Commit graph

1232 commits

Author SHA1 Message Date
Gergő Magyar
9721a3edd6
Merge branch 'main' into feat/cfg-layer-m1 2026-06-10 09:12:26 +01:00
Gergő Magyar
292f26ece3
fix(hooks): silence MCP-owned-DB augment skip for strict hook runners (#1913) (#2134)
* fix(hooks): silence MCP-owned-DB augment skip for strict hook runners

The PreToolUse augment-skip path wrote `[GitNexus] augment skipped: MCP
server owns DB` to stderr unconditionally on a normal (non-error) skip.
Strict hook runners that validate hook output (e.g. Codex `PreToolUse`)
treat that as noisy / "invalid pre-tool-use JSON output".

Gate the diagnostic behind GITNEXUS_DEBUG via a shared `isDebugEnabled()`
helper, so normal skips are silent by default (empty stdout AND stderr,
exit 0) and the reason stays recoverable with `GITNEXUS_DEBUG=1`. Applied
consistently to all three hand-maintained hook copies (claude,
antigravity, claude-plugin).

Tests:
- Unit (claude CJS + plugin): assert default-silent and debug-on behavior
  for the MCP-owned-DB skip and for the fail-closed (lsof ETIMEDOUT) skip
  that routes through the same gated line; the owner-detection tests run
  with GITNEXUS_DEBUG=1 so the skip discriminator stays observable.
- e2e (antigravity): the antigravity adapter shares the identical gated
  skip but only runs from its install dir, so cover it through the install
  pipeline with a faked DB-owner probe (strict empty-stdout/stderr +
  debug-on). Promote the fake-probe helpers (createHookToolDir / hookEnv,
  plus a module-private writeExecutable) into shared hook-test-helpers so
  unit + e2e reuse them.

Fixes #1913

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

* fix(hooks): unify GITNEXUS_DEBUG gating in main() catch handlers

The main() catch-handler in all three hook copies still gated its crash
log on truthy `if (process.env.GITNEXUS_DEBUG)`, while the skip diagnostic
the #1913 fix added is gated on the strict `isDebugEnabled()` helper
(=== '1' || === 'true'). That split meant GITNEXUS_DEBUG=0 or =false
suppressed the skip line yet still enabled crash logging — two conflicting
contract signals in the same file.

Switch the three catch handlers to isDebugEnabled() so GITNEXUS_DEBUG has
one strict meaning everywhere: exactly '1' or 'true' enables all
diagnostics; everything else (incl. '0', 'false', empty, unset) is silent.

Add boundary tests asserting the MCP-owner skip stays silent with
GITNEXUS_DEBUG='0' and 'false' (CJS + Plugin), pinning the strict contract.

Refs #1913

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

* fix(hooks): gate antigravity stale-index hint stderr behind GITNEXUS_DEBUG

The antigravity AfterTool handler mirrored the stale-index hint to stderr
unconditionally on a normal (non-error) success path — the last ungated
stderr write of the class issue #1913 targets, and a divergence from the
claude hook, which never mirrors this hint to stderr.

Gate the stderr mirror behind isDebugEnabled(). The hint still reaches the
agent via additionalContext (stdout JSON) — parts.push(hint) stays
unconditional — so there is no functional loss; only the by-default
terminal mirror moves behind GITNEXUS_DEBUG=1. This knowingly changes the
#1730 terminal-mirror behavior in favor of strict-runner cleanliness and
parity with the claude adapter.

Split the e2e assertion into a default-silent test (hint in
additionalContext, absent from stderr) and a GITNEXUS_DEBUG=1 test (hint
mirrored to stderr).

Refs #1913

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

* docs(hooks): document GITNEXUS_DEBUG=1 for hook diagnostics

GITNEXUS_DEBUG was documented only in the cursor integration README, so
the diagnostic escape hatch for the Claude Code / Antigravity hooks was
undiscoverable. Operators hitting a silent hook skip (MCP server owns the
DB, fail-closed probe timeout, or an already-current index) had no
documented way to surface the reason.

Add a Troubleshooting subsection explaining that the hooks stay silent on
normal skip paths for strict runners, that GITNEXUS_DEBUG=1 surfaces the
reason on stderr, and that only '1'/'true' enable diagnostics (stdout JSON
the agent consumes is unaffected).

Refs #1913

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

* test(hooks): update setup-antigravity unit test for gated stale-index hint

U2 (7995e921) gated the antigravity stale-index hint stderr mirror behind
GITNEXUS_DEBUG, but a second test — setup-antigravity.test.ts's "AfterTool
emits stale-index hint" — also asserted the hint on stderr by default and
was missed (it lives outside the two files validated locally; the full CI
matrix caught it).

