isWin ? 'where' : 'which', [command], {
-      encoding: 'utf-8',
-      timeout: PROBE_TIMEOUT_MS,
-      stdio: ['ignore', 'pipe', 'ignore'],
-      windowsHide: true,
-    });
-    return pickPathMatch(output, { isWin, gitnexusWrapper });
-  } catch {
-    return null;
+function resolveOnPath(
+  command,
+  preferExecExt = false,
+  { platform = process.platform, env = process.env } = {},
+) {
+  const pathValue = env.PATH || env.Path || env.path || '';
+  if (!pathValue) return null;
+  const isWin = platform === 'win32';
+  const exts = isWin
+    ? (env.PATHEXT || '.COM;.EXE;.BAT;.CMD')
+        .split(';')
+        .map((e) => e.trim())
+        .filter(Boolean)
+        .map((e) => (e.startsWith('.') ? e : `.${e}`))
+    : [''];
+  let weakHit = null;
+  // Split on the host's PATH delimiter. `platform` is injected only to choose the
+  // extension/exec-bit rules; the PATH string is always host-format, so it must
+  // split on the host delimiter (`path.delimiter`) — in production `platform` IS
+  // the host, so they coincide. (Deriving the delimiter from an injected platform
+  // would split a Windows drive-letter path `C:\…` at its colon under a POSIX
+  // injection.)
+  for (const dir of pathValue.split(path.delimiter).filter(Boolean)) {
+    for (const ext of exts) {
+      const candidate = path.join(dir, `${command}${ext}`);
+      try {
+        if (!fs.statSync(candidate).isFile()) continue;
+        if (!isWin) fs.accessSync(candidate, fs.constants.X_OK);
+        // Prefer a runnable .cmd/.bat/.exe shim; remember an exotic PATHEXT hit
+        // (e.g. .COM) only as a last resort if nothing better turns up.
+        if (isWin && preferExecExt && !/\.(cmd|bat|exe)$/i.test(ext)) {
+          weakHit = weakHit || candidate;
+          continue;
+        }
+        return candidate;
+      } catch {
+        /* not a runnable file here — try the next candidate */
+      }
+    }
   }
+  return weakHit;
 }
 
 // One spawn of `<command> --version` → { major, minor } (each null when
@@ -193,12 +221,12 @@ function formatPnpmDlxCommand(gitnexusArgs, options = {}, deps = {}) {
 function formatAnalyzeCommand(options = {}, deps = {}) {
   const suffix = options.embeddings ? ' --embeddings' : '';
   // Keep the stale-index hook budget tight by querying each tool at most once.
-  // A memoized PATH probe is shared with resolveInvocationMode (so `gitnexus`
-  // isn't probed twice), and pnpm's version is captured by a single
-  // `pnpm --version` that proves both presence (for mode resolution) and
-  // version (for the allow-build gate) — replacing the former `which pnpm` +
-  // `pnpm --version` double spawn. Injected deps (tests) and forced/global
-  // modes skip the pnpm probe.
+  // The memoized `probe` is a spawn-free PATH scan (resolveOnPath) shared with
+  // resolveInvocationMode, so `gitnexus` is scanned only once and no subprocess
+  // is spawned for presence. pnpm's *version* is still captured by a single
+  // `pnpm --version` (the allow-build gate needs the number), which also proves
+  // presence; the memoized scan only re-checks pnpm when that version is
+  // unreadable. Injected deps (tests) and forced/global modes skip the pnpm probe.
   const cache = new Map();
   const probe = (command, gitnexusWrapper) => {
     const key = `${command}:${gitnexusWrapper ? 1 : 0}`;
@@ -256,7 +284,7 @@ module.exports = {
   formatPnpmDlxCommand,
   resolveInvocationMode,
   buildRunnerArgv,
-  pickPathMatch,
+  resolveOnPath,
   getNpmMajorVersion,
   NPX_REF,
   PNPM_ALLOW_BUILD_BASE,

gitnexus/package-lock.json

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+      "resolved": "https://registry.npmjs.org/@oxc-project/types/-/types-0.133.0.tgz",
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@@ -1388,9 +1388,9 @@
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@@ -1405,9 +1405,9 @@
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@@ -1439,9 +1439,9 @@
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@@ -1456,9 +1456,9 @@
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@@ -1490,9 +1490,9 @@
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@@ -1524,9 +1524,9 @@
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@@ -1541,9 +1541,9 @@
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-      "version": "11.5.0",
-      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.5.0.tgz",
-      "integrity": "sha512-5YgH9UJd7wVb9hIouI2adWpgqrrICkt070Dnj8EUY1+B4B2P9eRLPAkAAo6NICA7CEhOIeBHl46u9zSNpNu7zA==",
+      "version": "11.5.1",
+      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.5.1.tgz",
+      "integrity": "sha512-RPimw/7aMdv2oqRrxKwvZXcPfwBrn/JZ2xYcY9Hus/6LaS3VOAKVWKWgNLCFSiOm1ESXinjsDlidVU7JlnCN2A==",
       "license": "BlueOak-1.0.0",
       "engines": {
         "node": "20 || >=22"
@@ -4292,13 +4456,13 @@
       }
     },
     "node_modules/rolldown": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/rolldown/-/rolldown-1.0.2.tgz",
-      "integrity": "sha512-oZx5zVDtVB44AW3eaifgDml1gWRDZGvjcfdxonE4swNPG98PrrXjaO/KrnUjzlMnztCCRVlUueA1kCXhARGk6g==",
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/rolldown/-/rolldown-1.0.3.tgz",
+      "integrity": "sha512-i00lAJ2ks1BYr7rjNjKC7BcqAS7nVfiT3QX1SI5aY+AFHblCmaUf9OE9dbdzDvW6dJxbi2ZCZiy9v3CcwOiX3g==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@oxc-project/types": "=0.132.0",
+        "@oxc-project/types": "=0.133.0",
         "@rolldown/pluginutils": "^1.0.0"
       },
       "bin": {
@@ -4308,21 +4472,21 @@
         "node": "^20.19.0 || >=22.12.0"
       },
       "optionalDependencies": {
-        "@rolldown/binding-android-arm64": "1.0.2",
-        "@rolldown/binding-darwin-arm64": "1.0.2",
-        "@rolldown/binding-darwin-x64": "1.0.2",
-        "@rolldown/binding-freebsd-x64": "1.0.2",
-        "@rolldown/binding-linux-arm-gnueabihf": "1.0.2",
-        "@rolldown/binding-linux-arm64-gnu": "1.0.2",
-        "@rolldown/binding-linux-arm64-musl": "1.0.2",
-        "@rolldown/binding-linux-ppc64-gnu": "1.0.2",
-        "@rolldown/binding-linux-s390x-gnu": "1.0.2",
-        "@rolldown/binding-linux-x64-gnu": "1.0.2",
-        "@rolldown/binding-linux-x64-musl": "1.0.2",
-        "@rolldown/binding-openharmony-arm64": "1.0.2",
-        "@rolldown/binding-wasm32-wasi": "1.0.2",
-        "@rolldown/binding-win32-arm64-msvc": "1.0.2",
-        "@rolldown/binding-win32-x64-msvc": "1.0.2"
+        "@rolldown/binding-android-arm64": "1.0.3",
+        "@rolldown/binding-darwin-arm64": "1.0.3",
+        "@rolldown/binding-darwin-x64": "1.0.3",
+        "@rolldown/binding-freebsd-x64": "1.0.3",
+        "@rolldown/binding-linux-arm-gnueabihf": "1.0.3",
+        "@rolldown/binding-linux-arm64-gnu": "1.0.3",
+        "@rolldown/binding-linux-arm64-musl": "1.0.3",
+        "@rolldown/binding-linux-ppc64-gnu": "1.0.3",
+        "@rolldown/binding-linux-s390x-gnu": "1.0.3",
+        "@rolldown/binding-linux-x64-gnu": "1.0.3",
+        "@rolldown/binding-linux-x64-musl": "1.0.3",
+        "@rolldown/binding-openharmony-arm64": "1.0.3",
+        "@rolldown/binding-wasm32-wasi": "1.0.3",
+        "@rolldown/binding-win32-arm64-msvc": "1.0.3",
+        "@rolldown/binding-win32-x64-msvc": "1.0.3"
       }
     },
     "node_modules/router": {
@@ -4694,7 +4858,6 @@
       "version": "7.2.0",
       "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
       "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
-      "dev": true,
       "license": "MIT",
       "dependencies": {
         "has-flag": "^4.0.0"
@@ -4703,6 +4866,19 @@
         "node": ">=8"
       }
     },
+    "node_modules/table-layout": {
+      "version": "4.1.1",
+      "resolved": "https://registry.npmjs.org/table-layout/-/table-layout-4.1.1.tgz",
+      "integrity": "sha512-iK5/YhZxq5GO5z8wb0bY1317uDF3Zjpha0QFFLA8/trAoiLbQD0HUbMesEaxyzUgDxi2QlcbM8IvqOlEjgoXBA==",
+      "license": "MIT",
+      "dependencies": {
+        "array-back": "^6.2.2",
+        "wordwrapjs": "^5.1.0"
+      },
+      "engines": {
+        "node": ">=12.17"
+      }
+    },
     "node_modules/tar": {
       "version": "7.5.13",
       "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.13.tgz",
@@ -4749,9 +4925,9 @@
       }
     },
     "node_modules/tinyglobby": {
-      "version": "0.2.16",
-      "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.16.tgz",
-      "integrity": "sha512-pn99VhoACYR8nFHhxqix+uvsbXineAasWm5ojXoN8xEwK5Kd3/TrhNn1wByuD52UxWRLy8pu+kRMniEi6Eq9Zg==",
+      "version": "0.2.17",
+      "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.17.tgz",
+      "integrity": "sha512-wXR/dYpcqKmfWpEdZjiKJOwCNFndD0DMnrW/cYjVGttEkBfVgcLFHoNrlj47mjOVic9yyNu65alsgF4NQyTa2g==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -5036,13 +5212,12 @@
       "version": "2.8.1",
       "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz",
       "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==",
-      "license": "0BSD",
-      "optional": true
+      "license": "0BSD"
     },
     "node_modules/tsx": {
-      "version": "4.22.3",
-      "resolved": "https://registry.npmjs.org/tsx/-/tsx-4.22.3.tgz",
-      "integrity": "sha512-mdoNxBC/cSQObGGVQ5Bpn5i+yv7j68gk3Nfm3wFjcJg3Z0Mix9jzAFfP12prmm5eVGmDKtp0yyArrs0Q+8gZHg==",
+      "version": "4.22.4",
+      "resolved": "https://registry.npmjs.org/tsx/-/tsx-4.22.4.tgz",
+      "integrity": "sha512-X8EX+XV4QR5xCsrgxaED954zTDfY8KqlDtskKEL0cHhyS/P8b4IFOvGDQpsC9Q1XnLq915wEfwwY/zzskCtmhg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -5115,6 +5290,15 @@
         "node": ">=14.17"
       }
     },
+    "node_modules/typical": {
+      "version": "7.3.0",
+      "resolved": "https://registry.npmjs.org/typical/-/typical-7.3.0.tgz",
+      "integrity": "sha512-ya4mg/30vm+DOWfBg4YK3j2WD6TWtRkCbasOJr40CseYENzCUby/7rIvXA99JGsQHeNxLbnXdyLLxKSv3tauFw==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.17"
+      }
+    },
     "node_modules/undici-types": {
       "version": "7.24.6",
       "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.24.6.tgz",
@@ -5168,17 +5352,17 @@
       }
     },
     "node_modules/vite": {
-      "version": "8.0.14",
-      "resolved": "https://registry.npmjs.org/vite/-/vite-8.0.14.tgz",
-      "integrity": "sha512-s4BJJ+5y1pYL6Otw51FHhVJQhPnuRinKig64g/1+EUNaJsd3gCKdD31IPFvswUgW9/60QT9oFHbZHbQK5imcxw==",
+      "version": "8.0.16",
+      "resolved": "https://registry.npmjs.org/vite/-/vite-8.0.16.tgz",
+      "integrity": "sha512-h9bXPmJichP5fLmVQo3PyaGSDE2n3aPuomeAlVRm0JLmt4rY6zmPKd59HYI4LNW8oTK7tlTsuC7l/m7awx9Jcw==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
         "lightningcss": "^1.32.0",
         "picomatch": "^4.0.4",
         "postcss": "^8.5.15",
-        "rolldown": "1.0.2",
-        "tinyglobby": "^0.2.16"
+        "rolldown": "1.0.3",
+        "tinyglobby": "^0.2.17"
       },
       "bin": {
         "vite": "bin/vite.js"
@@ -5246,19 +5430,19 @@
       }
     },
     "node_modules/vitest": {
-      "version": "4.1.7",
-      "resolved": "https://registry.npmjs.org/vitest/-/vitest-4.1.7.tgz",
-      "integrity": "sha512-flYyaFd2CgoCoU+0UKt3pxksgC+S02iTDN0n3LtqaMeXsI9SBcdNujc2k0DeFLzUn/0k538yNjOSdwgCqcrwJA==",
+      "version": "4.1.8",
+      "resolved": "https://registry.npmjs.org/vitest/-/vitest-4.1.8.tgz",
+      "integrity": "sha512-flY6ScbCIt9HThs+C5HS7jvGOB560DJtk/Z15IQROTA6zEy49Nh8T/dofWTQL+n3vswqn87sbJNiuqw1SDp5Ig==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@vitest/expect": "4.1.7",
-        "@vitest/mocker": "4.1.7",
-        "@vitest/pretty-format": "4.1.7",
-        "@vitest/runner": "4.1.7",
-        "@vitest/snapshot": "4.1.7",
-        "@vitest/spy": "4.1.7",
-        "@vitest/utils": "4.1.7",
+        "@vitest/expect": "4.1.8",
+        "@vitest/mocker": "4.1.8",
+        "@vitest/pretty-format": "4.1.8",
+        "@vitest/runner": "4.1.8",
+        "@vitest/snapshot": "4.1.8",
+        "@vitest/spy": "4.1.8",
+        "@vitest/utils": "4.1.8",
         "es-module-lexer": "^2.0.0",
         "expect-type": "^1.3.0",
         "magic-string": "^0.30.21",
@@ -5286,12 +5470,12 @@
         "@edge-runtime/vm": "*",
         "@opentelemetry/api": "^1.9.0",
         "@types/node": "^20.0.0 || ^22.0.0 || >=24.0.0",
-        "@vitest/browser-playwright": "4.1.7",
-        "@vitest/browser-preview": "4.1.7",
-        "@vitest/browser-webdriverio": "4.1.7",
-        "@vitest/coverage-istanbul": "4.1.7",
-        "@vitest/coverage-v8": "4.1.7",
-        "@vitest/ui": "4.1.7",
+        "@vitest/browser-playwright": "4.1.8",
+        "@vitest/browser-preview": "4.1.8",
+        "@vitest/browser-webdriverio": "4.1.8",
+        "@vitest/coverage-istanbul": "4.1.8",
+        "@vitest/coverage-v8": "4.1.8",
+        "@vitest/ui": "4.1.8",
         "happy-dom": "*",
         "jsdom": "*",
         "vite": "^6.0.0 || ^7.0.0 || ^8.0.0"
@@ -5367,6 +5551,15 @@
         "node": ">=8"
       }
     },
+    "node_modules/wordwrapjs": {
+      "version": "5.1.1",
+      "resolved": "https://registry.npmjs.org/wordwrapjs/-/wordwrapjs-5.1.1.tgz",
+      "integrity": "sha512-0yweIbkINJodk27gX9LBGMzyQdBDan3s/dEAiwBOj+Mf0PPyWL6/rikalkv8EeD0E8jm4o5RXEOrFTP3NXbhJg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.17"
+      }
+    },
     "node_modules/wrap-ansi": {
       "version": "7.0.0",
       "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",

gitnexus/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.5",
+  "version": "1.6.6",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",
@@ -48,7 +48,6 @@
     "test:integration": "vitest run test/integration",
     "test:watch": "vitest",
     "test:coverage": "vitest run --coverage",
-    "test:parity": "tsx scripts/run-parity.ts",
     "test:cross-platform": "tsx scripts/run-cross-platform.ts",
     "postinstall": "node scripts/materialize-vendor-grammars.cjs && node scripts/build-tree-sitter-dart.cjs && node scripts/build-tree-sitter-proto.cjs && node scripts/build-tree-sitter-swift.cjs",
     "prepare": "node scripts/build.js",
@@ -56,7 +55,7 @@
   },
   "dependencies": {
     "@huggingface/transformers": "^4.1.0",
-    "@ladybugdb/core": "^0.16.1",
+    "@ladybugdb/core": "^0.17.0",
     "@modelcontextprotocol/sdk": "^1.0.0",
     "@scarf/scarf": "^1.4.0",
     "cli-progress": "^3.12.0",
@@ -71,8 +70,8 @@
     "ignore": "^7.0.5",
     "js-yaml": "^4.1.1",
     "jsonc-parser": "^3.3.1",
-    "lru-cache": "^11.0.0",
     "mnemonist": "^0.40.3",
+    "onnxruntime-common": "^1.26.0",
     "onnxruntime-node": "^1.24.0",
     "pandemonium": "^2.4.0",
     "pino": "^10.3.1",

gitnexus/scripts/bench-scope-resolution.ts

@@ -4,10 +4,8 @@
  * isolating the resolution cost from parse / heritage / pipeline
  * overhead.
  *
- * Usage: REGISTRY_PRIMARY_PYTHON=1 npx tsx scripts/bench-scope-resolution.ts
+ * Usage: npx tsx scripts/bench-scope-resolution.ts
  */
-process.env.REGISTRY_PRIMARY_PYTHON = '1';
-
 import { generateId } from '../src/lib/utils.js';
 import { createKnowledgeGraph } from '../src/core/graph/graph.js';
 import { runScopeResolution } from '../src/core/ingestion/scope-resolution/index.js';

gitnexus/scripts/ci-list-migrated-languages.ts

@@ -1,24 +0,0 @@
-/**
- * CI helper — emits the `MIGRATED_LANGUAGES` set as a JSON matrix array for
- * GitHub Actions (`.github/workflows/ci-scope-parity.yml`).
- *
- * Consumed by the `discover` job in that workflow. Each entry has:
- *   - `slug`: lowercase language id, matching `test/integration/resolvers/<slug>.test.ts`.
- *   - `envvar`: uppercase suffix used to build the `REGISTRY_PRIMARY_<envvar>` toggle.
- *
- * Run with `npx tsx scripts/ci-list-migrated-languages.ts`. The script
- * writes a single JSON array to stdout (no wrapper object) so the
- * workflow can pipe it straight into `$GITHUB_OUTPUT`.
- */
-
-import { MIGRATED_LANGUAGES } from '../src/core/ingestion/registry-primary-flag.js';
-
-const entries = [...MIGRATED_LANGUAGES].map((slug) => {
-  const s = String(slug);
-  return {
-    slug: s,
-    envvar: s.toUpperCase().replace(/-/g, '_'),
-  };
-});
-
-process.stdout.write(JSON.stringify(entries));

gitnexus/scripts/cross-platform-tests.ts

@@ -33,7 +33,7 @@ const PLATFORM_LOGIC = [
   'test/unit/resolve-invocation.test.ts',
   'test/unit/platform-capabilities.test.ts',
   'test/unit/worker-pool-windows-quarantine.test.ts',
-  'test/unit/lbug-pool-win-fts-probe.test.ts',
+  'test/unit/lbug-pool-fts-load.test.ts',
   'test/unit/repo-manager.test.ts',
   'test/unit/repo-manager-finalize-invariant.test.ts',
   'test/unit/hooks.test.ts',

gitnexus/scripts/run-parity.ts

@@ -1,128 +0,0 @@
-/**
- * Consolidated scope-resolution parity runner.
- *
- * Replaces the per-language matrix in ci-scope-parity.yml with a single
- * job that runs all migrated languages sequentially in one process. This
- * eliminates 8× redundant checkout + npm ci + build cycles (the old
- * workflow created a separate GitHub Actions job per language).
- *
- * For each language in MIGRATED_LANGUAGES:
- *   1. Run its resolver test with REGISTRY_PRIMARY_<LANG>=0 (legacy DAG)
- *   2. Run its resolver test with REGISTRY_PRIMARY_<LANG>=1 (registry-primary)
- *
- * Both modes must pass. Failures are collected and reported at the end
- * so all regressions are visible in a single CI run (equivalent to the
- * old workflow's fail-fast: false behavior).
- *
- * Vitest output streams to the console in real time (stdio: 'inherit')
- * so CI logs show the actual test output directly. No per-invocation
- * timeout — the CI job-level timeout (30 min) is the outer guard.
- *
- * Usage:
- *   npx tsx scripts/run-parity.ts
- *   npx tsx scripts/run-parity.ts --language python   # single language
- */
-
-import { execFileSync } from 'child_process';
-import fs from 'fs';
-import path from 'path';
-import { fileURLToPath } from 'url';
-import { MIGRATED_LANGUAGES } from '../src/core/ingestion/registry-primary-flag.js';
-
-const __dirname = path.dirname(fileURLToPath(import.meta.url));
-const ROOT = path.resolve(__dirname, '..');
-
-interface ParityFailure {
-  lang: string;
-  mode: 'legacy' | 'registry-primary';
-}
-
-function envVarName(slug: string): string {
-  return `REGISTRY_PRIMARY_${slug.toUpperCase().replace(/-/g, '_')}`;
-}
-
-function testFilePath(slug: string): string {
-  return `test/integration/resolvers/${slug}.test.ts`;
-}
-
-function runVitest(testFile: string, env: Record<string, string>): boolean {
-  try {
-    execFileSync('npx', ['vitest', 'run', testFile], {
-      cwd: ROOT,
-      env: { ...process.env, ...env },
-      stdio: 'inherit',
-      shell: true,
-    });
-    return true;
-  } catch {
-    return false;
-  }
-}
-
-// Parse CLI args
-const args = process.argv.slice(2);
-const langFlag = args.indexOf('--language');
-const singleLang = langFlag >= 0 ? args[langFlag + 1] : undefined;
-
-if (langFlag >= 0 && singleLang === undefined) {
-  console.error('--language requires a value');
-  process.exit(1);
-}
-
-const languages = singleLang ? [singleLang] : [...MIGRATED_LANGUAGES].map(String);
-
-// Verify test files exist before running
-const missingFiles: string[] = [];
-for (const lang of languages) {
-  const file = path.resolve(ROOT, testFilePath(lang));
-  try {
-    fs.accessSync(file);
-  } catch {
-    missingFiles.push(`${testFilePath(lang)} (${lang})`);
-  }
-}
-
-if (missingFiles.length > 0) {
-  console.error('Missing resolver test files:');
-  for (const f of missingFiles) console.error(`  ${f}`);
-  process.exit(1);
-}
-
-console.log(`Scope-resolution parity: ${languages.length} language(s)`);
-console.log(`Languages: ${languages.join(', ')}\n`);
-
-const failures: ParityFailure[] = [];
-
-for (const lang of languages) {
-  const file = testFilePath(lang);
-  const envVar = envVarName(lang);
-
-  console.log(`\n── ${lang} — legacy DAG (${envVar}=0) ──`);
-  if (!runVitest(file, { [envVar]: '0' })) {
-    failures.push({ lang, mode: 'legacy' });
-  }
-
-  console.log(`\n── ${lang} — registry-primary (${envVar}=1) ──`);
-  if (!runVitest(file, { [envVar]: '1' })) {
-    failures.push({ lang, mode: 'registry-primary' });
-  }
-}
-
-// Summary
-const total = languages.length * 2;
-const passed = total - failures.length;
-
-console.log('\n═══════════════════════════════════════');
-console.log('PARITY SUMMARY');
-console.log('═══════════════════════════════════════');
-console.log(`Passed: ${passed}/${total}`);
-
-if (failures.length > 0) {
-  console.log(`\nFAILURES (${failures.length}):`);
-  for (const f of failures) {
-    console.log(`  ✗ ${f.lang} [${f.mode}]`);
-  }
-  process.exit(1);
-}
-
-console.log('\nAll parity checks passed.');

gitnexus/shadow-parity-dashboard/index.html

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

gitnexus/skills/gitnexus-debugging.md

@@ -16,10 +16,10 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 ## Workflow
 
 ```
-1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
-2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
+1. query({query: "<error or symptom>"})            → Find related execution flows
+2. context({name: "<suspect>"})                    → See callers/callees/processes
 3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
-4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
+4. cypher({query: "MATCH path..."})                 → Custom traces if needed
 ```
 
 > If "Index is stale" → run `node .gitnexus/run.cjs analyze` in terminal.
@@ -28,11 +28,11 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ```
 - [ ] Understand the symptom (error message, unexpected behavior)
-- [ ] gitnexus_query for error text or related code
+- [ ] query for error text or related code
 - [ ] Identify the suspect function from returned processes
-- [ ] gitnexus_context to see callers and callees
+- [ ] context to see callers and callees
 - [ ] Trace execution flow via process resource if applicable
-- [ ] gitnexus_cypher for custom call chain traces if needed
+- [ ] cypher for custom call chain traces if needed
 - [ ] Read source files to confirm root cause
 ```
 
@@ -40,7 +40,7 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 | Symptom              | GitNexus Approach                                          |
 | -------------------- | ---------------------------------------------------------- |
-| Error message        | `gitnexus_query` for error text → `context` on throw sites |
+| Error message        | `query` for error text → `context` on throw sites |
 | Wrong return value   | `context` on the function → trace callees for data flow    |
 | Intermittent failure | `context` → look for external calls, async deps            |
 | Performance issue    | `context` → find symbols with many callers (hot paths)     |
@@ -48,24 +48,24 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ## Tools
 
-**gitnexus_query** — find code related to error:
+**query** — find code related to error:
 
 ```
-gitnexus_query({query: "payment validation error"})
+query({query: "payment validation error"})
 → Processes: CheckoutFlow, ErrorHandling
 → Symbols: validatePayment, handlePaymentError, PaymentException
 ```
 
-**gitnexus_context** — full context for a suspect:
+**context** — full context for a suspect:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates (external API!)
 → Processes: CheckoutFlow (step 3/7)
 ```
 
-**gitnexus_cypher** — custom call chain traces:
+**cypher** — custom call chain traces:
 
 ```cypher
 MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
@@ -75,11 +75,11 @@ RETURN [n IN nodes(path) | n.name] AS chain
 ## Example: "Payment endpoint returns 500 intermittently"
 
 ```
-1. gitnexus_query({query: "payment error handling"})
+1. query({query: "payment error handling"})
    → Processes: CheckoutFlow, ErrorHandling
    → Symbols: validatePayment, handlePaymentError
 
-2. gitnexus_context({name: "validatePayment"})
+2. context({name: "validatePayment"})
    → Outgoing calls: verifyCard, fetchRates (external API!)
 
 3. READ gitnexus://repo/my-app/process/CheckoutFlow

gitnexus/skills/gitnexus-exploring.md

@@ -18,8 +18,8 @@ description: "Use when the user asks how code works, wants to understand archite
 ```
 1. READ gitnexus://repos                          → Discover indexed repos
 2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
-3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
-4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
+3. query({query: "<what you want to understand>"})  → Find related execution flows
+4. context({name: "<symbol>"})            → Deep dive on specific symbol
 5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
 ```
 
@@ -29,9 +29,9 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ```
 - [ ] READ gitnexus://repo/{name}/context
-- [ ] gitnexus_query for the concept you want to understand
+- [ ] query for the concept you want to understand
 - [ ] Review returned processes (execution flows)
-- [ ] gitnexus_context on key symbols for callers/callees
+- [ ] context on key symbols for callers/callees
 - [ ] READ process resource for full execution traces
 - [ ] Read source files for implementation details
 ```
@@ -47,18 +47,18 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ## Tools
 
-**gitnexus_query** — find execution flows related to a concept:
+**query** — find execution flows related to a concept:
 
 ```
-gitnexus_query({query: "payment processing"})
+query({query: "payment processing"})
 → Processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Symbols grouped by flow with file locations
 ```
 
-**gitnexus_context** — 360-degree view of a symbol:
+**context** — 360-degree view of a symbol:
 
 ```
-gitnexus_context({name: "validateUser"})
+context({name: "validateUser"})
 → Incoming calls: loginHandler, apiMiddleware
 → Outgoing calls: checkToken, getUserById
 → Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
@@ -68,10 +68,10 @@ gitnexus_context({name: "validateUser"})
 
 ```
 1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
-2. gitnexus_query({query: "payment processing"})
+2. query({query: "payment processing"})
    → CheckoutFlow: processPayment → validateCard → chargeStripe
    → RefundFlow: initiateRefund → calculateRefund → processRefund
-3. gitnexus_context({name: "processPayment"})
+3. context({name: "processPayment"})
    → Incoming: checkoutHandler, webhookHandler
    → Outgoing: validateCard, chargeStripe, saveTransaction
 4. Read src/payments/processor.ts for implementation details

gitnexus/skills/gitnexus-impact-analysis.md

@@ -17,9 +17,9 @@ description: "Use when the user wants to know what will break if they change som
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
+1. impact({target: "X", direction: "upstream"})  → What depends on this
 2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
-3. gitnexus_detect_changes()                               → Map current git changes to affected flows
+3. detect_changes()                               → Map current git changes to affected flows
 4. Assess risk and report to user
 ```
 
@@ -28,11 +28,11 @@ description: "Use when the user wants to know what will break if they change som
 ## Checklist
 
 ```
-- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
+- [ ] impact({target, direction: "upstream"}) to find dependents
 - [ ] Review d=1 items first (these WILL BREAK)
 - [ ] Check high-confidence (>0.8) dependencies
 - [ ] READ processes to check affected execution flows
-- [ ] gitnexus_detect_changes() for pre-commit check
+- [ ] detect_changes() for pre-commit check
 - [ ] Assess risk level and report to user
 ```
 
@@ -55,10 +55,10 @@ description: "Use when the user wants to know what will break if they change som
 
 ## Tools
 
-**gitnexus_impact** — the primary tool for symbol blast radius:
+**impact** — the primary tool for symbol blast radius:
 
 ```
-gitnexus_impact({
+impact({
   target: "validateUser",
   direction: "upstream",
   minConfidence: 0.8,
@@ -73,10 +73,10 @@ gitnexus_impact({
   - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_detect_changes** — git-diff based impact analysis:
+**detect_changes** — git-diff based impact analysis:
 
 ```
-gitnexus_detect_changes({scope: "staged"})
+detect_changes({scope: "staged"})
 
 → Changed: 5 symbols in 3 files
 → Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
@@ -86,7 +86,7 @@ gitnexus_detect_changes({scope: "staged"})
 ## Example: "What breaks if I change validateUser?"
 
 ```
-1. gitnexus_impact({target: "validateUser", direction: "upstream"})
+1. impact({target: "validateUser", direction: "upstream"})
    → d=1: loginHandler, apiMiddleware (WILL BREAK)
    → d=2: authRouter, sessionManager (LIKELY AFFECTED)
 

gitnexus/skills/gitnexus-pr-review.md

@@ -18,10 +18,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 1. gh pr diff <number>                                    → Get the raw diff
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+2. detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
 3. For each changed symbol:
-   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
-4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+   impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. context({name: "<key symbol>"})               → Understand callers/callees
 5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
 6. Summarize findings with risk assessment
 ```
@@ -32,10 +32,10 @@ description: "Use when the user wants to review a pull request, understand what
 
 ```
 - [ ] Fetch PR diff (gh pr diff or git diff base...head)
-- [ ] gitnexus_detect_changes to map changes to affected execution flows
-- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] detect_changes to map changes to affected execution flows
+- [ ] impact on each non-trivial changed symbol
 - [ ] Review d=1 items (WILL BREAK) — are callers updated?
-- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] context on key changed symbols to understand full picture
 - [ ] Check if affected processes have test coverage
 - [ ] Assess overall risk level
 - [ ] Write review summary with findings
@@ -63,20 +63,20 @@ description: "Use when the user wants to review a pull request, understand what
 
 ## Tools
 
-**gitnexus_detect_changes** — map PR diff to affected execution flows:
+**detect_changes** — map PR diff to affected execution flows:
 
 ```
-gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+detect_changes({scope: "compare", base_ref: "main"})
 
 → Changed: 8 symbols in 4 files
 → Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
 → Risk: MEDIUM
 ```
 
-**gitnexus_impact** — blast radius per changed symbol:
+**impact** — blast radius per changed symbol:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream"})
+impact({target: "validatePayment", direction: "upstream"})
 
 → d=1 (WILL BREAK):
   - processCheckout (src/checkout.ts:42) [CALLS, 100%]
@@ -86,20 +86,20 @@ gitnexus_impact({target: "validatePayment", direction: "upstream"})
   - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
 ```
 
-**gitnexus_impact with tests** — check test coverage:
+**impact with tests** — check test coverage:
 
 ```
-gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+impact({target: "validatePayment", direction: "upstream", includeTests: true})
 
 → Tests that cover this symbol:
   - validatePayment.test.ts [direct]
   - checkout.integration.test.ts [via processCheckout]
 ```
 
-**gitnexus_context** — understand a changed symbol's role:
+**context** — understand a changed symbol's role:
 
 ```
-gitnexus_context({name: "validatePayment"})
+context({name: "validatePayment"})
 
 → Incoming calls: processCheckout, webhookHandler
 → Outgoing calls: verifyCard, fetchRates
@@ -112,20 +112,20 @@ gitnexus_context({name: "validatePayment"})
 1. gh pr diff 42 > /tmp/pr42.diff
    → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
 
-2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+2. detect_changes({scope: "compare", base_ref: "main"})
    → Changed symbols: validatePayment, PaymentInput, formatAmount
    → Affected processes: CheckoutFlow, RefundFlow
    → Risk: MEDIUM
 
-3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+3. impact({target: "validatePayment", direction: "upstream"})
    → d=1: processCheckout, webhookHandler (WILL BREAK)
    → webhookHandler is NOT in the PR diff — potential breakage!
 
-4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+4. impact({target: "PaymentInput", direction: "upstream"})
    → d=1: validatePayment (in PR), createPayment (NOT in PR)
    → createPayment uses the old PaymentInput shape — breaking change!
 
-5. gitnexus_context({name: "formatAmount"})
+5. context({name: "formatAmount"})
    → Called by 12 functions — but change is backwards-compatible (added optional param)
 
 6. Review summary:

gitnexus/skills/gitnexus-refactoring.md

@@ -16,9 +16,9 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ## Workflow
 
 ```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
-2. gitnexus_query({query: "X"})                            → Find execution flows involving X
-3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
+1. impact({target: "X", direction: "upstream"})  → Map all dependents
+2. query({query: "X"})                            → Find execution flows involving X
+3. context({name: "X"})                           → See all incoming/outgoing refs
 4. Plan update order: interfaces → implementations → callers → tests
 ```
 
@@ -29,65 +29,65 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ### Rename Symbol
 
 ```
-- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
+- [ ] rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
 - [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
-- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
-- [ ] gitnexus_detect_changes() — verify only expected files changed
+- [ ] If satisfied: rename({..., dry_run: false}) — apply edits
+- [ ] detect_changes() — verify only expected files changed
 - [ ] Run tests for affected processes
 ```
 
 ### Extract Module
 
 ```
-- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
-- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
+- [ ] context({name: target}) — see all incoming/outgoing refs
+- [ ] impact({target, direction: "upstream"}) — find all external callers
 - [ ] Define new module interface
 - [ ] Extract code, update imports
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ### Split Function/Service
 
 ```
-- [ ] gitnexus_context({name: target}) — understand all callees
+- [ ] context({name: target}) — understand all callees
 - [ ] Group callees by responsibility
-- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
+- [ ] impact({target, direction: "upstream"}) — map callers to update
 - [ ] Create new functions/services
 - [ ] Update callers
-- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] detect_changes() — verify affected scope
 - [ ] Run tests for affected processes
 ```
 
 ## Tools
 
-**gitnexus_rename** — automated multi-file rename:
+**rename** — automated multi-file rename:
 
 ```
-gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
 → 12 edits across 8 files
 → 10 graph edits (high confidence), 2 ast_search edits (review)
 → Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
 ```
 
-**gitnexus_impact** — map all dependents first:
+**impact** — map all dependents first:
 
 ```
-gitnexus_impact({target: "validateUser", direction: "upstream"})
+impact({target: "validateUser", direction: "upstream"})
 → d=1: loginHandler, apiMiddleware, testUtils
 → Affected Processes: LoginFlow, TokenRefresh
 ```
 
-**gitnexus_detect_changes** — verify your changes after refactoring:
+**detect_changes** — verify your changes after refactoring:
 
 ```
-gitnexus_detect_changes({scope: "all"})
+detect_changes({scope: "all"})
 → Changed: 8 files, 12 symbols
 → Affected processes: LoginFlow, TokenRefresh
 → Risk: MEDIUM
 ```
 
-**gitnexus_cypher** — custom reference queries:
+**cypher** — custom reference queries:
 
 ```cypher
 MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
@@ -98,24 +98,24 @@ RETURN caller.name, caller.filePath ORDER BY caller.filePath
 
 | Risk Factor         | Mitigation                                |
 | ------------------- | ----------------------------------------- |
-| Many callers (>5)   | Use gitnexus_rename for automated updates |
+| Many callers (>5)   | Use rename for automated updates |
 | Cross-area refs     | Use detect_changes after to verify scope  |
-| String/dynamic refs | gitnexus_query to find them               |
+| String/dynamic refs | query to find them               |
 | External/public API | Version and deprecate properly            |
 
 ## Example: Rename `validateUser` to `authenticateUser`
 
 ```
-1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+1. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
    → 12 edits: 10 graph (safe), 2 ast_search (review)
    → Files: validator.ts, login.ts, middleware.ts, config.json...
 