Update it to the U2 contract: assert the hint via additionalContext with
stderr silent by default, plus a GITNEXUS_DEBUG=1 run asserting the
terminal mirror reappears.

Refs #1913

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

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-10 09:09:41 +01:00
Gergő Magyar
4f9d595c73
fix(docker): ship runtime-needed published assets (hooks/, skills/) into the image (#2130) (#2132)
* fix(docker): copy hooks/ into Dockerfile.cli runtime stage (#2130)

`gitnexus analyze` inside the official image (akonlabs/gitnexus,
ghcr.io/abhigyanpatwari/gitnexus) crashed at startup with:

    Error: Cannot find module '../../hooks/claude/resolve-analyze-cmd.cjs'
    Require stack:
    - /app/gitnexus/dist/cli/resolve-invocation.js

`dist/cli/resolve-invocation.js` does
`createRequire(import.meta.url)('../../hooks/claude/resolve-analyze-cmd.cjs')`
at module load (it is the single source of truth for the npm-11 npx-crash
invocation decision, #1939), and `analyze.ts` statically imports it. The
Dockerfile.cli runtime stage copied dist/node_modules/package.json/the
duckdb script/vendor but never `hooks/`, so the require throws before the
command does any work. `hooks/` is in package.json `files`, so npm already
ships it — Docker was the only distribution dropping it.

Fix: copy `hooks/` into the runtime stage, mirroring what npm publishes.

Also add `test/unit/dockerfile-runtime-asset-parity.test.ts`: a regression
guard that derives every out-of-dist `require()`/`createRequire()` target
from source and asserts each is a runtime-stage `COPY`. Scoped to the
require family (not `fs.access`/`new URL`), so it locks the #2130 class
without false-flagging the intentionally-omitted, gracefully-degrading
`web/` and `skills/` assets.

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

* fix(docker): also ship skills/ into the runtime image

Follow-up to the hooks/ fix: `skills/` is another published runtime asset
(in package.json `files`) the Docker image dropped. The CLI reads the
bundled SKILL.md templates from `<pkg>/skills/` for `gitnexus analyze
--skills` (ai-context skill generation) and `gitnexus setup`/`uninstall`
(installing skills into editor configs). Unlike the hooks/ require(), these
reads degrade SILENTLY when the dir is absent — `--skills` writes minimal
placeholder content (ai-context.ts), `setup` installs zero skills
(setup.ts readdir → []) — so the image looked fine but produced wrong
output. Copy `skills/` so the image is fully usable for all CLI tooling.

`web/` (also in `files`) is intentionally NOT shipped: this image never
builds gitnexus-web (the builder doesn't copy it, build.js logs "skipping
web UI"), so it is API-only by design — the UI is the separate
Dockerfile.web image / hosted app. The duckdb script is the only runtime
asset needed from scripts/, so that stays a single-file copy.

Extends the runtime-asset-parity guard with an explicit skills/ assertion.

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

* fix(test): correct stale docstring that listed skills/ as not copied

The 2nd commit on this branch added a skills/ COPY + an it('copies skills/…')
assertion, but the top-of-file docstring still grouped skills/ with web/ as
'intentionally not copied / out of scope'. Drop skills/ from that sentence and
note it is shipped (and covered by its own test). web/ remains the sole
fs-accessed-but-uncopied example. Documentation-only; assertions unchanged.

* fix(test): make runtime-stage detection case-insensitive on AS

Docker accepts a lowercase `as runtime`; the parity guard's stage-detection
regex was case-sensitive on `AS`, so a future Dockerfile reformat would empty
the parsed COPY set and trip the named assertions. Add the /i flag.

* fix(test): stop runtime-stage COPY parsing at the next FROM

runtimeStageCopiedSources scanned from the runtime FROM to EOF. Bound the scan
to the runtime stage (start after its FROM, break on the next FROM) so a build
stage added after runtime can't have its COPY lines misattributed. No-op today
(runtime is the last stage); the copied set is unchanged.

* fix(test): assert at least one runtime COPY is parsed (no vacuous pass)

If the runtime FROM or the /app/gitnexus/ source prefix ever stops matching,
the copied set goes empty and the parity assertion passes vacuously. Add an
explicit copied.length>0 guard so that failure mode is loud and named.

* fix(test): strip line comments before require-scanning

requiredExternalAssets() regex-scanned raw source, so a future doc-comment such
as a commented-out require('../../web/x') in a shallow src file would resolve
outside dist/ and spuriously fail the parity guard. Strip // line comments
first. Block comments are deliberately not stripped (a naive block strip mangles
slash-star inside string/glob literals). Verified the real-tree scanner output
is byte-identical with and without the strip, and resolve-invocation.ts's
multi-line createRequire is still detected. (Also swaps a stray non-ASCII glyph
in the prior commit's comment for ASCII.)