 2. Review ast_search edits (config.json: dynamic reference!)
 
-3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
+3. rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
    → Applied 12 edits across 8 files
 
-4. gitnexus_detect_changes({scope: "all"})
+4. detect_changes({scope: "all"})
    → Affected: LoginFlow, TokenRefresh
    → Risk: MEDIUM — run tests for these flows
 ```

gitnexus/src/cli/ai-context.ts

@@ -29,6 +29,12 @@ export interface AIContextOptions {
   skipAgentsMd?: boolean;
   noStats?: boolean;
   skipSkills?: boolean;
+  /**
+   * Default branch used by the generated regression-compare example (#243).
+   * Resolved by the CLI (CLI flag > `.gitnexusrc` > auto-detect > "main"); a
+   * plain caller that omits it gets "main", preserving prior behavior.
+   */
+  defaultBranch?: string;
 }
 
 const GITNEXUS_START_MARKER = '<!-- gitnexus:start -->';
@@ -89,6 +95,16 @@ async function findGroupsContainingRegistryName(registryName: string): Promise<s
   return hits;
 }
 
+/**
+ * Strip backticks from a branch name before it is embedded in a Markdown
+ * inline-code span (#1996 tri-review P1). validateBranchName already rejects
+ * backticks for CLI/config/auto-detect inputs; this is the last-line defense at
+ * the generation sink so the embedding is provably safe regardless of caller.
+ */
+export function markdownSafeBranch(branch: string): string {
+  return branch.replace(/`/g, '');
+}
+
 export function generateGitNexusContent(
   projectName: string,
   stats: RepoStats,
@@ -100,6 +116,14 @@ export function generateGitNexusContent(
   // index (#1945). Referenced by docs so a single CLI-neutral command resolves
   // the available runner (global `gitnexus` → `pnpm dlx` → `npx`) at call time.
   runnerPath: string = '.gitnexus/run.cjs',
+  // Default branch for the regression-compare example (#243). Configurable so
+  // projects on `develop`/`master`/etc. don't get `base_ref: "main"` rewritten
+  // back over their fix on every analyze. The value is embedded inside a
+  // Markdown inline-code span: validateBranchName rejects backticks upstream,
+  // and `markdownSafeBranch` strips any remaining backtick here as defense in
+  // depth, so JSON.stringify's quote/escape handling is sufficient and the
+  // branch cannot break out of the span (#1996 tri-review P1).
+  defaultBranch: string = 'main',
 ): string {
   const generatedRows =
     generatedSkills && generatedSkills.length > 0
@@ -150,18 +174,18 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 
 ## Always Do
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`gitnexus_impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run \`gitnexus_detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run \`detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows. For regression review, compare against the default branch: \`detect_changes({scope: "compare", base_ref: ${JSON.stringify(markdownSafeBranch(defaultBranch))}})\`.
 - **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use \`gitnexus_query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`gitnexus_context({name: "symbolName"})\`.
+- When exploring unfamiliar code, use \`query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`context({name: "symbolName"})\`.
 
 ## Never Do
 
-- NEVER edit a function, class, or method without first running \`gitnexus_impact\` on it.
+- NEVER edit a function, class, or method without first running \`impact\` on it.
 - NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use \`gitnexus_rename\` which understands the call graph.
-- NEVER commit changes without running \`gitnexus_detect_changes()\` to check affected scope.
+- NEVER rename symbols with find-and-replace — use \`rename\` which understands the call graph.
+- NEVER commit changes without running \`detect_changes()\` to check affected scope.
 
 ## Resources
 
@@ -430,6 +454,7 @@ export async function generateAIContextFiles(
     options?.noStats,
     options?.skipSkills,
     runnerPath,
+    options?.defaultBranch ?? 'main',
   );
   const createdFiles: string[] = [];
 
@@ -472,3 +497,56 @@ export async function generateAIContextFiles(
 
   return { files: createdFiles };
 }
+
+/**
+ * Refresh only the `base_ref: "..."` value inside the GitNexus block of an
+ * already-generated AGENTS.md / CLAUDE.md, in place (#1996 tri-review P2).
+ *
+ * The `alreadyUpToDate` analyze fast path returns before the normal
+ * {@link generateAIContextFiles} call, so a changed `.gitnexusrc` defaultBranch
+ * (or `--default-branch`) would otherwise not take effect until the next
+ * re-index. This does a surgical line update that preserves the rest of the
+ * block — including community-skill rows written by a prior `--skills` run —
+ * rather than regenerating (which would drop those rows on a no-`--skills` run).
+ *
+ * Best-effort: missing files, a missing/blank block, or a block with no
+ * `base_ref` line (e.g. a user-trimmed keep block) are silently skipped. Writes
+ * only when the value actually changes, so a routine up-to-date run is a no-op.
+ */
+export async function refreshBaseRefLine(
+  repoPath: string,
+  defaultBranch: string,
+  options?: { skipAgentsMd?: boolean },
+): Promise<{ files: string[] }> {
+  if (options?.skipAgentsMd) return { files: [] };
+  const replacement = `base_ref: ${JSON.stringify(markdownSafeBranch(defaultBranch))}`;
+  const updated: string[] = [];
+  for (const name of ['AGENTS.md', 'CLAUDE.md']) {
+    const filePath = path.join(repoPath, name);
+    if (!(await fileExists(filePath))) continue;
+    let content: string;
+    try {
+      content = await fs.readFile(filePath, 'utf-8');
+    } catch {
+      continue;
+    }
+    const startIdx = findSectionMarkerIndex(content, GITNEXUS_START_MARKER);
+    if (startIdx === -1) continue;
+    const endIdx = findSectionMarkerIndex(content, GITNEXUS_END_MARKER, startIdx);
+    if (endIdx === -1 || endIdx <= startIdx) continue;
+    const blockEnd = endIdx + GITNEXUS_END_MARKER.length;
+    const block = content.substring(startIdx, blockEnd);
+    // Only the generated regression example carries a base_ref line, and only
+    // one per block; replace its quoted value while leaving the rest untouched.
+    const newBlock = block.replace(/base_ref: "(?:[^"\\]|\\.)*"/, replacement);
+    if (newBlock === block) continue; // no base_ref line present, or already current
+    const newContent = content.substring(0, startIdx) + newBlock + content.substring(blockEnd);
+    try {
+      await fs.writeFile(filePath, newContent, 'utf-8');
+      updated.push(name);
+    } catch {
+      // best-effort — never fail analyze over a context refresh
+    }
+  }
+  return { files: updated };
+}

gitnexus/src/cli/analyze-config.ts

@@ -0,0 +1,426 @@
+/**
+ * Project-local `.gitnexusrc` support for `gitnexus analyze` (#243).
+ *
+ * Lets a repository commit recurring `analyze` defaults — default branch for the
+ * generated regression example, AI-context / skills opt-outs, embedding knobs —
+ * so contributors don't re-pass the same flags on every run. Design rules:
+ *
+ *   - Config is repo-local (`.gitnexusrc` at the resolved repo root). It is NOT
+ *     read from `.gitnexus/` because that directory is index storage and is
+ *     commonly gitignored.
+ *   - JSON only. No YAML, no `package.json` field, no global `~/.gitnexus` file
+ *     in this pass.
+ *   - CLI flags always override config (see {@link mergeAnalyzeOptions}).
+ *   - Fail closed: unknown keys, wrong value types, conflicting aliases, and
+ *     invalid JSON all throw {@link GitNexusRcError} so a typo never silently
+ *     no-ops. Errors are actionable and surface before any expensive analysis.
+ *   - Config values never reach a shell. Strings are validated against control
+ *     and hidden/bidirectional characters so they cannot inject markdown,
+ *     JSON, or hidden controls into generated context files.
+ *
+ * Both a flat shape and a nested `analyze` block are accepted:
+ *
+ *     { "defaultBranch": "develop", "skipContextFiles": true }
+ *     { "analyze": { "defaultBranch": "develop", "skipSkills": true } }
+ *
+ * When both set the same option, the nested `analyze` block wins (deterministic,
+ * documented precedence). Conflicting *aliases at the same level* (e.g. both
+ * `defaultBranch` and `branch`) are rejected.
+ */
+
+import fs from 'node:fs';
+import path from 'node:path';
+import type { AnalyzeOptions } from './analyze.js';
+
+export const GITNEXUS_RC_FILENAME = '.gitnexusrc';
+
+/** Final fallback when no branch is configured or detectable. */
+export const DEFAULT_BRANCH_FALLBACK = 'main';
+
+/** Git refs longer than this are almost certainly a mistake / injection attempt. */
+const BRANCH_MAX_LENGTH = 255;
+
+/**
+ * Thrown for any `.gitnexusrc` problem (missing-file is NOT an error — it
+ * returns `undefined`). The message is user-facing and names the file so the
+ * CLI can print it verbatim before starting the progress bar.
+ */
+export class GitNexusRcError extends Error {
+  constructor(message: string) {
+    super(message);
+    this.name = 'GitNexusRcError';
+  }
+}
+
+type ValueKind =
+  | 'boolean'
+  | 'boolean-negate'
+  | 'string'
+  | 'numeric-string'
+  | 'embeddings'
+  | 'branch';
+
+interface KeySpec {
+  /** The `AnalyzeOptions` field this config key normalizes into. */
+  target: keyof AnalyzeOptions;
+  kind: ValueKind;
+}
+
+/**
+ * Allowed `.gitnexusrc` keys and how each maps onto `AnalyzeOptions`.
+ *
+ * Aliases intentionally collapse onto a shared target:
+ *   - `branch` is the legacy alias for `defaultBranch` (issue-comment shape).
+ *   - `skipContextFiles` / `skipAiContext` are aliases for `skipAgentsMd` — they
+ *     suppress the AGENTS.md / CLAUDE.md block ONLY. They do not imply
+ *     `skipSkills`, and they are weaker than `indexOnly` (which skips all
+ *     file injection). This matches the existing CLI semantics exactly.
+ *   - `noStats` is the negation of `stats`.
+ */
+const KEY_SPECS: Record<string, KeySpec> = {
+  defaultBranch: { target: 'defaultBranch', kind: 'branch' },
+  branch: { target: 'defaultBranch', kind: 'branch' },
+  skipAgentsMd: { target: 'skipAgentsMd', kind: 'boolean' },
+  skipContextFiles: { target: 'skipAgentsMd', kind: 'boolean' },
+  skipAiContext: { target: 'skipAgentsMd', kind: 'boolean' },
+  skipSkills: { target: 'skipSkills', kind: 'boolean' },
+  indexOnly: { target: 'indexOnly', kind: 'boolean' },
+  stats: { target: 'stats', kind: 'boolean' },
+  noStats: { target: 'stats', kind: 'boolean-negate' },
+  embeddings: { target: 'embeddings', kind: 'embeddings' },
+  dropEmbeddings: { target: 'dropEmbeddings', kind: 'boolean' },
+  name: { target: 'name', kind: 'string' },
+  allowDuplicateName: { target: 'allowDuplicateName', kind: 'boolean' },
+  maxFileSize: { target: 'maxFileSize', kind: 'numeric-string' },
+  workerTimeout: { target: 'workerTimeout', kind: 'numeric-string' },
+  walCheckpointThreshold: { target: 'walCheckpointThreshold', kind: 'numeric-string' },
+  workers: { target: 'workers', kind: 'numeric-string' },
+  embeddingThreads: { target: 'embeddingThreads', kind: 'numeric-string' },
+  embeddingBatchSize: { target: 'embeddingBatchSize', kind: 'numeric-string' },
+  embeddingSubBatchSize: { target: 'embeddingSubBatchSize', kind: 'numeric-string' },
+  embeddingDevice: { target: 'embeddingDevice', kind: 'string' },
+};
+
+/** Top-level container key for the nested form; not itself an `AnalyzeOptions` field. */
+const NESTED_KEY = 'analyze';
+
+const ALLOWED_KEYS_HINT = `Allowed keys: ${Object.keys(KEY_SPECS).join(', ')} (or a nested "${NESTED_KEY}" object).`;
+
+/**
+ * Reject control characters and hidden / bidirectional Unicode in a string
+ * value. These have no legitimate place in a branch name, registry name, or
+ * device string, and would otherwise let a committed config smuggle invisible
+ * controls into generated AGENTS.md / CLAUDE.md content.
+ */
+const isHiddenOrControl = (codePoint: number): boolean =>
+  codePoint < 0x20 ||
+  codePoint === 0x7f ||
+  (codePoint >= 0x200b && codePoint <= 0x200f) || // zero-width + LRM/RLM
+  (codePoint >= 0x202a && codePoint <= 0x202e) || // bidi embeddings/overrides
+  (codePoint >= 0x2060 && codePoint <= 0x2064) || // word-joiner + invisible math
+  (codePoint >= 0x2066 && codePoint <= 0x206f) || // bidi isolates + deprecated
+  codePoint === 0xfeff; // BOM / zero-width no-break space
+
+const assertNoHiddenChars = (value: string, source: string): void => {
+  for (const ch of value) {
+    const cp = ch.codePointAt(0);
+    if (cp !== undefined && isHiddenOrControl(cp)) {
+      throw new GitNexusRcError(
+        `${source}: value contains control or hidden/bidirectional characters, which are not allowed.`,
+      );
+    }
+  }
+};
+
+/**
+ * Validate a user-supplied branch name (from CLI or `.gitnexusrc`). Returns the
+ * trimmed name or throws {@link GitNexusRcError}. Conservative but accepts the
+ * shapes real branches use (`feature/foo-bar`, `release/1.2`, `develop`).
+ */
+export function validateBranchName(value: string, source: string): string {
+  const trimmed = value.trim();
+  if (!trimmed) {
+    throw new GitNexusRcError(`${source}: branch name must not be empty.`);
+  }
+  if (trimmed.length > BRANCH_MAX_LENGTH) {
+    throw new GitNexusRcError(`${source}: branch name is too long (max ${BRANCH_MAX_LENGTH}).`);
+  }
+  assertNoHiddenChars(trimmed, source);
+  if (/\s/.test(trimmed)) {
+    throw new GitNexusRcError(`${source}: branch name must not contain whitespace.`);
+  }
+  // git ref-name rules (subset): reject characters git itself forbids in refs.
+  if (/[~^:?*[\\]/.test(trimmed)) {
+    throw new GitNexusRcError(
+      `${source}: branch name contains characters not allowed in a git ref (~ ^ : ? * [ \\).`,
+    );
+  }
+  if (trimmed.startsWith('-')) {
+    throw new GitNexusRcError(`${source}: branch name must not start with "-".`);
+  }
+  if (trimmed.includes('..')) {
+    throw new GitNexusRcError(`${source}: branch name must not contain "..".`);
+  }
+  // Git permits a backtick in a ref, but the branch is embedded inside a
+  // Markdown inline-code span in the generated AGENTS.md/CLAUDE.md regression
+  // example, where a backtick would close the span early and let the rest of
+  // the template render as instruction text. Reject it at this single
+  // chokepoint so all three tiers (CLI flag, .gitnexusrc, auto-detect via
+  // sanitizeDetectedBranch) are covered (#1996 tri-review P1).
+  if (trimmed.includes('`')) {
+    throw new GitNexusRcError(
+      `${source}: branch name must not contain a backtick (it would break the generated Markdown).`,
+    );
+  }
+  return trimmed;
+}
+
+/**
+ * Best-effort validation for an auto-detected branch (from git). Never throws —
+ * returns `undefined` for anything unusable so the resolver falls back to the
+ * next precedence tier.
+ */
+export function sanitizeDetectedBranch(value: string | null | undefined): string | undefined {
+  if (!value) return undefined;
+  try {
+    return validateBranchName(value, 'detected branch');
+  } catch {
+    return undefined;
+  }
+}
+
+const normalizeValue = (kind: ValueKind, value: unknown, key: string): unknown => {
+  const source = `${GITNEXUS_RC_FILENAME} "${key}"`;
+  switch (kind) {
+    case 'boolean':
+      if (typeof value !== 'boolean') {
+        throw new GitNexusRcError(`${source} must be a boolean (true/false).`);
+      }
+      return value;
+    case 'boolean-negate':
+      if (typeof value !== 'boolean') {
+        throw new GitNexusRcError(`${source} must be a boolean (true/false).`);
+      }
+      return !value;
+    case 'branch':
+      if (typeof value !== 'string') {
+        throw new GitNexusRcError(`${source} must be a string branch name.`);
+      }
+      return validateBranchName(value, source);
+    case 'string': {
+      if (typeof value !== 'string') {
+        throw new GitNexusRcError(`${source} must be a string.`);
+      }
+      const trimmed = value.trim();
+      if (!trimmed) {
+        throw new GitNexusRcError(`${source} must not be empty.`);
+      }
+      assertNoHiddenChars(trimmed, source);
+      // `name` flows into the generated AGENTS.md/CLAUDE.md as `**${name}**` and
+      // inside `gitnexus://repo/${name}/…` code spans, so a Markdown-significant
+      // character would break those spans or inject emphasis/links/HTML into
+      // agent-instruction content (#1996 tri-review P1). `_` is intentionally
+      // allowed (legitimate in repo names; intraword `_` is not emphasis).
+      // embeddingDevice (the other `string`-kind option) only ever holds a
+      // fixed device token, so this guard never rejects a valid value there.
+      if (/[`*[\]<>]/.test(trimmed)) {
+        throw new GitNexusRcError(
+          `${source} must not contain Markdown-significant characters (\` * [ ] < >).`,
+        );
+      }
+      return trimmed;
+    }
+    case 'numeric-string': {
+      // Mirror Commander's contract: these options reach the existing CLI
+      // validation as strings. Accept a JSON number or a string; normalize to a
+      // string and let the downstream per-flag validation enforce ranges so the
+      // error messages stay in one place.
+      if (typeof value === 'number') {
+        if (!Number.isFinite(value)) {
+          throw new GitNexusRcError(`${source} must be a finite number.`);
+        }
+        return String(value);
+      }
+      if (typeof value === 'string') {
+        const trimmed = value.trim();
+        if (!trimmed) {
+          throw new GitNexusRcError(`${source} must not be empty.`);
+        }
+        return trimmed;
+      }
+      throw new GitNexusRcError(`${source} must be a number or numeric string.`);
+    }
+    case 'embeddings': {
+      // Mirror `--embeddings [limit]`: boolean toggles, a non-negative integer
+      // sets the node cap (normalized to a string, as Commander would supply).
+      if (typeof value === 'boolean') return value;
+      if (typeof value === 'number') {
+        if (!Number.isInteger(value) || value < 0) {
+          throw new GitNexusRcError(
+            `${source} must be true/false or a non-negative integer (node cap; 0 disables the cap).`,
+          );
+        }
+        return String(value);
+      }
+      throw new GitNexusRcError(
+        `${source} must be a boolean or a non-negative integer (node cap; 0 disables the cap).`,
+      );
+    }
+    default:
+      // Exhaustive — kept for forward-compat if a new kind is added.
+      throw new GitNexusRcError(`${source}: unsupported config value kind.`);
+  }
+};
+
+/**
+ * Normalize one level (flat top-level or the nested `analyze` block) into a
+ * partial `AnalyzeOptions`. Rejects unknown keys and two aliases that configure
+ * the same option at the same level.
+ */
+const normalizeLevel = (
+  obj: Record<string, unknown>,
+  { allowNestedKey }: { allowNestedKey: boolean },
+): Partial<AnalyzeOptions> => {
+  const out: Partial<AnalyzeOptions> = {};
+  const setBy = new Map<keyof AnalyzeOptions, string>();
+
+  for (const [key, value] of Object.entries(obj)) {
+    if (allowNestedKey && key === NESTED_KEY) continue; // handled separately
+    // `Object.hasOwn`, not a truthiness check: a plain-object lookup like
+    // `KEY_SPECS["__proto__"]` returns an inherited member (Object.prototype,
+    // truthy) and would slip past `if (!spec)`, hitting the wrong error branch
+    // instead of the documented "Unknown key" message (#1996 tri-review P3).
+    if (!Object.hasOwn(KEY_SPECS, key)) {
+      throw new GitNexusRcError(
+        `Unknown key "${key}" in ${GITNEXUS_RC_FILENAME}. ${ALLOWED_KEYS_HINT}`,
+      );
+    }
+    const spec = KEY_SPECS[key];
+    const prev = setBy.get(spec.target);
+    if (prev && prev !== key) {
+      throw new GitNexusRcError(
+        `${GITNEXUS_RC_FILENAME}: "${prev}" and "${key}" both configure the same option; set only one.`,
+      );
+    }
+    setBy.set(spec.target, key);
+    (out as Record<string, unknown>)[spec.target] = normalizeValue(spec.kind, value, key);
+  }
+
+  return out;
+};
+
+/**
+ * Locate, read, parse, validate, and normalize `.gitnexusrc` at `repoRoot`.
+ *
+ * @returns the normalized config defaults, or `undefined` when no file exists
+ *          (the normal case). Throws {@link GitNexusRcError} on any problem.
+ */
+export function loadAnalyzeConfig(repoRoot: string): Partial<AnalyzeOptions> | undefined {
+  const filePath = path.join(repoRoot, GITNEXUS_RC_FILENAME);
+
+  let raw: string;
+  try {
+    raw = fs.readFileSync(filePath, 'utf-8');
+  } catch (err) {
+    if ((err as NodeJS.ErrnoException)?.code === 'ENOENT') return undefined;
+    throw new GitNexusRcError(`Could not read ${GITNEXUS_RC_FILENAME}: ${(err as Error).message}`);
+  }
+
+  // Strip a leading UTF-8 BOM: Node's 'utf-8' decode keeps it, and JSON.parse
+  // then fails with a confusing "Unexpected token" on an otherwise-valid file
+  // (#1996 tri-review). Only one leading BOM is stripped; in-string control
+  // rejection still applies to the parsed values.
+  if (raw.charCodeAt(0) === 0xfeff) raw = raw.slice(1);
+
+  let parsed: unknown;
+  try {
+    parsed = JSON.parse(raw);
+  } catch (err) {
+    throw new GitNexusRcError(
+      `${GITNEXUS_RC_FILENAME} is not valid JSON: ${(err as Error).message}. ` +
+        `Expected a JSON object such as {"defaultBranch": "develop", "skipContextFiles": true}.`,
+    );
+  }
+
+  if (parsed === null || typeof parsed !== 'object' || Array.isArray(parsed)) {
+    throw new GitNexusRcError(`${GITNEXUS_RC_FILENAME} must contain a JSON object.`);
+  }
+
+  const obj = parsed as Record<string, unknown>;
+  const flat = normalizeLevel(obj, { allowNestedKey: true });
+
+  let nested: Partial<AnalyzeOptions> = {};
+  if (Object.prototype.hasOwnProperty.call(obj, NESTED_KEY)) {
+    const nestedRaw = obj[NESTED_KEY];
+    if (nestedRaw === null || typeof nestedRaw !== 'object' || Array.isArray(nestedRaw)) {
+      throw new GitNexusRcError(`${GITNEXUS_RC_FILENAME} "${NESTED_KEY}" must be a JSON object.`);
+    }
+    nested = normalizeLevel(nestedRaw as Record<string, unknown>, { allowNestedKey: false });
+  }
+
+  // Nested `analyze` block overrides flat top-level keys for the same option.
+  return { ...flat, ...nested };
+}
+
+/**
+ * Merge CLI options over `.gitnexusrc` defaults. CLI wins whenever it provides a
+ * value — including an explicit `false` (so an explicit CLI off-switch beats a
+ * config `true`). Config fills only the genuinely-unset (`undefined`) options.
+ *
+ * `stats` is special: Commander always materializes it (`true` by default,
+ * `false` only when `--no-stats` is passed), so plain `??` can't tell "default
+ * on" from "explicitly on". The rule is: a passed `--no-stats` (`stats: false`)
+ * always wins; otherwise the config value applies. There is intentionally no
+ * `--stats` counter-flag, so config can only turn stats off, not force it back
+ * on against a `--no-stats`.
+ *
+ * `defaultBranch` is NOT resolved here — see {@link resolveDefaultBranch}, which
+ * applies the CLI > config > auto-detect > "main" precedence chain.
+ */
+export function mergeAnalyzeOptions(
+  cli: AnalyzeOptions,
+  config: Partial<AnalyzeOptions> | undefined,
+): AnalyzeOptions {
+  if (!config) return cli;
+
+  const merged: AnalyzeOptions = { ...cli };
+  for (const key of Object.keys(config) as (keyof AnalyzeOptions)[]) {
+    if (key === 'stats' || key === 'defaultBranch') continue; // handled below / by resolver
+    if (merged[key] === undefined) {
+      (merged as Record<string, unknown>)[key] = config[key];
+    }
+  }
+
+  if (config.stats !== undefined && cli.stats !== false) {
+    merged.stats = config.stats;
+  }
+
+  return merged;
+}
+
+/**
+ * Resolve the default branch threaded into generated context, applying the
+ * precedence chain:
+ *
+ *   CLI `--default-branch` > `.gitnexusrc` `defaultBranch`/`branch`
+ *     > auto-detected `origin/HEAD` > {@link DEFAULT_BRANCH_FALLBACK} ("main").
+ *
+ * User-supplied values (CLI, config) are validated strictly and throw on bad
+ * input. The auto-detected value is best-effort and silently ignored if
+ * unusable.
+ */
+export function resolveDefaultBranch(input: {
+  cliBranch?: string;
+  configBranch?: string;
+  detectedBranch?: string | null;
+}): string {
+  if (input.cliBranch !== undefined) {
+    return validateBranchName(input.cliBranch, '--default-branch');
+  }
+  if (input.configBranch !== undefined) {
+    return validateBranchName(input.configBranch, `${GITNEXUS_RC_FILENAME} "defaultBranch"`);
+  }
+  const detected = sanitizeDetectedBranch(input.detectedBranch);
+  if (detected) return detected;
+  return DEFAULT_BRANCH_FALLBACK;
+}

gitnexus/src/cli/analyze.ts

@@ -9,6 +9,7 @@
  */
 
 import path from 'path';
+import os from 'os';
 import { spawn } from 'child_process';
 import v8 from 'v8';
 import cliProgress from 'cli-progress';
@@ -26,7 +27,14 @@ import {
   AnalysisNotFinalizedError,
   assertAnalysisFinalized,
 } from '../storage/repo-manager.js';
-import { getGitRoot, hasGitDir } from '../storage/git.js';
+import { getGitRoot, hasGitDir, getDefaultBranch } from '../storage/git.js';
+import {
+  loadAnalyzeConfig,
+  mergeAnalyzeOptions,
+  resolveDefaultBranch,
+  validateBranchName,
+  GitNexusRcError,
+} from './analyze-config.js';
 import { runFullAnalysis } from '../core/run-analyze.js';
 import { getMaxFileSizeBannerMessage } from '../core/ingestion/utils/max-file-size.js';
 import { warnMissingOptionalGrammars } from './optional-grammars.js';
@@ -35,6 +43,7 @@ import fs from 'fs/promises';
 import { cliError } from './cli-message.js';
 import { formatElapsed } from './format-elapsed.js';
 import { isHfDownloadFailure } from '../core/embeddings/hf-env.js';
+import { isLocalEmbeddingRuntimeBlockerMessage } from '../core/embeddings/runtime-support.js';
 import { warnIfNpm11NpxRisk } from './resolve-invocation.js';
 
 // Capture stderr.write at module load BEFORE anything (LadybugDB native
@@ -51,6 +60,22 @@ const writeFatalToStderr = (label: string, err: unknown): void => {
   const message = isErr ? err.message : String(err);
   realStderrWrite(`\n  ${label}: ${message}\n`);
   if (isErr && err.stack) realStderrWrite(`${err.stack}\n`);
+  // Walk and print the `cause` chain. The phase runner wraps the underlying
+  // failure as `new Error("Phase 'X' failed: …", { cause })`, so the original
+  // error (e.g. a WorkerPoolDispatchError carrying the worker-side stack from
+  // #2068) is only reachable via `.cause`. Without this the user sees the
+  // wrapper's main-thread stack and never the real frame. `cause.stack` already
+  // begins with the cause's message, so we print the stack alone (not message +
+  // stack) to avoid repeating it. Depth-bounded so a cyclic `cause` can't loop
+  // (the phase runner wraps one level; the bound leaves headroom for future
+  // nesting); uses realStderrWrite so the redirected console.error's ANSI
+  // clear-line wrapping can't erase it (#1169).
+  const MAX_CAUSE_DEPTH = 5;
+  let cause: unknown = isErr ? (err as { cause?: unknown }).cause : undefined;
+  for (let depth = 0; depth < MAX_CAUSE_DEPTH && cause instanceof Error; depth++) {
+    realStderrWrite(`\n  Caused by: ${cause.stack ?? cause.message}\n`);
+    cause = (cause as { cause?: unknown }).cause;
+  }
 };
 
 let fatalHandlersInstalled = false;
@@ -76,13 +101,45 @@ const installFatalHandlers = (): void => {
   });
 };
 
-const HEAP_MB = 16384;
+/** Historical floor for the re-exec heap cap — the auto-sizer never goes below
+ *  this, so small boxes / CI never regress. */
+const DEFAULT_HEAP_MB = 16384;
+
+/**
+ * RAM-aware re-exec heap cap (MB): `0.75 × effective RAM`, clamped to
+ * `>= DEFAULT_HEAP_MB`. Kept BELOW physical RAM on purpose — a cap `>=` RAM makes
+ * V8 collect lazily and inflate the heap into swap-thrash (observed analyzing the
+ * Linux kernel at a 30GB cap on a 31GB box). `constrainedBytes` is the cgroup
+ * limit or `null`; it is honored only as a real, smaller-than-physical cap, because
+ * `process.constrainedMemory()` returns a huge sentinel when UNCONSTRAINED.
+ */
+export function computeHeapCapMb(totalBytes: number, constrainedBytes: number | null): number {
+  const effectiveBytes =
+    constrainedBytes !== null && constrainedBytes > 0 && constrainedBytes < totalBytes
+      ? constrainedBytes
+      : totalBytes;
+  const effectiveMb = Math.floor(effectiveBytes / (1024 * 1024));
+  return Math.max(DEFAULT_HEAP_MB, Math.floor(0.75 * effectiveMb));
+}
+
+function readConstrainedBytes(): number | null {
+  if (typeof process.constrainedMemory !== 'function') return null;
+  const c = process.constrainedMemory();
+  return typeof c === 'number' && c > 0 ? c : null;
+}
+
+const HEAP_MB = computeHeapCapMb(os.totalmem(), readConstrainedBytes());
 const TEST_RESPAWN_HEAP_MB = Number(process.env.GITNEXUS_TEST_RESPAWN_HEAP_MB);
 const RESPAWN_HEAP_MB =
   Number.isFinite(TEST_RESPAWN_HEAP_MB) && TEST_RESPAWN_HEAP_MB > 0
     ? Math.floor(TEST_RESPAWN_HEAP_MB)
     : HEAP_MB;
 const HEAP_FLAG = `--max-old-space-size=${RESPAWN_HEAP_MB}`;
+/** Larger semi-space (young-gen) cuts minor-GC frequency + promotion churn during
+ *  the multi-million-node graph build/emit. Allowed in NODE_OPTIONS (unlike
+ *  --stack-size), so it propagates to the re-exec env cleanly. */
+const SEMI_SPACE_MB = 128;
+const SEMI_FLAG = `--max-semi-space-size=${SEMI_SPACE_MB}`;
 /** Increase default stack size (KB) to prevent stack overflow on deep class hierarchies. */
 const STACK_KB = 4096;
 const STACK_FLAG = `--stack-size=${STACK_KB}`;
@@ -432,7 +489,8 @@ const forceHeapOOMForTestIfEnabled = (): void => {
 // `gitnexus/src/core/lbug/lbug-config.ts` in sync with this value.
 const RECOMMENDED_WAL_CHECKPOINT_THRESHOLD = 64 * 1024 * 1024;
 
-/** Re-exec the process with a 16GB heap and larger stack if we're currently below that. */
+/** Re-exec the process with the RAM-aware auto heap cap + larger semi-space/stack
+ *  if we're currently below that. A user-supplied NODE_OPTIONS heap wins (no re-exec). */
 async function ensureHeap(): Promise<boolean> {
   const nodeOpts = process.env.NODE_OPTIONS || '';
   if (nodeOpts.includes('--max-old-space-size')) return false;
@@ -440,25 +498,26 @@ async function ensureHeap(): Promise<boolean> {
   const v8Heap = v8.getHeapStatistics().heap_size_limit;
   if (v8Heap >= HEAP_MB * 1024 * 1024 * 0.9) return false;
 
-  // --stack-size is a V8 flag not allowed in NODE_OPTIONS on Node 24+,
-  // so pass it only as a direct CLI argument, not via the environment.
-  const cliFlags = [HEAP_FLAG];
+  // --stack-size is a V8 flag not allowed in NODE_OPTIONS on Node 24+, so pass it
+  // only as a direct CLI argument. --max-semi-space-size IS allowed in NODE_OPTIONS.
+  const cliFlags = [HEAP_FLAG, SEMI_FLAG];
   if (!nodeOpts.includes('--stack-size')) cliFlags.push(STACK_FLAG);
 
   const childArgs = [...cliFlags, ...process.argv.slice(1)];
   const childEnv = {
     ...process.env,
-    NODE_OPTIONS: `${nodeOpts} ${HEAP_FLAG}`.trim(),
+    NODE_OPTIONS: `${nodeOpts} ${HEAP_FLAG} ${SEMI_FLAG}`.trim(),
   };
   if (shouldBridgeRespawnProgressTty()) childEnv[RESPAWN_PROGRESS_ENV] = '1';
   const childExit = await runRespawnedAnalyze(childArgs, childEnv);
   if (childExit.status !== 0 || childExit.signal) {
     if (childProcessLikelyOom(childExit)) {
       cliError(
-        `  Analysis likely ran out of memory.\n` +
-          `  Retry with a larger heap if your machine allows it:\n` +
-          `    NODE_OPTIONS="--max-old-space-size=24576" gitnexus analyze [your-args]\n` +
-          `    (Windows: set NODE_OPTIONS=--max-old-space-size=24576 && gitnexus analyze [your-args])\n` +
+        `  Analysis likely ran out of memory (heap cap auto-sized to ${RESPAWN_HEAP_MB}MB ≈ 0.75x RAM).\n` +
+          `  This repository's working set exceeds available RAM. Use a machine with more RAM,\n` +
+          `  or override the cap (a cap above physical RAM causes swap-thrash — use with care):\n` +
+          `    NODE_OPTIONS="--max-old-space-size=<MB>" gitnexus analyze [your-args]\n` +
+          `    (Windows: set NODE_OPTIONS=--max-old-space-size=<MB> && gitnexus analyze [your-args])\n` +
           `  If this persists, it may be a native crash unrelated to heap size.\n`,
         { recoveryHint: 'heap-oom-respawn' },
       );
@@ -466,8 +525,7 @@ async function ensureHeap(): Promise<boolean> {
       cliError(
         `  Analysis aborted in a native worker or native binding path.\n` +
           `  Try one of these recovery paths:\n` +
-          `    gitnexus analyze --workers 0\n` +
-          `    npm uninstall -g gitnexus && npm install -g gitnexus@latest\n` +
+          `    npm uninstall -g gitnexus && npm install -g gitnexus@latest (rebuilds native bindings)\n` +
           `    Use Node 22 LTS if you are on a newer non-LTS runtime.\n`,
         { recoveryHint: 'native-worker-abort' },
       );
@@ -492,6 +550,7 @@ const ANALYZE_CLI_ENV_KEYS = [
   'GITNEXUS_VERBOSE',
   'GITNEXUS_PROFILE_DEFERRED',
   'GITNEXUS_PROFILE_DEFERRED_SLOW_MS',
+  'GITNEXUS_DEBUG_HEAP',
   'GITNEXUS_MAX_FILE_SIZE',
   'GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS',
   'GITNEXUS_WAL_CHECKPOINT_THRESHOLD',
@@ -554,6 +613,13 @@ export interface AnalyzeOptions {
   stats?: boolean;
   /** Skip installing standard GitNexus skill files to .claude/skills/gitnexus/. */
   skipSkills?: boolean;
+  /**
+   * Default branch for the generated regression-compare example (#243). From
+   * `--default-branch`; may also be supplied via `.gitnexusrc`. Resolved to a
+   * concrete branch (CLI > `.gitnexusrc` > auto-detected origin/HEAD > "main")
+   * before being threaded into the generated AGENTS.md / CLAUDE.md content.
+   */
+  defaultBranch?: string;
   /** Pure index mode: skip all file injection (AGENTS.md, CLAUDE.md, skills). */
   indexOnly?: boolean;
   /** Index the folder even when no .git directory is present. */
@@ -583,7 +649,7 @@ export interface AnalyzeOptions {
   workerTimeout?: string;
   /** Control LadybugDB WAL auto-checkpoint threshold during analyze. */
   walCheckpointThreshold?: string;
-  /** Parse worker pool size; 0 disables workers (sequential fallback). */
+  /** Parse worker pool size (>=1); 0 is rejected (no sequential mode). */
   workers?: string;
   embeddingThreads?: string;
   embeddingBatchSize?: string;
@@ -638,16 +704,116 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
   }
 };
 
-const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions): Promise<void> => {
-  if (options?.verbose) {
+const analyzeCommandImpl = async (
+  inputPath?: string,
+  cliOptions?: AnalyzeOptions,
+): Promise<void> => {
+  console.log('\n  GitNexus Analyzer\n');
+
+  // ── Resolve the target repo root ──────────────────────────────────
+  // Resolved FIRST because `.gitnexusrc` is read from the repo root (not the
+  // caller's cwd), and config can set defaults that the validation below
+  // consumes. `--skip-git` is a CLI-only flag (never a config key), so the raw
+  // CLI options are authoritative for repo-root resolution.
+  let repoPath: string;
+  if (inputPath) {
+    repoPath = path.resolve(inputPath);
+  } else if (cliOptions?.skipGit) {
+    // --skip-git: treat cwd as the index root, do not walk up to a parent git repo.
+    repoPath = path.resolve(process.cwd());
+  } else {
+    const gitRoot = getGitRoot(process.cwd());
+    if (!gitRoot) {
+      console.log(
+        '  Not inside a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n',
+      );
+      process.exitCode = 1;
+      return;
+    }
+    repoPath = gitRoot;
+  }
+
+  const repoHasGit = hasGitDir(repoPath);
+  if (!repoHasGit && !cliOptions?.skipGit) {
+    console.log(
+      '  Not a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n',
+    );
+    process.exitCode = 1;
+    return;
+  }
+  if (!repoHasGit) {
+    console.log(
+      '  Warning: no .git directory found — commit-tracking and incremental updates disabled.\n',
+    );
+  }
+
+  // Validate an explicit `--default-branch` up front so its errors are
+  // attributed to the flag (with a CLI-specific recovery hint) rather than to
+  // `.gitnexusrc`, which the user may not even have (#1996 tri-review).