* fix(test): account for aliased + computed module-load requires (fail-closed)

The parity scanner only matched string-literal require/createRequire, so it
missed module-load requires via aliased createRequire bindings and computed
paths — and already failed to see community-processor.ts's
`_require(leidenPath)` -> vendor/leiden, making the "every out-of-dist asset"
claim untrue.

Broaden the scan:
- Discover per-file createRequire bindings (requireCJS, _require, …) and match
  their literal-arg calls; keep the createRequire(...)('…') IIFE form.
- Detect COMPUTED (non-literal) requires and gate them on MODULE-LOAD position
  (brace-depth 0), so the four in-function computed requires that target
  node_modules/package.json (optional-grammars, native-check, capabilities,
  parse-cache) are correctly out of charter and ignored. A module-load computed
  require must be vetted in KNOWN_COMPUTED_REQUIRES (seed: community-processor ->
  vendor/leiden) or the test FAILS CLOSED for manual review.
- Allowlist entries are coverage-checked via isCovered, never trusted: a new
  test removes the `vendor` COPY from a fixture and asserts leiden surfaces as
  uncovered (so deleting a COPY can't silently pass — the #2130 class).
- Exclude `<id>.resolve(...)` (a path lookup, not a load).
- Upgrade the comment stripper to a string-aware pass that removes line AND
  block comments without mangling slash-star inside string/glob literals — the
  computed branch needs JSDoc requires (e.g. javascript/index.ts) gone, and the
  literal scan output stays byte-identical.

Honest claim wording: the 4th test now says coverage = resolvable + vetted
module-load requires, unrecognized computed requires fail for review. Adds
unit tests for fail-closed, aliased-literal, and in-function-ignored paths.

* fix(test): also scan shipped .cjs/.mjs assets for sibling requires

The guard only scanned src/**/*.ts, so hand-written shipped runtime files were
invisible — and they DO require siblings: hooks/claude/gitnexus-hook.cjs and
hooks/antigravity/gitnexus-antigravity-hook.cjs each require('./hook-lock.cjs'),
'./hook-db-lock-probe.cjs', './resolve-analyze-cmd.cjs'. Add a second pass over
shipped .cjs/.mjs assets (the runtime COPY set minus dep/data roots), resolving
each relative require against the asset's OWN package-relative dir and checking
COPY coverage — by prefix, NOT on-disk existence: the antigravity hook's
'./hook-lock.cjs' resolves to hooks/antigravity/hook-lock.cjs (which doesn't
physically exist; hook-lock.cjs lives under hooks/claude) yet is covered by the
whole-hooks COPY. All 6 shipped sibling requires resolve under the hooks COPY.

* fix(docker): move hooks/skills COPYs past the DuckDB FTS RUN

The hooks/ and skills/ COPYs sat between the vendor COPY and the DuckDB
FTS-extension install RUN, so any edit to hook/skill content invalidated that
RUN's cache layer — which performs a one-time network INSTALL of the extension
(~tens of seconds per affected build). The COPYs have no input dependency on the
DuckDB step; relocate them to after it (before USER node) so stable
infrastructure layers are not rebuilt on hook/skill churn. Image contents are
unchanged. The runtime-asset-parity guard still detects both (its scan covers
the whole runtime stage), and the two are consolidated under one comment.

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-10 08:38:37 +01:00
Gergő Magyar
9d61fd137b
Merge branch 'main' into feat/cfg-layer-m1 2026-06-10 08:15:36 +01:00
Gergő Magyar
e46651e42c
fix(embeddings): create VECTOR index via conn.query, not the prepared path (#2114)
`gitnexus analyze` silently failed to create the LadybugDB VECTOR/HNSW index because `CALL CREATE_VECTOR_INDEX(...)` was run through the prepared `conn.prepare()` path, which rejects multi-statement procedures — degrading semantic search to exact-scan. Route index creation through `conn.query()` via a new adapter-owned `createVectorIndex` (mirrors `createFTSIndex`), make the previously-swallowed error visible (`{ err }` logging), add an in-process idempotency cache, and add real-`@ladybugdb/core` regression coverage.