+  if (cliOptions?.defaultBranch !== undefined) {
+    try {
+      validateBranchName(cliOptions.defaultBranch, '--default-branch');
+    } catch (err) {
+      cliError(`  ${err instanceof Error ? err.message : String(err)}\n`, {
+        recoveryHint: 'default-branch-invalid',
+      });
+      process.exitCode = 1;
+      return;
+    }
+  }
+
+  // ── Load .gitnexusrc and merge: CLI flags override config (#243) ───
+  // Parse/validate before the progress bar so a malformed config produces an
+  // actionable error and exits before any expensive analysis starts.
+  let options: AnalyzeOptions;
+  let resolvedDefaultBranch: string;
+  try {
+    const fileConfig = loadAnalyzeConfig(repoPath);
+    options = mergeAnalyzeOptions(cliOptions ?? {}, fileConfig);
+
+    // Resolve the default branch threaded into generated context:
+    //   CLI --default-branch > .gitnexusrc defaultBranch/branch
+    //     > auto-detected origin/HEAD > "main".
+    // Only shell out to git when no branch was configured AND the generated
+    // context will actually use it, keeping the common path free of an extra
+    // git call. Detection is best-effort and never blocks analyze.
+    const cliBranch = cliOptions?.defaultBranch;
+    const configBranch = fileConfig?.defaultBranch;
+    const willGenerateContext = !options.indexOnly && !options.skipAgentsMd;
+    let detectedBranch: string | null = null;
+    if (
+      cliBranch === undefined &&
+      configBranch === undefined &&
+      repoHasGit &&
+      !cliOptions?.skipGit &&
+      willGenerateContext
+    ) {
+      try {
+        detectedBranch = getDefaultBranch(repoPath);
+      } catch {
+        detectedBranch = null;
+      }
+    }
+    resolvedDefaultBranch = resolveDefaultBranch({ cliBranch, configBranch, detectedBranch });
+  } catch (err) {
+    const msg =
+      err instanceof GitNexusRcError
+        ? err.message
+        : `Invalid .gitnexusrc: ${err instanceof Error ? err.message : String(err)}`;
+    cliError(`  ${msg}\n`, { recoveryHint: 'gitnexusrc-invalid' });
+    process.exitCode = 1;
+    return;
+  }
+
+  if (options.verbose) {
     process.env.GITNEXUS_VERBOSE = '1';
   }
 
-  if (options?.maxFileSize) {
+  if (options.maxFileSize) {
     process.env.GITNEXUS_MAX_FILE_SIZE = options.maxFileSize;
   }
 
-  if (options?.workerTimeout) {
+  if (options.workerTimeout) {
     const workerTimeoutSeconds = Number(options.workerTimeout);
     if (!Number.isFinite(workerTimeoutSeconds) || workerTimeoutSeconds < 1) {
       cliError('  --worker-timeout must be at least 1 second.\n');
@@ -659,7 +825,7 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
     );
   }
 
-  if (options?.walCheckpointThreshold !== undefined) {
+  if (options.walCheckpointThreshold !== undefined) {
     const parsed = parseWalCheckpointThreshold(options.walCheckpointThreshold);
     if (parsed === undefined) {
       cliError('  --wal-checkpoint-threshold must be an integer >= -1.\n');
@@ -676,12 +842,13 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
   // values back-to-back and observe the value they passed, not whatever the
   // previous call leaked.
   let workerPoolSize: number | undefined;
-  if (options?.workers !== undefined) {
+  if (options.workers !== undefined) {
     const parsedWorkers = Number(options.workers);
-    if (!Number.isInteger(parsedWorkers) || parsedWorkers < 0) {
+    if (!Number.isInteger(parsedWorkers) || parsedWorkers < 1) {
       cliError(
-        '  --workers must be a non-negative integer. ' +
-          'Pass 0 to disable the worker pool (sequential fallback).\n',
+        '  --workers must be a positive integer (>= 1). ' +
+          'GitNexus parses through a worker pool only — there is no sequential ' +
+          'mode, so 0 is not allowed. Omit --workers for an auto-sized pool.\n',
       );
       process.exitCode = 1;
       return;
@@ -694,7 +861,7 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
   // sibling-validation pattern (exit before bar.start() — otherwise
   // process.exit() leaves the progress bar's hidden cursor uncleared).
   let embeddingsNodeLimit: number | undefined;
-  if (typeof options?.embeddings === 'string') {
+  if (typeof options.embeddings === 'string') {
     const parsed = Number(options.embeddings);
     if (!Number.isInteger(parsed) || parsed < 0) {
       cliError(
@@ -706,7 +873,7 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
     }
     embeddingsNodeLimit = parsed;
   }
-  const embeddingsEnabled = !!options?.embeddings;
+  const embeddingsEnabled = !!options.embeddings;
 
   const setPositiveEnv = (
     optionName: string,
@@ -728,23 +895,23 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
     !setPositiveEnv(
       '--embedding-threads',
       'GITNEXUS_EMBEDDING_THREADS',
-      options?.embeddingThreads,
+      options.embeddingThreads,
     ) ||
     !setPositiveEnv(
       '--embedding-batch-size',
       'GITNEXUS_EMBEDDING_BATCH_SIZE',
-      options?.embeddingBatchSize,
+      options.embeddingBatchSize,
     ) ||
     !setPositiveEnv(
       '--embedding-sub-batch-size',
       'GITNEXUS_EMBEDDING_SUB_BATCH_SIZE',
-      options?.embeddingSubBatchSize,
+      options.embeddingSubBatchSize,
     )
   ) {
     return;
   }
 
-  if (options?.embeddingDevice) {
+  if (options.embeddingDevice) {
     const allowed = new Set(['auto', 'cpu', 'dml', 'cuda', 'wasm']);
     if (!allowed.has(options.embeddingDevice)) {
       cliError('  --embedding-device must be one of: auto, cpu, dml, cuda, wasm.\n');
@@ -754,7 +921,7 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
     process.env.GITNEXUS_EMBEDDING_DEVICE = options.embeddingDevice;
   }
 
-  if (options?.repairFts && options?.force) {
+  if (options.repairFts && options.force) {
     cliError(
       '  Cannot combine `--repair-fts` with `--force`. ' +
         'Use `--repair-fts` for fast FTS-only repair, or `--force` for a full rebuild.\n',
@@ -763,52 +930,18 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
     return;
   }
 
-  console.log('\n  GitNexus Analyzer\n');
-
   // `--index-only` is the stronger contract — it suppresses every form of file
   // injection, including community skill writes that `--skills` would normally
   // produce. Surface the override explicitly so users don't wonder why a
   // pipeline re-index ran but no skill files appeared. The pipeline still
-  // re-runs (see `force: options?.force || options?.skills` below); the warning
+  // re-runs (see `force: options.force || options.skills` below); the warning
   // is purely about the dropped post-index write step.
-  if (options?.indexOnly && options?.skills) {
+  if (options.indexOnly && options.skills) {
     console.log(
       '  Note: --index-only overrides --skills; community skill files will not be written.\n',
     );
   }
 
-  let repoPath: string;
-  if (inputPath) {
-    repoPath = path.resolve(inputPath);
-  } else if (options?.skipGit) {
-    // --skip-git: treat cwd as the index root, do not walk up to a parent git repo.
-    repoPath = path.resolve(process.cwd());
-  } else {
-    const gitRoot = getGitRoot(process.cwd());
-    if (!gitRoot) {
-      console.log(
-        '  Not inside a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n',
-      );
-      process.exitCode = 1;
-      return;
-    }
-    repoPath = gitRoot;
-  }
-
-  const repoHasGit = hasGitDir(repoPath);
-  if (!repoHasGit && !options?.skipGit) {
-    console.log(
-      '  Not a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n',
-    );
-    process.exitCode = 1;
-    return;
-  }
-  if (!repoHasGit) {
-    console.log(
-      '  Warning: no .git directory found \u2014 commit-tracking and incremental updates disabled.\n',
-    );
-  }
-
   // If the target repo contains files an optional grammar would parse but
   // that grammar's native binding is absent, warn before analysis so users
   // learn why those files end up unparsed instead of silently getting a
@@ -938,36 +1071,39 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
 
   // ── Run shared analysis orchestrator ───────────────────────────────
   try {
-    const skipAll = options?.indexOnly;
-    const skipAgentsMd = skipAll || options?.skipAgentsMd;
-    const skipSkills = skipAll || options?.skipSkills;
+    const skipAll = options.indexOnly;
+    const skipAgentsMd = skipAll || options.skipAgentsMd;
+    const skipSkills = skipAll || options.skipSkills;
     const result = await runFullAnalysis(
       repoPath,
       {
         // Pipeline re-index — OR'd with --skills because skill generation
         // needs a fresh pipelineResult. Has no bearing on the registry
         // collision guard (see allowDuplicateName below).
-        force: options?.force || options?.skills,
-        repairFts: options?.repairFts,
+        force: options.force || options.skills,
+        repairFts: options.repairFts,
         embeddings: embeddingsEnabled,
         embeddingsNodeLimit,
-        dropEmbeddings: options?.dropEmbeddings,
-        verbose: options?.verbose,
-        skipGit: options?.skipGit,
+        dropEmbeddings: options.dropEmbeddings,
+        verbose: options.verbose,
+        skipGit: options.skipGit,
         skipAgentsMd,
         skipSkills,
+        // Resolved default branch (CLI > .gitnexusrc > auto-detect > "main")
+        // threaded into the generated regression-compare example (#243).
+        defaultBranch: resolvedDefaultBranch,
         // commander.js `.option('--no-stats', …)` registers the flag as
         // `options.stats` (boolean, default true; `false` when the user
-        // passed --no-stats). Reading `options?.noStats` here returns
+        // passed --no-stats). Reading `options.noStats` here returns
         // undefined every time, so the flag was a no-op on the markdown
         // rewrite path before this fix. See #1477.
-        noStats: options?.stats === false,
-        registryName: options?.name,
+        noStats: options.stats === false,
+        registryName: options.name,
         // Registry-collision bypass — its own CLI flag, intentionally NOT
         // overloading --force. A user who hits the collision guard should
         // be able to accept the duplicate name without also paying the
         // cost of a full pipeline re-index. See #829 review round 2.
-        allowDuplicateName: options?.allowDuplicateName,
+        allowDuplicateName: options.allowDuplicateName,
         // Worker pool size threaded from --workers, replacing the previous
         // GITNEXUS_WORKER_POOL_SIZE env mutation. `undefined` defers to the
         // env / auto-formula fallback inside the pipeline.
@@ -987,6 +1123,21 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
       // that half-finalized state, runFullAnalysis returns alreadyUpToDate
       // on the next invocation unless we check the registry here too.
       await assertAnalysisFinalized(repoPath);
+      // The fast path skips context regeneration, but a changed `.gitnexusrc`
+      // defaultBranch / `--default-branch` must still take effect. Surgically
+      // refresh just the `base_ref` line in AGENTS.md/CLAUDE.md in place,
+      // preserving the rest of the block (incl. --skills community rows). No-op
+      // when the value already matches, so a routine up-to-date run is silent
+      // (#1996 tri-review P2).
+      let baseRefRefreshed: string[] = [];
+      try {
+        const { refreshBaseRefLine } = await import('./ai-context.js');
+        baseRefRefreshed = (
+          await refreshBaseRefLine(repoPath, resolvedDefaultBranch, { skipAgentsMd })
+        ).files;
+      } catch {
+        /* best-effort — never fail the fast path over a context refresh */
+      }
       clearInterval(elapsedTimer);
       process.removeListener('SIGINT', sigintHandler);
       console.log = origLog;
@@ -996,6 +1147,11 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
       console.error = origError;
       bar.stop();
       console.log('  Already up to date\n');
+      if (baseRefRefreshed.length > 0) {
+        console.log(
+          `  Updated base_ref to "${resolvedDefaultBranch}" in ${baseRefRefreshed.join(', ')}\n`,
+        );
+      }
       // Safe to return without process.exit(0) — the early-return path in
       // runFullAnalysis never opens LadybugDB, so no native handles prevent exit.
       return;
@@ -1069,9 +1225,13 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
             {
               skipAgentsMd,
               skipSkills,
+              // Same resolved branch as the main run (#243) so the --skills
+              // re-generation of AGENTS.md/CLAUDE.md does not revert base_ref
+              // to "main".
+              defaultBranch: resolvedDefaultBranch,
               // Mirror runFullAnalysis `noStats` bridge (#1477) — same expression;
               // exercised on the `--skills` path by analyze-no-stats-bridge.test.ts.
-              noStats: options?.stats === false,
+              noStats: options.stats === false,
             },
           );
         }
@@ -1191,6 +1351,20 @@ const analyzeCommandImpl = async (inputPath?: string, options?: AnalyzeOptions):
       return;
     }
 
+    // Local embedding runtime unsupported on this platform (macOS Intel ships no
+    // darwin/x64 ONNX native binding, #1515). The guard threw before importing
+    // transformers.js, so this is a clean, actionable GitNexus message. Checked
+    // before the network-heuristic isHfDownloadFailure branch below (and before
+    // the generic module-not-found "installation may be corrupt" hint) so the
+    // explicit platform message always takes priority.
+    if (isLocalEmbeddingRuntimeBlockerMessage(msg)) {
+      cliError(`  ${msg.replace(/\n/g, '\n  ')}\n`, {
+        recoveryHint: 'local-embedding-unsupported',
+      });
+      process.exitCode = 1;
+      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.

gitnexus/src/cli/cli-message.ts

@@ -49,9 +49,12 @@ export type RecoveryHint =
   | 'heap-oom-respawn'
   | 'native-worker-abort'
   | 'hf-endpoint-unreachable'
+  | 'local-embedding-unsupported'
   | 'large-repo'
   | 'npm-resolution'
-  | 'module-not-found';
+  | 'module-not-found'
+  | 'gitnexusrc-invalid'
+  | 'default-branch-invalid';
 
 /**
  * Common shape for the optional structured-field bag passed to

gitnexus/src/cli/doctor.ts

@@ -1,6 +1,7 @@
 import { getRuntimeCapabilities, getRuntimeFingerprint } from '../core/platform/capabilities.js';
 import { resolveEmbeddingConfig } from '../core/embeddings/config.js';
 import { isHttpMode } from '../core/embeddings/http-client.js';
+import { getLocalEmbeddingRuntimeBlocker } from '../core/embeddings/runtime-support.js';
 import { checkLbugNative } from '../core/lbug/native-check.js';
 import { getExtensionInstallPolicy } from '../core/lbug/extension-loader.js';
 import { t } from './i18n/index.js';
@@ -50,6 +51,33 @@ export function padDisplayEnd(value: string, columns: number): string {
 
 const label = (key: Parameters<typeof t>[0], width: number): string => padDisplayEnd(t(key), width);
 
+/**
+ * Embedding-runtime support status for the `doctor` Embeddings section.
+ * Pure and DI-friendly so it can be unit-tested without running the whole
+ * command. Delegates the platform decision to
+ * {@link getLocalEmbeddingRuntimeBlocker} so the wording stays in one place.
+ *
+ * - HTTP mode: always supported (never touches the native runtime).
+ * - Local mode on an unsupported platform (macOS Intel, #1515): reports the
+ *   blocker as `detail` so the caller can surface the full guidance.
+ */
+export function localEmbeddingDoctorStatus(opts: {
+  httpMode: boolean;
+  platform?: NodeJS.Platform;
+  arch?: NodeJS.Architecture;
+}): { status: string; detail: string | null } {
+  if (opts.httpMode) {
+    return { status: '✓ http endpoint configured', detail: null };
+  }
+  const platform = opts.platform ?? process.platform;
+  const arch = opts.arch ?? process.arch;
+  const blocker = getLocalEmbeddingRuntimeBlocker({ platform, arch });
+  if (blocker) {
+    return { status: `✗ local embeddings unavailable on ${platform}/${arch}`, detail: blocker };
+  }
+  return { status: '✓ local embeddings supported', detail: null };
+}
+
 export const doctorCommand = async () => {
   const fingerprint = getRuntimeFingerprint();
   const capabilities = getRuntimeCapabilities();
@@ -102,4 +130,13 @@ export const doctorCommand = async () => {
   console.log(
     `  ${label('doctor.labels.subBatch', 12)}${t('doctor.chunks', { count: embeddingConfig.subBatchSize })}`,
   );
+  // Surface local-runtime support so macOS Intel users see up front that local
+  // embeddings can't load here (the bundled ONNX Runtime ships no darwin/x64
+  // native binding, #1515) — rather than discovering it only when
+  // `analyze --embeddings` fails. Literal label like the 'native' line above.
+  const support = localEmbeddingDoctorStatus({ httpMode: isHttpMode() });
+  console.log(`  ${padDisplayEnd('Support:', 12)}${support.status}`);
+  if (support.detail) {
+    process.stderr.write(`\n${support.detail.replace(/^/gm, '  ')}\n\n`);
+  }
 };

gitnexus/src/cli/i18n/en.ts

@@ -175,7 +175,7 @@ export const en = {
   'help.option.analyze.walCheckpointThreshold':
     'LadybugDB WAL auto-checkpoint threshold in bytes during analyze (integer >= -1; default: 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB).',
   'help.option.analyze.workers':
-    'Parse worker pool size. Default: cores-1 capped at 16. Pass 0 to disable workers (sequential).',
+    'Parse worker pool size (>=1). Default: cores-1 capped at 16, auto-sized to the repo.',
   'help.option.analyze.embeddingThreads': 'Limit local ONNX embedding CPU threads',
   'help.option.analyze.embeddingBatchSize': 'Number of nodes per embedding batch',
   'help.option.analyze.embeddingSubBatchSize': 'Number of chunks per embedding model call',
@@ -189,7 +189,7 @@ export const en = {
   'help.option.clean.lbugSidecars': 'Clean quarantined LadybugDB missing-shadow WAL sidecars',
   'help.option.wiki.force': 'Force full regeneration even if up to date',