Fixes #2114.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-10 07:59:37 +01:00
Gergő Magyar
113b7ca899
Merge branch 'main' into feat/cfg-layer-m1 2026-06-10 06:34:16 +01:00
dependabot[bot]
43e6a3f688
chore(deps)(deps): bump js-yaml from 4.1.1 to 4.2.0 in /gitnexus (#2097)
Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 4.1.1 to 4.2.0.
- [Changelog](https://github.com/nodeca/js-yaml/blob/master/CHANGELOG.md)
- [Commits](https://github.com/nodeca/js-yaml/commits)

---
updated-dependencies:
- dependency-name: js-yaml
  dependency-version: 4.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-10 06:33:39 +01:00
dependabot[bot]
581943bbe5
chore(deps)(deps-dev): bump @types/node in /gitnexus (#2128)
Bumps [@types/node](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/node) from 25.9.1 to 25.9.2.
- [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases)
- [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/node)

---
updated-dependencies:
- dependency-name: "@types/node"
  dependency-version: 25.9.2
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2026-06-10 06:32:57 +01:00
Gergő Magyar
1cf65b339c
chore: release v1.6.7 (#2126)
Bump gitnexus 1.6.6 -> 1.6.7, add the 1.6.7 CHANGELOG section (14 PRs since v1.6.6), and sync the Claude plugin manifests (plugin.json + marketplace.json) to 1.6.7.
2026-06-09 21:37:33 +01:00
gitnexus-release-bot[bot]
d0452d26a1
chore(vendor): rebuild native prebuilds (tree-sitter-c,tree-sitter-dart,tree-sitter-proto,tree-sitter-kotlin,tree-sitter-swift) (#2125)
Built by https://github.com/abhigyanpatwari/GitNexus/actions/runs/27230510159

Co-authored-by: gitnexus-release-bot[bot] <gitnexus-release-bot[bot]@users.noreply.github.com>
2026-06-09 20:57:37 +01:00
Gergő Magyar
247ea431de
fix(ci): make the prebuild PR push re-run-safe (--force-with-lease -> --force) (#2123) 2026-06-09 20:28:08 +01:00
Gergő Magyar
4682a477d8
feat(mcp): paginate list_repos to avoid client token truncation (#2119) (#2120)
* feat(mcp): paginate list_repos to avoid client token truncation (#2119)

list_repos returned every indexed repository in one unpaginated array,
which large/LLM MCP clients truncate by token limit — so agents with
hundreds of indexed repos could not enumerate them all (the data
transmits fully; the consuming client drops it).

Add bounded limit/offset pagination to the list_repos tool:
- result changes from a bare array to
  { repositories, pagination: { total, limit, offset, returned,
  hasMore, nextOffset } }; default page 50, max 200 (shared constants)
- reject malformed limit/offset; clamp limit above the max
- deterministic order (lower-cased name, then path) over one registry
  snapshot per call, so paging never skips or duplicates an entry
- covers both stdio and remote /api/mcp (shared createMCPServer/callTool)

The internal listRepos() method (5 callers), GET /api/repos, and the
`gitnexus list` CLI are unchanged. The array->object tool-result shape
is a deliberate contract change, documented in CHANGELOG.

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

* fix(mcp): reject list_repos limit above the max instead of clamping (#2119)

parseListReposPagination silently clamped limit>max to the maximum while
throwing on every other out-of-bounds value (limit<1, offset<0, non-integer,
NaN). A client that advanced offset by its requested limit (rather than
pagination.nextOffset) then silently skipped repositories and saw
hasMore:false — defeating the "never skips" guarantee. Reject an over-max
limit too, so validation is symmetric and a caller never gets a smaller page
than it asked for without a clear error. Updates the schema/description, the
helper + ListReposPagination JSDoc, the guide note, and the two clamp tests.

Resolves the cross-engine-corroborated P2 (Codex + adversarial lane) and the
maintainability lane's clamp-vs-throw inconsistency from the PR #2120 review.

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

* refactor(mcp): name the list_repos return type and mark the parser @internal

Extract the inline listRepos() element shape into an exported RepoListing
interface and use it for both listRepos() and listReposPage().repositories,
replacing the opaque Awaited<ReturnType<LocalBackend['listRepos']>> expression
the maintainability review flagged. Tag parseListReposPagination @internal
(it is exported only for unit testing). Pure type/JSDoc change; no behavior.

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

* refactor(eval-server): type formatListReposResult to the paginated shape

Narrow formatListReposResult's parameter from `any` to
{ repositories: RepoListing[]; pagination?: ListReposPagination } and drop the
dead bare-array branch — after #2119 callTool('list_repos') always returns the
paginated object, so the Array.isArray shim was unreachable. Add a list_repos
continuation hint to the eval-server's getNextStepHint (parity with the MCP
server), and cover the previously-untested non-empty + hasMore:false formatter
branch. Migrates the two bare-array formatter tests to the object shape.

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

* test(mcp): harden list_repos pagination coverage

- Exercise the #2054 sibling-clone guarantee through the real callTool tool
  path (in the #2054 describe, which has temp-dir cleanup), proving siblings
  and remoteUrl survive listReposPage's sort+slice — not only listRepos().
- Assert total + limit on the middle-page test (a total miscalculation at a
  non-zero offset would otherwise slip past it).
- Cover the benign boundaries: negative-zero offset (accepted as page 0) and a
  MAX_SAFE_INTEGER offset (empty page).
- Replace the integration test's '\n\n---' split with a string-aware brace
  scan, so a repo path containing braces can never truncate the JSON parse.

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

* docs(skills): sync the list_repos pagination example to the guide mirrors

The .claude and gitnexus-claude-plugin guide mirrors only carried the one-line
table note; add the full "Paginating list_repos" section (shape + multi-page
traversal example + notes) so all three guide copies are byte-consistent with
the canonical gitnexus/skills/gitnexus-guide.md.

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

* chore: drop list_repos CHANGELOG entries from this PR

Restore gitnexus/CHANGELOG.md to match main so this PR contributes no
changelog change; the changelog is curated separately from feature PRs.

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

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 19:59:54 +01:00
Gergő Magyar
bd90d5bf90
fix(ci): green the tree-sitter prebuild matrix (npm-bundled prebuilds + arm64 runtime) (#2122)
First real dispatch of build-tree-sitter-prebuilds failed every job from two
independent root causes:

1. `c` (kind:'npm'): tree-sitter-c's npm tarball bundles prebuilds/ for all 6
   tuples, so the post-build `find ... -print -quit` picked a non-host tuple
   (win32-x64 on a linux runner) and the "built X, expected Y" assertion failed.
   Clear $pkgdir/prebuilds before prebuildify so only the freshly-built host
   tuple remains. (kotlin is npm too but ships no prebuilds, so it dodged this.)

2. every linux-arm64: validate installed tree-sitter@0.21.1 with
   --ignore-scripts, but that tarball ships no linux-arm64 prebuild, so
   require("tree-sitter") threw "No native build was found ... arch=arm64". The
   grammar's own arm64 .node loaded fine. Drop --ignore-scripts and add node-gyp
   + node-addon-api so the runtime source-builds where upstream ships no prebuild;
   prebuild-covered tuples still use the prebuild. The grammar-vs-runtime ABI
   check still fires at setLanguage.
2026-06-09 19:39:10 +01:00
Gergő Magyar
6ab3f64443
fix(ci): drop the broken -t 22 from prebuildify (build-tree-sitter-prebuilds) (#2121)
The native build step ran `prebuildify --napi --strip -t 22`, but prebuildify
parses the bare `-t 22` as the NUMBER 22 and crashes in resolveTargets
(`TypeError: v.indexOf is not a function`) — so every matrix job (c/dart/proto/
kotlin × 6 tuples) failed on its first real run. N-API prebuilds are
Node-version-agnostic, so `-t <node-version>` is both wrong and the cause; drop
it. Verified locally: `prebuildify --napi --strip` builds the vendored c source
cleanly into prebuilds/<tuple>/tree-sitter-c.node and exports
napi_register_module_v1.
2026-06-09 19:02:06 +01:00
Gergő Magyar
cef63dd044
feat(install): toolchain-free tree-sitter via vendored prebuilds (#2113)
* feat(install): toolchain-free tree-sitter via vendored GitNexus-built prebuilds

Eliminate the C/C++-toolchain requirement at install for the at-risk grammars
(dart, proto, kotlin) by generating + vendoring native prebuilds, mirroring the
existing vendored tree-sitter-swift. The 10 grammars that already ship 6 upstream
prebuilds stay npm dependencies (toolchain-free AND dependency-review-tracked).

- .github/workflows/build-tree-sitter-prebuilds.yml: a registry-parameterized
  workflow that builds {dart,proto,kotlin} x {linux,darwin,win32}-{x64,arm64}
  prebuilds natively, validates each loads + parses on its arch, and opens a PR
  vendoring them. A `guard` job gates the heavy matrix to run ONLY on dispatch
  or a real grammar-version change — ordinary code PRs cost zero matrix minutes.
- dart/proto: prefer a committed prebuild; fall back to today's source build
  when none matches (no behavior change until prebuilds are vendored).
- kotlin: vendor it (Swift parity) instead of compiling the third-party
  optionalDependency from source at the user's install — supersedes #2110's
  optionalDependency mechanism. The ~23 MB parser.c is NOT vendored (the
  workflow builds from the published package); only node-types + bindings +
  prebuilds are. Removed from optionalDependencies; lock regenerated; probe,
  parser-loader note, README/.devcontainer docs, and the #2110 tests updated.