   'help.option.wiki.provider':
-    'LLM provider: openai, openrouter, azure, custom, cursor, claude, or codex (default: openai)',
+    'LLM provider: openai, openrouter, azure, custom, cursor, claude, codex, or opencode (default: openai)',
   'help.option.wiki.model': 'LLM model or Azure deployment name (default: minimax/minimax-m2.5)',
   'help.option.wiki.baseUrl':
     'LLM API base URL. Azure v1: https://{resource}.openai.azure.com/openai/v1',

gitnexus/src/cli/i18n/zh-CN.ts

@@ -164,7 +164,7 @@ export const zhCN = {
   'help.option.analyze.walCheckpointThreshold':
     'analyze 期间 LadybugDB WAL 自动 checkpoint 阈值（字节，整数 >= -1；默认：67108864 = 64 MiB；-1 保持 Ladybug 默认约 16 MiB）。',
   'help.option.analyze.workers':
-    '解析 worker 池大小。默认：cores-1，最多 16。传 0 禁用 worker（顺序执行）。',
+    '解析 worker 池大小（>=1）。默认：cores-1，最多 16，按仓库规模自适应。',
   'help.option.analyze.embeddingThreads': '限制本地 ONNX 嵌入 CPU 线程数',
   'help.option.analyze.embeddingBatchSize': '每个嵌入批次的节点数',
   'help.option.analyze.embeddingSubBatchSize': '每次嵌入模型调用的分块数',
@@ -178,7 +178,7 @@ export const zhCN = {
   'help.option.clean.lbugSidecars': '清理已隔离的 LadybugDB missing-shadow WAL sidecar',
   'help.option.wiki.force': '即使已是最新也强制完整重新生成',
   'help.option.wiki.provider':
-    'LLM 提供商：openai、openrouter、azure、custom、cursor、claude 或 codex（默认：openai）',
+    'LLM 提供商：openai、openrouter、azure、custom、cursor、claude、codex 或 opencode（默认：openai）',
   'help.option.wiki.model': 'LLM 模型或 Azure deployment 名称（默认：minimax/minimax-m2.5）',
   'help.option.wiki.baseUrl':
     'LLM API base URL。Azure v1：https://{resource}.openai.azure.com/openai/v1',

gitnexus/src/cli/index.ts

@@ -44,6 +44,11 @@ program
       '(no-op when --index-only is also set).',
   )
   .option('--skip-agents-md', 'Skip updating the gitnexus section in AGENTS.md and CLAUDE.md')
+  .option(
+    '--default-branch <branch>',
+    'Default branch used in the generated regression-compare example (base_ref). ' +
+      'Falls back to .gitnexusrc, then auto-detected origin/HEAD, then "main".',
+  )
   .option('--no-stats', 'Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md')
   .option(
     '--skip-skills',
@@ -82,7 +87,7 @@ program
   )
   .option(
     '--workers <n>',
-    'Parse worker pool size. Default: cores-1 capped at 16. Pass 0 to disable workers (sequential).',
+    'Parse worker pool size (>=1). Default: cores-1 capped at 16, auto-sized to the repo.',
   )
   .option('--embedding-threads <n>', 'Limit local ONNX embedding CPU threads')
   .option('--embedding-batch-size <n>', 'Number of nodes per embedding batch')
@@ -150,7 +155,7 @@ program
   .option('-f, --force', 'Force full regeneration even if up to date')
   .option(
     '--provider <provider>',
-    'LLM provider: openai, openrouter, azure, custom, cursor, claude, or codex (default: openai)',
+    'LLM provider: openai, openrouter, azure, custom, cursor, claude, codex, or opencode (default: openai)',
   )
   .option('--model <model>', 'LLM model or Azure deployment name (default: minimax/minimax-m2.5)')
   .option(

gitnexus/src/cli/skill-gen.ts

@@ -649,9 +649,9 @@ const renderSkillMarkdown = (
         : community.label;
   lines.push('## How to Explore');
   lines.push('');
-  lines.push(`1. \`gitnexus_context({name: "${firstEntry}"})\` \u2014 see callers and callees`);
+  lines.push(`1. \`context({name: "${firstEntry}"})\` \u2014 see callers and callees`);
   lines.push(
-    `2. \`gitnexus_query({query: "${community.label.toLowerCase()}"})\` \u2014 find related execution flows`,
+    `2. \`query({query: "${community.label.toLowerCase()}"})\` \u2014 find related execution flows`,
   );
   lines.push('3. Read key files listed above for implementation details');
   lines.push('');

gitnexus/src/cli/wiki.ts

@@ -58,14 +58,21 @@ function parsePositiveIntegerOption(
 
 function isLocalProvider(
   provider: LLMProvider | undefined,
-): provider is 'cursor' | 'claude' | 'codex' {
-  return provider === 'cursor' || provider === 'claude' || provider === 'codex';
+): provider is 'cursor' | 'claude' | 'codex' | 'opencode' {
+  return (
+    provider === 'cursor' ||
+    provider === 'claude' ||
+    provider === 'codex' ||
+    provider === 'opencode'
+  );
 }
 
-function localModelConfigKey(provider: 'cursor' | 'claude' | 'codex') {
+function localModelConfigKey(provider: 'cursor' | 'claude' | 'codex' | 'opencode') {
   if (provider === 'cursor') return 'cursorModel';
   if (provider === 'claude') return 'claudeModel';
-  return 'codexModel';
+  if (provider === 'codex') return 'codexModel';
+  if (provider === 'opencode') return 'opencodeModel';
+  throw new Error(`Unsupported local provider: ${provider satisfies never}`);
 }
 
 /**
@@ -248,7 +255,7 @@ const wikiCommandImpl = async (inputPath?: string, options?: WikiCommandOptions)
       if (!llmConfig.apiKey && !isLocalProvider(llmConfig.provider)) {
         console.log('  Error: No LLM API key found.');
         console.log('  Set OPENAI_API_KEY or GITNEXUS_API_KEY environment variable,');
-        console.log('  or pass --api-key <key>, or use --provider cursor|claude|codex.\n');
+        console.log('  or pass --api-key <key>, or use --provider cursor|claude|codex|opencode.\n');
         process.exitCode = 1;
         return;
       }
@@ -256,16 +263,17 @@ const wikiCommandImpl = async (inputPath?: string, options?: WikiCommandOptions)
     } else {
       console.log("  No LLM configured. Let's set it up.\n");
       console.log(
-        '  Supports OpenAI, OpenRouter, Azure, any OpenAI-compatible API, Cursor CLI, Claude CLI, or Codex CLI.\n',
+        '  Supports OpenAI, OpenRouter, Azure, any OpenAI-compatible API, Cursor CLI, Claude CLI, Codex CLI, or OpenCode CLI.\n',
       );
 
       // Check if local agent CLIs are available.
       const hasCursor = detectCursorCLI();
       const hasClaude = detectLocalCLI('claude');
       const hasCodex = detectLocalCLI('codex');
+      const hasOpenCode = detectLocalCLI('opencode');
       const localChoices: Array<{
         choice: string;
-        provider: 'cursor' | 'claude' | 'codex';
+        provider: 'cursor' | 'claude' | 'codex' | 'opencode';
       }> = [];
 
       // Provider selection
@@ -298,6 +306,14 @@ const wikiCommandImpl = async (inputPath?: string, options?: WikiCommandOptions)
         });
         console.log(`  [${choice}] Codex CLI (local, uses your Codex login)`);
       }
+      if (hasOpenCode) {
+        const choice = String(nextChoice++);
+        localChoices.push({
+          choice,
+          provider: 'opencode',
+        });
+        console.log(`  [${choice}] OpenCode CLI (local, uses your OpenCode login/config)`);
+      }
       console.log('');
 
       const maxChoice = String(nextChoice - 1);

gitnexus/src/core/embeddings/embedder.ts

@@ -14,12 +14,11 @@ if (!process.env.ORT_LOG_LEVEL) {
   process.env.ORT_LOG_LEVEL = '3';
 }
 
-import {
-  pipeline,
-  env,
-  type FeatureExtractionPipeline,
-  type ProgressInfo,
-} from '@huggingface/transformers';
+// Type-only import: erased at compile time so loading this module never pulls
+// in @huggingface/transformers (and its native onnxruntime-node binding) at
+// runtime. The runtime values (pipeline, env) are dynamically imported inside
+// initEmbedder, after the platform guard has passed (#1515).
+import type { FeatureExtractionPipeline, ProgressInfo } from '@huggingface/transformers';
 import { existsSync } from 'fs';
 import { execFileSync } from 'child_process';
 import { join, dirname } from 'path';
@@ -28,6 +27,7 @@ import { DEFAULT_EMBEDDING_CONFIG, type EmbeddingConfig, type ModelProgress } fr
 import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
 import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry } from './hf-env.js';
+import { getLocalEmbeddingRuntimeBlocker } from './runtime-support.js';
 import { logger } from '../logger.js';
 
 /**
@@ -143,6 +143,17 @@ export const initEmbedder = async (
     );
   }
 
+  // Fail fast on platforms where the bundled native ONNX Runtime binding is not
+  // shipped (macOS Intel, #1515). Must run before any transformers.js /
+  // onnxruntime-node import or resolution — otherwise the native module load
+  // crashes with a raw "Cannot find module ...onnxruntime_binding.node" that
+  // ONNX_WEB_BACKEND=wasm cannot rescue (#1516). HTTP mode was already handled
+  // above, so this only blocks the local-runtime path.
+  const runtimeBlocker = getLocalEmbeddingRuntimeBlocker();
+  if (runtimeBlocker) {
+    throw new Error(runtimeBlocker);
+  }
+
   // Return existing instance if available
   if (embedderInstance) {
     return embedderInstance;
@@ -166,6 +177,10 @@ export const initEmbedder = async (
 
   initPromise = (async () => {
     try {
+      // Lazy-load transformers.js only after the runtime guard has passed, so
+      // unsupported platforms never reach the native ONNX import (#1515).
+      const { pipeline, env } = await import('@huggingface/transformers');
+
       // Configure transformers.js environment
       env.allowLocalModels = false;
       // Bridge user-controlled env vars to transformers.js: HF_HOME →

gitnexus/src/core/embeddings/runtime-support.ts

@@ -0,0 +1,79 @@
+/**
+ * Local embedding runtime support guard.
+ *
+ * The bundled local embedding stack (`@huggingface/transformers` →
+ * `onnxruntime-node`) only ships native ONNX Runtime bindings for a subset of
+ * platform/arch pairs. On macOS Intel (`darwin`/`x64`), `onnxruntime-node`
+ * ships no `bin/napi-v6/darwin/x64/onnxruntime_binding.node`, so *importing*
+ * transformers.js throws a raw `Cannot find module ...onnxruntime_binding.node`
+ * before any device/backend selection can run (#1515). `ONNX_WEB_BACKEND=wasm`
+ * cannot rescue this — the failure is at native-module import time, not backend
+ * selection (#1516).
+ *
+ * This module is intentionally free of any native or transformers.js import (at
+ * module scope or inside its functions) so it can be consulted *before* the
+ * dynamic import that would crash. HTTP embedding mode never touches the native
+ * runtime, so callers in HTTP mode must skip this guard.
+ */
+
+/**
+ * Stable lead line of the macOS-Intel blocker message. Also used to recognise
+ * the thrown error in the CLI error handler without coupling to the full
+ * wording (see {@link isLocalEmbeddingRuntimeBlockerMessage}).
+ */
+const LOCAL_EMBEDDING_BLOCKER_LEAD =
+  'Local semantic embeddings are unavailable on macOS Intel (darwin/x64).';
+
+export interface LocalEmbeddingRuntimeOptions {
+  platform?: NodeJS.Platform;
+  arch?: NodeJS.Architecture;
+}
+
+/**
+ * Return a human-readable explanation when the *local* embedding runtime cannot
+ * load on this platform, or `null` when local embeddings are expected to work.
+ *
+ * Only `darwin`/`x64` is blocked today: it is the one platform/arch pair where
+ * the bundled `onnxruntime-node` ships no native binding (#1515). Every other
+ * platform returns `null` and follows the normal device-probe path, so genuine
+ * ONNX failures on supported platforms are never masked by this message.
+ *
+ * Accepts an explicit `{ platform, arch }` for testing; defaults to the current
+ * process values.
+ */
+export const getLocalEmbeddingRuntimeBlocker = (
+  options: LocalEmbeddingRuntimeOptions = {},
+): string | null => {
+  const platform = options.platform ?? process.platform;
+  const arch = options.arch ?? process.arch;
+
+  if (platform === 'darwin' && arch === 'x64') {
+    return [
+      LOCAL_EMBEDDING_BLOCKER_LEAD,
+      'The bundled ONNX Runtime package (onnxruntime-node) does not ship a',
+      'darwin/x64 native binding, so the local embedding model cannot load here.',
+      'ONNX_WEB_BACKEND=wasm does not help: the failure happens while importing',
+      'the native runtime, before any backend can be selected. Forcing',
+      'GITNEXUS_EMBEDDING_DEVICE=wasm (or cpu) does not help either, for the same reason.',
+      '',
+      'Use one of these instead:',
+      '  - Run analyze without --embeddings (all other indexing still works).',
+      '  - Point GITNEXUS_EMBEDDING_URL (with GITNEXUS_EMBEDDING_MODEL) at an',
+      '    OpenAI-compatible /v1/embeddings endpoint to embed over HTTP.',
+      '  - Run GitNexus on Linux or in Docker, where the native binding ships.',
+      '  - Run GitNexus on Apple Silicon (darwin/arm64), which ships a binding.',
+      '  - Use a future GitNexus build that restores darwin/x64 ONNX support.',
+    ].join('\n');
+  }
+
+  return null;
+};
+
+/**
+ * True when `message` is the macOS-Intel local-embedding blocker produced by
+ * {@link getLocalEmbeddingRuntimeBlocker}. Lets the CLI surface a clean,
+ * actionable message instead of a raw stack trace, without coupling to the
+ * full wording.
+ */
+export const isLocalEmbeddingRuntimeBlockerMessage = (message: string): boolean =>
+  message.includes(LOCAL_EMBEDDING_BLOCKER_LEAD);

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

@@ -55,6 +55,7 @@ const METHOD_ANNOTATION_TO_HTTP: Record<string, string> = {
 interface SpringRouteBinding {
   method: string;
   path: string;
+  ownerPrefix?: string;
 }
 
 interface SpringMethodInfo {
@@ -395,6 +396,25 @@ function joinPath(prefix: string, methodPath: string): string {
   return `/${cleanPrefix}/${cleanSub}`;
 }
 
+function joinInheritedSpringPath(
+  controllerPrefix: string,
+  inheritedPath: string,
+  inheritedOwnerPrefix = '',
+): string {
+  const joined = joinPath(controllerPrefix, inheritedPath);
+  const cleanPrefix = controllerPrefix.replace(/^\/+/, '').replace(/\/+$/, '');
+  const cleanOwnerPrefix = inheritedOwnerPrefix.replace(/^\/+/, '').replace(/\/+$/, '');
+  const cleanInherited = inheritedPath.replace(/^\/+/, '');
+  if (!cleanPrefix) return joined;
+  if (
+    cleanPrefix === cleanOwnerPrefix &&
+    (cleanInherited === cleanPrefix || cleanInherited.startsWith(`${cleanPrefix}/`))
+  ) {
+    return `/${cleanInherited}`;
+  }
+  return joined;
+}
+
 function getNodeName(node: Parser.SyntaxNode): string | null {
   return node.childForFieldName('name')?.text ?? null;
 }
@@ -634,6 +654,7 @@ function scanSpringProject(files: readonly HttpScanInput[]): HttpFileDetections[
       const routes = method.routes.map((route) => ({
         method: route.method,
         path: type.classPrefix ? joinPath(type.classPrefix, route.path) : route.path,
+        ownerPrefix: type.classPrefix,
       }));
       if (routes.length > 0) methodMap.set(method.name, routes);
     }
@@ -651,7 +672,7 @@ function scanSpringProject(files: readonly HttpScanInput[]): HttpFileDetections[
         const routes = routeMap.get(method.name) ?? [];
         return routes.map((route) => ({
           method: route.method,
-          path: joinPath(type.classPrefix, route.path),
+          path: joinInheritedSpringPath(type.classPrefix, route.path, route.ownerPrefix),
         }));
       });
 

gitnexus/src/core/ingestion/ast-cache.ts

@@ -1,77 +0,0 @@
-import { LRUCache } from 'lru-cache';
-import Parser from 'tree-sitter';
-
-import { logger } from '../logger.js';
-/**
- * Minimal structural shape consumers need when reading Trees back
- * through a phase-dependency boundary. Declared here so phases that
- * receive ASTCache via `getPhaseOutput<...>` don't hand-roll their
- * own inline structural types that silently drift when ASTCache's
- * contract changes.
- *
- * Typed as `unknown` at the Tree boundary because consumers on the
- * other side of the phase-output map don't share tree-sitter's type
- * graph (e.g. COBOL's standalone processor).
- */
-export interface ASTCacheReader {
-  get(filePath: string): unknown;
-  clear(): void;
-}
-
-// Define the interface for the Cache
-export interface ASTCache extends ASTCacheReader {
-  get: (filePath: string) => Parser.Tree | undefined;
-  set: (filePath: string, tree: Parser.Tree) => void;
-  clear: () => void;
-  stats: () => { size: number; maxSize: number };
-}
-
-export const createASTCache = (maxSize: number = 50): ASTCache => {
-  const effectiveMax = Math.max(maxSize, 1);
-  // Initialize the cache with a 'dispose' handler
-  // This is the magic: When an item is evicted (dropped), this runs automatically.
-  const cache = new LRUCache<string, Parser.Tree>({
-    max: effectiveMax,
-    dispose: (tree) => {
-      try {
-        // NOTE: web-tree-sitter has tree.delete(); native tree-sitter
-        // trees are GC-managed and .delete is absent (no-op here).
-        //
-        // Single-owner invariant (load-bearing under WASM): a given
-        // Parser.Tree reference must live in AT MOST ONE ASTCache
-        // that disposes. The parse-phase chunk-local cache clears
-        // between chunks; the cross-phase `scopeTreeCache` (also an
-        // ASTCache today) holds the same Tree by reference. Under
-        // native tree-sitter this is benign (dispose is a no-op).
-        // If/when GitNexus adopts web-tree-sitter for sequential
-        // parsing, the cross-phase cache must either (a) skip
-        // writing Trees that are already owned by a disposing cache,
-        // or (b) use tree.copy() per entry. Failing to pick one
-        // will hand freed memory to scope-resolution.
-        (tree as unknown as { delete?: () => void }).delete?.();
-      } catch (e) {
-        logger.warn({ e }, 'Failed to delete tree from WASM memory');
-      }
-    },
-  });
-
-  return {
-    get: (filePath: string) => {
-      const tree = cache.get(filePath);
-      return tree; // Returns undefined if not found
-    },
-
-    set: (filePath: string, tree: Parser.Tree) => {
-      cache.set(filePath, tree);
-    },
-
-    clear: () => {
-      cache.clear();
-    },
-
-    stats: () => ({
-      size: cache.size,
-      maxSize: effectiveMax,
-    }),
-  };
-};

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

@@ -7,8 +7,8 @@
  * call-processor so that the classification logic lives in one place.
  *
  * Heritage (mixins: include/extend/prepend) was previously routed here
- * but is now handled by heritageExtractor.extractFromCall before the
- * call router runs.  The router still returns 'skip' for these calls.
+ * but is now emitted by the scope-resolution pipeline. The router still