DO NOT MERGE until vendor/tree-sitter-kotlin/prebuilds/ is populated by the
build-tree-sitter-prebuilds workflow: until then Kotlin is unavailable (vendored
with no source-build fallback). dart/proto remain fully functional throughout.

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

* test(install): guard 6/6 N-API prebuild coverage for every grammar

Regression guard so a toolchain-less install can never silently lose a tree-sitter
language on a supported platform-arch:

- Vendored grammars (vendor/tree-sitter-*): every one MUST ship a loadable N-API
  prebuild for all 6 tuples {linux,darwin,win32}-{x64,arm64}. Asserts the
  napi_register_module_v1 entry symbol in each .node (cross-platform, no need to
  run the binary). Currently RED for dart/proto/kotlin until the
  build-tree-sitter-prebuilds workflow populates their prebuilds/ — this is the
  must-fill-before-merge gate (swift already passes 6/6).
- npm-dependency grammars: asserts upstream ships 6/6 N-API too, catching a
  future platform drop. tree-sitter-c is allow-listed at 4/6 (missing
  linux-arm64/win32-arm64) pending #2116; the guard also fails if that gap is
  silently closed (prompting allow-list removal).

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

* feat(install): vendor tree-sitter-c at 0.21.4 with GitNexus-built prebuilds (#2116)

tree-sitter-c is the one grammar dependency upstream ships incomplete prebuilds
for (4/6 — no linux-arm64/win32-arm64), AND it is a REQUIRED grammar: its own
`install` (node-gyp-build) compiles from source when no prebuild matches and
exits non-zero, so on a toolchain-less ARM host `npm install gitnexus` HARD-FAILS
at the c step — during npm's dependency phase, before any GitNexus postinstall
runs (so a postinstall "supplement" can't help).

Fix: vendor c prebuild-only at the pinned 0.21.4 (Kotlin pattern), with all six
prebuilds GitNexus-cross-built, and drop it from `dependencies`:
- vendor/tree-sitter-c/ (bindings + node-types + manifest + prebuilds); build
  probe scripts/build-tree-sitter-c.cjs; added to the build workflow registry
  (kind 'npm' — built from c@0.21.4 source).
- materialize-vendor-grammars.cjs: c is REQUIRED, so it is always materialized,
  even under GITNEXUS_SKIP_OPTIONAL_GRAMMARS (it needs no toolchain).
- Removed from package.json dependencies + lockfile (nothing else needs npm c —
  tree-sitter-cpp's dep on c is dev-only and not installed). Preserves the #1242
  ABI pin: vendoring 0.21.4 keeps the good ABI while closing the ARM gap.
- parser-loader note + the prebuild-coverage guard + a cli-commands assertion
  updated; c moves from the npm-gap allow-list into the vendored 6/6 cohort.

Verified: tsc clean, 31 unit tests pass, c loads/parses; the guard is RED for
c/dart/proto/kotlin until the workflow populates prebuilds (the must-fill gate).
Closes the operational risk in #2116.

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

* fix(ci): source-build fallback for vendored c/kotlin so CI is healthy pre-prebuilds

The vendored prebuild-only grammars (c, kotlin) had empty prebuilds/ until the
build-tree-sitter-prebuilds workflow runs, so they could not load in CI — and
C is hard-required by cross-platform tests (tree-sitter-languages/parsing on
ubuntu+macos+windows), which I cannot pre-build for macos/windows locally. The
robust fix is a source-build fallback that works on every CI runner (all have a
toolchain), mirroring dart/proto:

- Vendor the grammar source (binding.gyp + src/) for c and kotlin; their build
  scripts now PREFER a committed prebuild (toolchain-free) and fall back to
  `node-gyp rebuild` from the vendored source when no prebuild matches. Verified
  both compile against the hoisted node-addon-api@^8 and the runtime loads.
- prebuild-coverage guard is now bootstrap-tolerant: a grammar that vendors its
  source (binding.gyp) may have an incomplete prebuild set (the workflow fills
  it); a prebuild-only grammar (swift) still must ship all six. Any present
  prebuild must still be N-API. Guard goes green; it re-tightens per-grammar as
  the workflow populates prebuilds.
- actionlint: silence a false-positive SC2016 (JS template literals inside the
  single-quoted `node -e` validate block).

Note: kotlin's generated parser.c is large (~23 MB on disk; compresses heavily
in git). Once the workflow populates all six kotlin prebuilds, the source serves
only as the fallback and could be slimmed if desired.