+ * returns 'skip' for these calls so they don't become spurious call edges.
  *
  * NOTE: This file is intentionally duplicated in gitnexus-web/ because the
  * two packages have separate build targets (Node native vs WASM/browser).
@@ -24,9 +24,10 @@ export type CallRoutingResult = RubyCallRouting | null;
 
 /**
  * Per-language call router.
- * IMPORTANT: Call-routed imports bypass preprocessImportPath(), so any router that
- * returns an importPath MUST validate it independently (length cap, control-char
- * rejection). See routeRubyCall for the reference implementation.
+ * IMPORTANT: Call-routed imports are NOT sanitized by the standard import-path
+ * cleaner, so any router that returns an importPath MUST validate it
+ * independently (length cap, control-char rejection). See routeRubyCall for the
+ * reference implementation.
  */
 export type CallRouter = (calledName: string, callNode: SyntaxNode) => CallRoutingResult;
 
@@ -82,10 +83,10 @@ export function routeRubyCall(calledName: string, callNode: SyntaxNode): RubyCal
     return { kind: 'import', importPath, isRelative };
   }
 
-  // ── include / extend / prepend — heritage (now handled by heritageExtractor) ─
-  // Call-based heritage is intercepted by heritageExtractor.extractFromCall
-  // before the call router runs.  Return SKIP_RESULT so these calls don't
-  // fall through to normal call processing.
+  // ── include / extend / prepend — heritage (emitted by scope-resolution) ─
+  // Call-based heritage (Ruby mixins) is emitted by the scope-resolution
+  // pipeline. Return SKIP_RESULT so these calls don't fall through to normal
+  // call processing and become spurious call edges.
   if (calledName === 'include' || calledName === 'extend' || calledName === 'prepend') {
     return SKIP_RESULT;
   }

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

@@ -78,100 +78,3 @@ export interface CallExtractionConfig {
    */
   typeAsReceiverHeuristic?: boolean;
 }
-
-// ---------------------------------------------------------------------------
-// Call-resolution DAG types
-// ---------------------------------------------------------------------------
-//
-// The call-resolution pipeline is a typed DAG:
-//
-//   extract-call  ──▶  classify-form  ──▶  infer-receiver  ──▶  select-dispatch  ──▶  resolve-target  ──▶  emit-edge
-//
-// Provider hooks plug in at infer-receiver and select-dispatch; shared stages
-// stay language-agnostic. Stages 1-2 run in the parse worker; stages 3-6 run
-// on the main thread. DAG-internal types below are main-thread-only and never
-// serialize to the graph.
-
-/**
- * DAG stage 3 output: call record with receiver type and source discriminant.
- *
- * `receiverTypeName` is resolved via TypeEnv → constructor-map → class-as-receiver →
- * mixed-chain, or synthesized by `inferImplicitReceiver`. `receiverSource` tags
- * which path won and drives MRO strategy selection in stage 4.
- *
- * Invariants:
- * - `receiverSource` MUST match how `receiverTypeName` was resolved; every
- *   discriminant must have a live reader and writer.
- * - `hint` is opaque to shared stages; only the same provider's `selectDispatch` reads it.
- *
- * @see language-provider.ts § inferImplicitReceiver, selectDispatch
- */
-export interface ReceiverEnriched {
-  readonly calledName: string;
-  readonly callForm: 'free' | 'member' | 'constructor' | undefined;
-  readonly receiverName: string | undefined;
-  readonly receiverTypeName: string | undefined;
-  readonly receiverSource:
-    | 'none'
-    | 'typed-binding'
-    | 'constructor-map'
-    | 'class-as-receiver'
-    | 'mixed-chain'
-    | 'implicit-self';
-  /** Free-form hint from the provider hook; opaque to shared stages. */
-  readonly hint?: string;
-}
-
-/**
- * Provider hook output for `LanguageProvider.inferImplicitReceiver` (DAG stage 3).
- *
- * Overlay applied to `ReceiverEnriched` when an implicit receiver is synthesized.
- * Ruby example: bare `serialize` inside `Account#call_serialize` →
- * `{ callForm: 'member', receiverName: 'self', receiverTypeName: 'Account',
- *   receiverSource: 'implicit-self', hint: 'instance' }`
- *
- * Invariants:
- * - `receiverSource` is always `'implicit-self'` — the only variant this type produces.
- * - `callForm` is always `'member'` — the rewrite converts bare-call to method invocation.
- * - `hint` is opaque to shared stages; consumed by the same language's `selectDispatch`.
- */
-export interface ImplicitReceiverOverride {
-  readonly callForm: 'free' | 'member' | 'constructor';
-  readonly receiverName: string;
-  readonly receiverTypeName: string;
-  readonly receiverSource: Extract<ReceiverEnriched['receiverSource'], 'implicit-self'>;
-  /** Free-form language tag (e.g. Ruby sets 'singleton' for `def self.foo`
-   *  method bodies). Consumed by the same language's `selectDispatch` hook. */
-  readonly hint?: string;
-}
-
-/**
- * DAG stage 4 output: dispatch strategy for resolving the target method.
- *
- * Encodes which resolver branch to try first and an optional fallback.
- * Stage 5 delegates to `resolveMemberCall`, `resolveFreeCall`, or
- * `resolveStaticCall` based on `primary`.
- *
- * - `primary`: `'owner-scoped'` = MRO walk, `'free'` = arity-tiered global lookup,
- *   `'constructor'` = type instantiation.
- * - `fallback`: Only `'free-arity-narrowed'` exists; used by Ruby implicit-self
- *   to degrade to arity-tiered free lookup when the MRO walk misses.
- * - `ancestryView`: Ruby `'ruby-mixin'` only. `'singleton'` walks extend providers
- *   only; a miss NEVER falls through to file-scoped lookup (enforced in
- *   resolveCallTarget). `'instance'` is the default.
- *
- * Common patterns:
- *   - `{primary: 'constructor'}` — constructor call
- *   - `{primary: 'owner-scoped'}` — member call with known type
- *   - `{primary: 'owner-scoped', fallback: 'free-arity-narrowed', ancestryView: 'instance'}` — Ruby implicit-self
- *   - `{primary: 'owner-scoped', ancestryView: 'singleton'}` — Ruby class-method call
- *
- * @see language-provider.ts § selectDispatch
- * @see call-processor.ts § defaultDispatchDecision, resolveCallTarget
- */
-export interface DispatchDecision {
-  readonly primary: 'owner-scoped' | 'free' | 'constructor';
-  readonly fallback?: 'free-arity-narrowed';
-  readonly ancestryView?: 'instance' | 'singleton';
-  readonly hint?: string;
-}

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

@@ -45,10 +45,33 @@ export const cClassConfig: ClassExtractionConfig = {
 export const cppClassConfig: ClassExtractionConfig = {
   language: SupportedLanguages.CPlusPlus,
   typeDeclarationNodes: ['class_specifier', 'struct_specifier', 'enum_specifier'],
-  ancestorScopeNodeTypes: ['namespace_definition', 'class_specifier', 'struct_specifier'],
+  // #1995: `union_specifier` is included so a type nested in a NAMED union
+  // (`union U1 { struct Inner {...} }`) qualifies as `U1.Inner`. Anonymous unions
+  // have no `name` child → extractScopeSegmentsFromNode returns [] → they correctly
+  // contribute nothing (members inject into the enclosing scope). C uses the
+  // separate cClassConfig (no qualifiedNodeId), so it is intentionally untouched.
+  ancestorScopeNodeTypes: [
+    'namespace_definition',
+    'class_specifier',
+    'struct_specifier',
+    'union_specifier',
+  ],
   // #1978: key nested-type nodes by their fully-qualified path (Outer.Inner) so
   // same-tail nested types in one TU stay distinct instead of silently merging.
   qualifiedNodeId: true,
+  // #1995: anonymous namespaces have no `name` child, so the generic scope walker
+  // drops them (empty segment) and two `namespace { struct Inner {} }` blocks in one
+  // TU collapse onto a single `Inner` node. Give each anonymous namespace_definition
+  // a deterministic per-block discriminator (its start byte — stable across the
+  // sequential and worker full-file parses) so the nested types stay distinct.
+  // Returning `undefined` for every other scope — named namespaces (incl. `inline
+  // namespace`), classes, structs, named unions — falls through to the default
+  // name-based extraction, leaving them unchanged. Anonymous UNIONS are not matched
+  // here (members inject into the enclosing scope), so they keep yielding [].
+  extractScopeSegments: (node) =>
+    node.type === 'namespace_definition' && !node.childForFieldName?.('name')
+      ? [`@anon${node.startIndex}`]
+      : undefined,
   extractName: (node) => {
     const nameNode = node.childForFieldName?.('name');
     if (!nameNode) return undefined;

gitnexus/src/core/ingestion/class-extractors/generic.ts

@@ -164,6 +164,14 @@ export function createClassExtractor(config: ClassExtractionConfig): ClassExtrac
       return extract(node, { name: simpleName })?.qualifiedName ?? null;
     },
 
+    // #1991: qualify a non-typeDeclaration scope node (e.g. a Ruby `module` → Trait)
+    // by the same ancestor-scope walk the node-id path uses, so two same-tail nested
+    // mixin modules stay distinct. extract()/extractQualifiedName cannot be reused —
+    // they bail on non-typeDeclarations (a module is not in typeDeclarationNodes).
+    qualifyScopeName(node: SyntaxNode, simpleName: string): string {
+      return buildQualifiedName(node, simpleName);
+    },
+
     shouldSkipClassCapture(context): boolean {
       return config.shouldSkipClassCapture?.(context) ?? false;
     },

gitnexus/src/core/ingestion/class-types.ts

@@ -44,6 +44,14 @@ export interface ClassExtractor {
     },
   ): ExtractedClassSymbol | null;
   extractQualifiedName(node: SyntaxNode, simpleName: string): string | null;
+  /**
+   * #1991: qualify a scope-defining node that maps to a class-like registry label
+   * (e.g. a Ruby `module` → Trait) but is NOT a typeDeclaration, so it cannot go
+   * through extract()/extractQualifiedName (which bail on non-typeDeclarations).
+   * Walks the same ancestor scopes as the node-id path. Optional — only providers
+   * that materialize such nodes implement it.
+   */
+  qualifyScopeName?(node: SyntaxNode, simpleName: string): string;
   shouldSkipClassCapture?(
     context: ClassCaptureContext & { nodeLabel: ClassLikeNodeLabel },
   ): boolean;

gitnexus/src/core/ingestion/emit-references.ts

@@ -267,9 +267,14 @@ function buildRelationship(
 
 /**
  * Map a `Reference.kind` to an existing `RelationshipType`. Read/write
- * both fold into `ACCESSES`; `type-reference` + `import-use` both fold
- * into `USES`. This keeps the graph schema additive — no new
+ * both fold into `ACCESSES`; `type-reference`, `import-use`, and `macro`
+ * all fold into `USES`. This keeps the graph schema additive — no new
  * RelationshipType values are introduced by this module.
+ *
+ * `macro` folds into `USES` (not `CALLS`) deliberately: a macro
+ * invocation targets a `Macro` node, not a callable function, so keeping
+ * it out of the `CALLS` keyspace preserves the invariant that `CALLS`
+ * edges denote function/method dispatch.
  */
 function mapKindToType(kind: Reference['kind']): RelationshipType {
   switch (kind) {
@@ -282,6 +287,7 @@ function mapKindToType(kind: Reference['kind']): RelationshipType {
       return 'INHERITS';
     case 'type-reference':
     case 'import-use':
+    case 'macro':
       return 'USES';
   }
 }

gitnexus/src/core/ingestion/export-detection.ts

@@ -4,7 +4,8 @@
  * Determines whether a symbol (function, class, etc.) is exported/public
  * in its language. This is a pure function — safe for use in worker threads.
  *
- * Shared between parse-worker.ts (worker pool) and parsing-processor.ts (sequential fallback).
+ * Used by the language providers during worker parsing (parse-worker.ts) — the
+ * sole parse path. (Sequential parsing was removed.)
  */
 
 import { findSiblingChild, type SyntaxNode } from './utils/ast-helpers.js';

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

@@ -2,15 +2,59 @@
 
 import { SupportedLanguages } from 'gitnexus-shared';
 import type { FieldExtractionConfig } from '../generic.js';
+import type { FieldVisibility } from '../../field-types.js';
+import type { SyntaxNode } from '../../utils/ast-helpers.js';
 import { hasKeyword } from './helpers.js';
 import { extractSimpleTypeName } from '../../type-extractors/shared.js';
 
 /**
  * Dart field extraction config.
  *
- * Dart class fields appear as declaration nodes inside class_body.
+ * Dart class fields appear as `declaration` nodes inside `class_body`.
+ * Two shapes carry the field name(s):
+ *   - instance / plain fields → `initialized_identifier_list`
+ *     (`int z = 0;`, `int a = 1, b = 2;`)
+ *   - `static const` / `static final` / `const` fields → `static_final_declaration_list`
+ *     (`static const a = 1;`, `static final String b = 'x', c = 'y';`)
+ * Both shapes may declare SEVERAL fields in one declaration, so name extraction
+ * is multi-name (`extractNames`). The structure query (`DART_QUERIES`) emits one
+ * `@definition.property` per name for both shapes; this config enriches each.
+ *
  * Visibility is convention-based: underscore prefix = private.
  */
+
+/** All field names declared by a `declaration` node, across both Dart shapes. */
+function extractDartFieldNames(node: SyntaxNode): string[] {
+  const names: string[] = [];
+  for (let i = 0; i < node.namedChildCount; i++) {
+    const child = node.namedChild(i);
+    if (!child) continue;
+
+    // instance / plain fields: initialized_identifier_list > initialized_identifier > identifier
+    if (child.type === 'initialized_identifier_list') {
+      for (let j = 0; j < child.namedChildCount; j++) {
+        const init = child.namedChild(j);
+        if (init?.type === 'initialized_identifier') {
+          const ident = init.firstNamedChild;
+          if (ident?.type === 'identifier') names.push(ident.text);
+        }
+      }
+    }
+
+    // static const / final fields: static_final_declaration_list > static_final_declaration > identifier
+    if (child.type === 'static_final_declaration_list') {
+      for (let j = 0; j < child.namedChildCount; j++) {
+        const decl = child.namedChild(j);
+        if (decl?.type === 'static_final_declaration') {
+          const ident = decl.firstNamedChild;
+          if (ident?.type === 'identifier') names.push(ident.text);
+        }
+      }
+    }
+  }
+  return names;
+}
+
 export const dartConfig: FieldExtractionConfig = {
   language: SupportedLanguages.Dart,
   typeDeclarationNodes: ['class_definition'],
@@ -18,31 +62,20 @@ export const dartConfig: FieldExtractionConfig = {
   bodyNodeTypes: ['class_body'],
   defaultVisibility: 'public',
 
+  // One AST `declaration` node may declare several fields (`int a, b;`,
+  // `static final String b = 'x', c = 'y';`), so use the multi-name path.
   extractName(node) {
-    // declaration > initialized_identifier_list > initialized_identifier > identifier
-    for (let i = 0; i < node.namedChildCount; i++) {
-      const child = node.namedChild(i);
-      if (child?.type === 'initialized_identifier_list') {
-        for (let j = 0; j < child.namedChildCount; j++) {
-          const init = child.namedChild(j);
-          if (init?.type === 'initialized_identifier') {
-            const ident = init.firstNamedChild;
-            if (ident?.type === 'identifier') return ident.text;
-          }
-        }
-      }
-      if (child?.type === 'initialized_identifier') {
-        const ident = child.firstNamedChild;
-        if (ident?.type === 'identifier') return ident.text;
-      }
-    }
-    // fallback: look for direct identifier
-    const name = node.childForFieldName('name');
-    return name?.text;
+    return extractDartFieldNames(node)[0];
+  },
+
+  extractNames(node) {
+    return extractDartFieldNames(node);
   },
 
   extractType(node) {
-    // declaration > type_identifier (first named child usually)
+    // declaration > type_identifier (the type annotation, present for both the
+    // instance-field shape and `static final String b = …`). `static const a = 1;`
+    // has no annotation → undefined (untyped).
     for (let i = 0; i < node.namedChildCount; i++) {
       const child = node.namedChild(i);
       if (child && (child.type === 'type_identifier' || child.type === 'function_type')) {
@@ -52,22 +85,16 @@ export const dartConfig: FieldExtractionConfig = {
     return undefined;
   },
 
-  extractVisibility(node) {
-    // Dart uses _ prefix for private
-    // Walk to find the identifier name
-    for (let i = 0; i < node.namedChildCount; i++) {
-      const child = node.namedChild(i);
-      if (child?.type === 'initialized_identifier_list') {
-        for (let j = 0; j < child.namedChildCount; j++) {
-          const init = child.namedChild(j);
-          if (init?.type === 'initialized_identifier') {
-            const ident = init.firstNamedChild;
-            if (ident?.text?.startsWith('_')) return 'private';
-          }
-        }
-      }
-    }
-    return 'public';
+  // Per-name: Dart convention is underscore-prefixed = private. A single
+  // declaration can mix visibilities (`static const _p = 1, q = 2;`), so the
+  // decision is keyed on the individual field name.
+  extractVisibilityForName(_node, name): FieldVisibility {
+    return name.startsWith('_') ? 'private' : 'public';
+  },
+
+  extractVisibility(node): FieldVisibility {
+    const first = extractDartFieldNames(node)[0];
+    return first?.startsWith('_') ? 'private' : 'public';
   },
 
   isStatic(node) {
@@ -75,6 +102,8 @@ export const dartConfig: FieldExtractionConfig = {
   },
 
   isReadonly(node) {
+    // `final` / `const` (both `final_builtin`/`const_builtin` nodes whose text
+    // is `final`/`const`) are read-only.
     return hasKeyword(node, 'final') || hasKeyword(node, 'const');
   },
 };

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

@@ -3,6 +3,8 @@
 import { SupportedLanguages } from 'gitnexus-shared';
 import type { FieldExtractionConfig } from '../generic.js';
 import { extractSimpleTypeName } from '../../type-extractors/shared.js';
+import type { FieldVisibility } from '../../field-types.js';
+import type { SyntaxNode } from '../../utils/ast-helpers.js';
 
 /**
  * Go field extraction config.