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

* fix(docker): re-materialize+rebuild vendored grammars after npm prune

`npm prune --omit=dev` in the gitnexus CLI image drops anything not in
package.json's dependency tree — including the VENDORED tree-sitter grammars
(materialized by postinstall, not declared deps) and their built bindings. The
`serve` image analyzes/parses repos at runtime, so re-run the grammar postinstall
after the prune (in the toolchain-equipped builder) to restore them. Load-bearing
for tree-sitter-c, a core REQUIRED grammar now vendored (#2116): as a former
dependency it survived prune; vendored, it would not. Also restores
swift/dart/proto/kotlin, which were silently pruned from the image before.

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

* feat(grammars): unify tree-sitter-swift with the vendored-source build pipeline

Swift was the last grammar handled differently — it shipped only upstream
prebuilds, while c/dart/proto/kotlin vendor their grammar source and use a
prefer-prebuild -> source-build-fallback activation script. Vendor swift's
source so all five are handled identically (one uniform build path).

- vendor/tree-sitter-swift: add binding.gyp (win-hardened), bindings/node/
  binding.cc, src/parser.c (ABI-14 default, ~18 MB), src/scanner.c, and
  src/tree_sitter/ headers. The 6/6 prebuilds are retained. The legacy
  parser_abi13.c alternate is intentionally not vendored.
- build-tree-sitter-swift.cjs: rewrite the prebuild probe into the dart-style
  prefer-prebuild then source-build fallback (keeps the GITNEXUS_SKIP gate and
  the never-exit-non-zero postinstall invariant).
- build-tree-sitter-prebuilds.yml: register swift (kind 'vendored'); add its
  package.json to the version-gated pull_request paths and a validate snippet.
- prebuild-coverage guard auto-moves swift into the source-fallback cohort
  (binding.gyp now present); refresh the stale "swift is prebuild-only" comments.
- tests: add build-tree-sitter-swift-probe.test.ts; fix the pre-existing
  build-tree-sitter-kotlin-probe.test.ts breakage (it still asserted the old
  probe strings after kotlin's dart-style conversion); assert swift's vendored
  source in cli-commands.test.ts.
- docs: README / .devcontainer / kotlin vendor README — swift's prebuilds are
  now GitNexus-cross-built from vendored source like the rest, not upstream-only.

Verified: swift source-builds against node-addon-api@8 -> N-API binary -> loads
against the pinned tree-sitter@0.21.1 (ABI 14) -> parses cleanly.

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

* feat(publish): gate a lean prebuilds-only npm tarball behind a coverage guard

Vendoring grammar source (parser.c) alongside the prebuilds means the npm
tarball now carries ~50 MB of generated source it almost never compiles (every
supported platform-arch has a prebuild). Prepare to drop it from the published
package once all prebuilds exist — safely.

- .npmignore: add a GATED, commented-out "lean publish" block that excludes the
  source-build inputs (parser.c/scanner.c/tree_sitter/binding.gyp/binding.cc) but
  keeps prebuilds/ + the runtime files. Uncommenting ships prebuilds-only.
- scripts/assert-publish-grammar-coverage.cjs: a prepack guard that refuses to
  pack/publish if the source exclusion is active while any vendored grammar still
  lacks 6/6 prebuilds (which would ship a grammar with no loadable binding). Wired
  into `prepack` (runs on npm pack + publish, incl. the publish.yml dry-run) and
  exposed as `npm run assert-publish-coverage`.
- test: pure-core decision cases + a real-repo publish-safety check that fails CI
  if .npmignore is activated prematurely.

Net: the prebuilds already publish today (files: ["vendor"]); this makes the
future switch to a prebuilds-only tarball a one-line uncomment that can't ship a
dead grammar. The guard currently reports "source + prebuilds" (only swift has
6/6 prebuilds so far) and passes.

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

* refactor(grammars): consolidate the 5 build-tree-sitter-*.cjs into one

The per-grammar activation scripts (c/dart/proto/swift/kotlin) were ~95%
identical — same prefer-prebuild → source-build → never-fail flow, differing only
in name, target_name, required-vs-optional, and the display label in warnings.

- scripts/build-tree-sitter-grammars.cjs: one registry-driven script. Bare call
  builds all (postinstall); `... <name>` builds only the named grammars (so the
  probe test can isolate one). c is `required: true` (ignores the opt-out gate);
  the rest honor GITNEXUS_SKIP_OPTIONAL_GRAMMARS. Per-grammar try/catch + a final
  process.exit(0) preserve the postinstall never-exit-non-zero invariant.
- package.json: postinstall is now `materialize && build-tree-sitter-grammars.cjs`
  (was five chained `build-tree-sitter-<name>.cjs` calls).
- tests: replace the two near-identical *-probe.test.ts files with one
  parameterized build-tree-sitter-grammars-probe.test.ts that also covers the
  required-vs-optional opt-out split and an unknown-grammar arg.
- update cli-commands.test.ts postinstall assertions + the vendor c/kotlin/swift
  README + swift provenance to reference the consolidated script.