@@ -13,14 +15,52 @@ import { extractSimpleTypeName } from '../../type-extractors/shared.js';
  * Visibility in Go is based on the first character: uppercase = exported (public),
  * lowercase = unexported (package).
  */
+function goVisibilityForName(name: string): FieldVisibility {
+  const first = name.charAt(0);
+  return first === first.toUpperCase() && first !== first.toLowerCase() ? 'public' : 'package';
+}
+
+function extractGoFieldNames(node: SyntaxNode): string[] {
+  const names: string[] = [];
+  for (let i = 0; i < node.namedChildCount; i++) {
+    const child = node.namedChild(i);
+    if (child?.type === 'field_identifier') names.push(child.text);
+  }
+  return names;
+}
+
 export const goConfig: FieldExtractionConfig = {
   language: SupportedLanguages.Go,
-  typeDeclarationNodes: ['type_declaration'],
+  typeDeclarationNodes: ['type_declaration', 'struct_type'],
   fieldNodeTypes: ['field_declaration'],
   bodyNodeTypes: ['field_declaration_list'],
   defaultVisibility: 'package',
 
+  extractOwnerName(node) {
+    if (node.type === 'struct_type') {
+      return node.parent?.type === 'type_spec'
+        ? node.parent.childForFieldName('name')?.text
+        : undefined;
+    }
+    const typeSpec = node.namedChildren.find((child) => child.type === 'type_spec');
+    return typeSpec?.childForFieldName('name')?.text;
+  },
+
+  findBodyNodes(node) {
+    if (node.type === 'struct_type') {
+      const body = node.namedChildren.find((child) => child.type === 'field_declaration_list');
+      return body ? [body] : [];
+    }
+    const typeSpec = node.namedChildren.find((child) => child.type === 'type_spec');
+    const typeNode = typeSpec?.childForFieldName('type');
+    const body = typeNode?.namedChildren.find((child) => child.type === 'field_declaration_list');
+    return body ? [body] : [];
+  },
+
   extractName(node) {
+    const firstName = extractGoFieldNames(node)[0];
+    if (firstName) return firstName;
+
     // field_declaration > name:(field_identifier)
     const name = node.childForFieldName('name');
     if (name) return name.text;
@@ -32,6 +72,8 @@ export const goConfig: FieldExtractionConfig = {
     return undefined;
   },
 
+  extractNames: extractGoFieldNames,
+
   extractType(node) {
     // field_declaration > type:(type_identifier | pointer_type | ...)
     const typeNode = node.childForFieldName('type');
@@ -54,6 +96,10 @@ export const goConfig: FieldExtractionConfig = {
     return 'package';
   },
 
+  extractVisibilityForName(_node, name) {
+    return goVisibilityForName(name);
+  },
+
   isStatic(_node) {
     return false; // Go has no static fields
   },

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

@@ -5,6 +5,7 @@ import type { FieldExtractionConfig } from '../generic.js';
 import { findVisibility, hasKeyword, hasModifier, typeFromField } from './helpers.js';
 import { extractSimpleTypeName } from '../../type-extractors/shared.js';
 import type { FieldVisibility } from '../../field-types.js';
+import type { SyntaxNode } from '../../utils/ast-helpers.js';
 
 // ---------------------------------------------------------------------------
 // Java
@@ -73,13 +74,49 @@ export const javaConfig: FieldExtractionConfig = {
 
 const KOTLIN_VIS = new Set<FieldVisibility>(['public', 'private', 'protected', 'internal']);
 
+/** A property_declaration is a companion-object member when its nearest
+ *  class-body ancestor is the body of a companion_object (F52, issue #1919).
+ *  Companion members are addressed statically through the enclosing class
+ *  (`C.TAG`), so they are marked static. */
+function isInsideKotlinCompanion(node: SyntaxNode): boolean {
+  for (let cur = node.parent; cur !== null; cur = cur.parent) {
+    if (cur.type === 'class_body') return cur.parent?.type === 'companion_object';
+    if (cur.type === 'companion_object') return true;
+  }
+  return false;
+}
+
 export const kotlinConfig: FieldExtractionConfig = {
   language: SupportedLanguages.Kotlin,
-  typeDeclarationNodes: ['class_declaration', 'object_declaration'],
+  // F52: include companion_object so a companion property's innermost
+  // class-container owner (findEnclosingClassNode returns the companion_object)
+  // is recognized as a type declaration and its nested class_body is walked.
+  // The structure query already creates the Property node and owns it on the
+  // ENCLOSING class for anonymous companions / on the named companion Class —
+  // this entry only drives field-metadata enrichment, so it does NOT change
+  // ownership or emit a second node (no double-count).
+  typeDeclarationNodes: ['class_declaration', 'object_declaration', 'companion_object'],
   fieldNodeTypes: ['property_declaration'],
   bodyNodeTypes: ['class_body'],
   defaultVisibility: 'public',
 
+  // F52: an anonymous `companion object { ... }` has no name child, so the
+  // generic factory's `childForFieldName('name')` owner lookup is empty and
+  // `extract()` would bail before walking the body. Supply a stable owner
+  // name (the named companion's identifier, else "Companion") so the body IS
+  // walked; the resulting FieldInfo map is keyed by field NAME only, so the
+  // owner name does not affect which Property node gets enriched.
+  extractOwnerName(node) {
+    const typeIdentifierText = node.namedChildren.find((c) => c.type === 'type_identifier')?.text;
+    if (node.type === 'companion_object') {
+      // Anonymous companions have no type_identifier — fall back to "Companion".
+      return typeIdentifierText ?? 'Companion';
+    }
+    const name = node.childForFieldName('name');
+    if (name) return name.text;
+    return typeIdentifierText;
+  },
+
   extractName(node) {
     // property_declaration > variable_declaration > simple_identifier
     for (let i = 0; i < node.namedChildCount; i++) {
@@ -124,9 +161,11 @@ export const kotlinConfig: FieldExtractionConfig = {
     return findVisibility(node, KOTLIN_VIS, 'public', 'modifiers');
   },
 
-  isStatic(_node) {
-    // Kotlin doesn't have static; companion object members are handled separately
-    return false;
+  isStatic(node) {
+    // Kotlin has no `static`, but companion-object members are accessed
+    // statically through the enclosing class (`C.TAG`) — mark them static
+    // so the field metadata reflects that (F52).
+    return isInsideKotlinCompanion(node);
   },
 
   isReadonly(node) {

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

@@ -2,7 +2,7 @@
 
 import { SupportedLanguages } from 'gitnexus-shared';
 import type { FieldExtractionConfig } from '../generic.js';
-import { hasKeyword, findVisibility } from './helpers.js';
+import { hasKeyword, hasModifier, findVisibility } from './helpers.js';
 import { extractSimpleTypeName } from '../../type-extractors/shared.js';
 import type { FieldVisibility } from '../../field-types.js';
 
@@ -17,18 +17,33 @@ const SWIFT_VIS = new Set<FieldVisibility>([
 /**
  * Swift field extraction config.
  *
- * Handles property_declaration inside class_body / protocol_body.
+ * Handles property_declaration inside class_body / protocol_body and
+ * protocol_property_declaration inside protocol_body (F75 — protocol property
+ * requirements like "var title: String { get }").
+ *
  * tree-sitter-swift uses property_declaration for stored/computed properties.
+ * A protocol property requirement parses to its own node type,
+ * protocol_property_declaration, whose name lives in a "name:" pattern field
+ * (pattern > value_binding_pattern + simple_identifier(bound_identifier)), its
+ * type in a sibling type_annotation, and its "{ get }" / "{ get set }" in a
+ * protocol_property_requirements child. Note: Swift reuses the "name:" field
+ * across many positions (func name, every parameter label, parameter/return
+ * type), so the name is synthesized from the simple_identifier inside the
+ * pattern rather than read blindly off "name:".
  */
 export const swiftConfig: FieldExtractionConfig = {
   language: SupportedLanguages.Swift,
   typeDeclarationNodes: ['class_declaration', 'protocol_declaration'],
-  fieldNodeTypes: ['property_declaration'],
+  fieldNodeTypes: ['property_declaration', 'protocol_property_declaration'],
   bodyNodeTypes: ['class_body', 'protocol_body'],
   defaultVisibility: 'internal',
 
   extractName(node) {
-    // property_declaration > pattern > simple_identifier
+    // property_declaration > pattern > simple_identifier, and
+    // protocol_property_declaration > name: (pattern ... simple_identifier).
+    // For protocol_property_declaration the pattern wraps a leading
+    // value_binding_pattern ("var") plus the simple_identifier — the loop
+    // below skips the binding keyword and returns the identifier.
     for (let i = 0; i < node.namedChildCount; i++) {
       const child = node.namedChild(i);
       if (child?.type === 'pattern') {
@@ -62,7 +77,19 @@ export const swiftConfig: FieldExtractionConfig = {
   },
 
   isStatic(node) {
-    return hasKeyword(node, 'static') || hasKeyword(node, 'class');
+    // `static`/`class` (type-level) modifiers live inside a `modifiers`
+    // wrapper for both property_declaration and protocol_property_declaration
+    // (e.g. `static var shared: P { get }`), so check the wrapper too.
+    // `hasKeyword` compares each direct child by `.text` equality: it matches a
+    // single-modifier wrapper (`modifiers.text === 'static'`) but fails for a
+    // multi-modifier wrapper (`private static` → `modifiers.text === 'private static'`),
+    // which `hasModifier` handles by descending into the wrapper's children.
+    return (
+      hasKeyword(node, 'static') ||
+      hasKeyword(node, 'class') ||
+      hasModifier(node, 'modifiers', 'static') ||
+      hasModifier(node, 'modifiers', 'class')
+    );
   },
 
   isReadonly(node) {

gitnexus/src/core/ingestion/field-extractors/generic.ts

@@ -33,6 +33,10 @@ export interface FieldExtractionConfig {
   bodyNodeTypes: string[];
   /** Default visibility when no modifier is present */
   defaultVisibility: FieldVisibility;
+  /** Extract owner type name from a type declaration node. */
+  extractOwnerName?: (node: SyntaxNode) => string | undefined;
+  /** Find body nodes inside a type declaration node. */
+  findBodyNodes?: (node: SyntaxNode) => SyntaxNode[];
   /**
    * Extract field name from a field declaration node.
    * Use this for nodes that declare exactly one field.
@@ -49,6 +53,8 @@ export interface FieldExtractionConfig {
   extractType: (node: SyntaxNode) => string | undefined;
   /** Extract visibility from a field declaration node */
   extractVisibility: (node: SyntaxNode) => FieldVisibility;
+  /** Extract visibility for one field name from a multi-name declaration. */
+  extractVisibilityForName?: (node: SyntaxNode, name: string) => FieldVisibility;
   /** Check if a field is static */
   isStatic: (node: SyntaxNode) => boolean;
   /** Check if a field is readonly/final/const */
@@ -84,10 +90,9 @@ export function createFieldExtractor(config: FieldExtractionConfig): FieldExtrac
     extract(node: SyntaxNode, context: FieldExtractorContext): ExtractedFields | null {
       if (!this.isTypeDeclaration(node)) return null;
 
-      const nameNode = node.childForFieldName('name');
-      if (!nameNode) return null;
+      const ownerFqn = config.extractOwnerName?.(node) ?? node.childForFieldName('name')?.text;
+      if (!ownerFqn) return null;
 
-      const ownerFqn = nameNode.text;
       const fields: FieldInfo[] = [];
 
       // Find body container(s)
@@ -110,6 +115,8 @@ export function createFieldExtractor(config: FieldExtractionConfig): FieldExtrac
     // ------------------------------------------------------------------
 
     private findBodies(node: SyntaxNode): SyntaxNode[] {
+      if (config.findBodyNodes) return config.findBodyNodes(node);
+
       const result: SyntaxNode[] = [];
       // Try named 'body' field first
       const bodyField = node.childForFieldName('body');
@@ -179,7 +186,7 @@ export function createFieldExtractor(config: FieldExtractionConfig): FieldExtrac
       return {
         name,
         type,
-        visibility: config.extractVisibility(node),
+        visibility: config.extractVisibilityForName?.(node, name) ?? config.extractVisibility(node),
         isStatic: config.isStatic(node),
         isReadonly: config.isReadonly(node),
         sourceFile: context.filePath,

gitnexus/src/core/ingestion/filesystem-walker.ts

@@ -6,10 +6,6 @@ import { glob } from 'glob';
 import { createIgnoreFilter } from '../../config/ignore-service.js';
 
 import { logger } from '../logger.js';
-export interface FileEntry {
-  path: string;
-  content: string;
-}
 
 /** Lightweight entry — path + size from stat, no content in memory */
 export interface ScannedFile {
@@ -153,21 +149,3 @@ export const readFileContents = async (
 
   return contents;
 };
-
-/**
- * Legacy API — scans and reads everything into memory.
- * Used by sequential fallback path only.
- */
-export const walkRepository = async (
-  repoPath: string,
-  onProgress?: (current: number, total: number, filePath: string) => void,
-): Promise<FileEntry[]> => {
-  const scanned = await walkRepositoryPaths(repoPath, onProgress);
-  const contents = await readFileContents(
-    repoPath,
-    scanned.map((f) => f.path),
-  );
-  return scanned
-    .filter((f) => contents.has(f.path))
-    .map((f) => ({ path: f.path, content: contents.get(f.path)! }));
-};

gitnexus/src/core/ingestion/finalize-orchestrator.ts

@@ -51,6 +51,8 @@ import {
   finalize,
 } from 'gitnexus-shared';
 import type { ScopeResolutionIndexes } from './model/scope-resolution-indexes.js';
+import { parseTruthyEnv } from './utils/env.js';
+import { TransitionalScopeTree } from '../../storage/scope-index-store.js';
 
 // ─── Public entry point ─────────────────────────────────────────────────────
 
@@ -114,14 +116,20 @@ export function finalizeScopeModel(
     moduleEntries.push({ filePath: file.filePath, moduleScopeId: file.moduleScope });
   }
 
-  const scopeTree = buildScopeTree(allScopes);
+  // Out-of-core scope index: when enabled, build a TransitionalScopeTree
+  // (validated + fully resident now; sealed to disk by run.ts just before emit so
+  // the heavy Scope.bindings payload is reclaimed). Default off → the in-heap
+  // buildScopeTree result exactly, byte-identical.
+  const scopeTree = parseTruthyEnv(process.env.GITNEXUS_DISK_SCOPE_INDEX)
+    ? new TransitionalScopeTree(allScopes)
+    : buildScopeTree(allScopes);
   const defs = buildDefIndex(allDefs);
   const qualifiedNames = buildQualifiedNameIndex(allDefs);
   const moduleScopes = buildModuleScopeIndex(moduleEntries);
 
   // ── Step 3: MethodDispatchIndex. Today we lack per-language MRO
   // strategies wired into this orchestrator (that belongs with the
-  // HeritageMap bridge, a separate piece of work). Ship an EMPTY index
+  // MRO bridge, a separate piece of work). Ship an EMPTY index
   // so the bundle shape is consistent; the callbacks return `[]` for
   // every owner and `implementsOf` returns `[]`. Populating this
   // properly is tracked alongside the per-language provider hooks.

gitnexus/src/core/ingestion/heritage-extractors/configs/cpp.ts

@@ -1,21 +0,0 @@
-// gitnexus/src/core/ingestion/heritage-extractors/configs/cpp.ts
-
-import type { SupertypeShapeDescriptor } from '../../heritage-types.js';
-
-/**
- * C++ base-class supertype shapes (legacy CPP_QUERIES bank only).
- *
- * A `base_class_clause` entry can be a bare `type_identifier`, a
- * `template_type` (`Base<T>`), or a `qualified_identifier` (`ns::Base`,
- * possibly itself wrapping a `template_type`). Entries may be prefixed by an
- * `access_specifier`; tree-sitter's bracketed alternation matches the base
- * node regardless of the preceding access specifier, so a single pattern
- * covers both `: Base` and `: public Base`.
- *
- * NOTE: the registry/scope-resolution path emits its own normalized
- * `@reference.inherits` captures (see languages/cpp/captures.ts); this
- * descriptor only repairs the legacy heritage-query bank.
- */
-export const cppHeritageShapes: SupertypeShapeDescriptor = {
-  shapes: ['type_identifier', 'template_type', 'qualified_identifier'],
-};

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

@@ -1,38 +0,0 @@
-// gitnexus/src/core/ingestion/heritage-extractors/configs/csharp.ts
-
-import type { SupertypeShapeDescriptor } from '../../heritage-types.js';
-
-/**
- * C# base-list supertype shapes.
- *
- * Every `base_list` entry (class/record/struct/interface) is captured as
- * `@heritage.extends`; EXTENDS-vs-IMPLEMENTS is decided downstream by
- * `resolveExtendsType`, so the query does not pre-split. Entries can be a bare
- * `identifier`, a `generic_name` (`IFoo<T>`), a `qualified_name` (`ns.Base`,
- * and also `global::System.IDisposable` — a dotted name qualified by an
- * `alias_qualified_name` parses as a `qualified_name` whose first part is the
- * alias), an `alias_qualified_name` (a *bare* alias-qualified base with no
- * dotted suffix: `global::IDisposable`, `MyAlias::Foo`), or a
- * `primary_constructor_base_type` (`Base(args)` on a record).
- *
- * NOTE: `scoped_type` is intentionally NOT listed. Per
- * tree-sitter-c-sharp/src/node-types.json, `scoped_type` is a `type` subtype
- * that wraps a `ref_type` (the `scoped ref`/`scoped in` parameter modifier);
- * it is referenced only by the hidden `type` supertype and never appears as a
- * `base_list` entry, so adding it would be a dead, untested shape. The
- * alias-qualified base shapes that *do* occur are `qualified_name` (dotted) and
- * `alias_qualified_name` (bare) — verified by parsing
- * `class A : System.Exception, global::System.IDisposable, MyAlias::Foo {}`.
- * `normalizeSupertypeName` collapses `alias_qualified_name` to the simple name
- * via its `name` field (an `identifier`). See
- * `test/integration/heritage-supertype-shapes.test.ts`.
- */
-export const csharpHeritageShapes: SupertypeShapeDescriptor = {
-  shapes: [
-    'identifier',
-    'generic_name',
-    'qualified_name',
-    'alias_qualified_name',
-    'primary_constructor_base_type',
-  ],
-};