Behavior is preserved (warnings normalized to one consistent format). Removes 5
scripts + 1 test file; adds 1 script + 1 test.

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

* fix(ingestion): lazy-load tree-sitter-c to prevent module-load crash

tree-sitter-c is now vendored prebuild-only (#2116) with 0/6 committed
prebuilds, so on a toolchain-less or `--ignore-scripts` install C has no native
binding. Three modules loaded it via a hard top-level `import C from
'tree-sitter-c'`, which throws ERR_MODULE_NOT_FOUND at module-load — crashing
`analyze` before parser-loader's optional/severity:error degradation can run.
This is the #2091/#2093 bug class (previously fixed for swift/dart/kotlin); C was
left static because it used to be an always-present npm dependency.

- languages/c/query.ts: load via the lazy guarded getLanguageGrammar(C), mirroring
  swift/query.ts; the main-thread isLanguageAvailable filter ensures the getters
  are reached only when C is present.
- workers/parse-worker.ts: guarded `_require('tree-sitter-c')` + conditional
  languageMap spread, like swift/dart/kotlin.
- group/extractors/include-extractor.ts: guarded `_require`; getLanguageForFile
  returns null for .c/.h when absent, so C include-extraction degrades to a no-op
  (C++ unaffected).
- extend the registry-import-closure regression test (#2091/#2093) to assert C
  also loads lazily at registry static-import time.

* fix(ci): repin attest-build-provenance to the real v2.4.0 SHA

The workflow pinned actions/attest-build-provenance@bd77c077… commented
`# v2.4.0`, but v2.4.0 is e8998f94… (verified via the GitHub API); bd77c077…
is an untagged mid-stream commit, so the SLSA-attestation step ran unvetted
action code and the comment misrepresented what runs. Repin to the real
v2.4.0 commit and drop the `# PLACEHOLDER-PIN` markers on both this line and
the setup-python pin (a26af69b… is already the correct v5.6.0 — only its
comment was stale). Update the header NOTE accordingly.

* fix(ci): skip the prebuild-PR aggregate when release App secrets are absent

The aggregate job mints a GitHub App token as its first step; with
RELEASE_APP_ID/RELEASE_APP_PRIVATE_KEY unset it hard-failed AFTER a full
(up-to-6-runner) native build. Since the `secrets` context isn't available in
a job-level `if:`, the guard job now computes a `release_app` boolean output
(a step can read secrets) and emits an actionable `::notice::`; aggregate
gates on it and skips cleanly, while the build job's artifacts still upload
(run with open_pr=false for artifacts-only).

* chore(ci): drop package-lock.json from the prebuild paths filter; widen build timeout

`gitnexus/package-lock.json` changes on nearly every dependency PR, so it
fired the prebuild workflow's guard job on unrelated churn (the matrix stayed
correctly skipped — `gitnexus/package.json` already covers the transition-window
pin, so removing the lock only drops guard noise). Also bump the native build
job timeout 30 -> 45 min for headroom compiling the 23 MB kotlin / 18 MB swift
parser.c, especially under arm emulation.

* fix(ci): event-gate the aggregate open-PR condition explicitly

`inputs.open_pr` is null on pull_request events, and the prior
`inputs.open_pr != false` leg relied on GHA's direction-ambiguous null
coercion (Codex F4) to decide whether to open the prebuild PR. Gate
explicitly on the event: a non-fork pull_request that bumped a grammar
version opens the prebuild PR (the documented flow), and `open_pr` is only
consulted on workflow_dispatch — so a manual run with open_pr=false stays
artifacts-only and no event's behavior rests on coercion.

* fix(publish): validate the effective npm-pack contents in the coverage guard

The publish guard inferred "is source shipped?" from a single .npmignore toggle
line, which a partial/out-of-order edit could defeat (exclude binding.gyp but
leave parser.c → unbuildable yet "source-shipping"). It now inspects the
EFFECTIVE tarball via `npm pack --dry-run --ignore-scripts --json` (the
--ignore-scripts avoids re-entering this guard through prepack): a grammar
"ships source" only when EVERY on-disk source-build input (binding.gyp +
binding.cc + parser.c + scanner.c when present + a tree_sitter header) is
actually in the packed file list.

This also surfaced that the gated lean-publish .npmignore block was inert:
package.json's `files: ["vendor"]` allow-list overrides .npmignore for the
vendored subtree, so those exclusion lines never dropped anything. Replace the
dead toggle with documentation of the real mechanism (narrow the `files` field)
and note the guard enforces safety on the effective pack regardless of how the
slim is done.

* test(prebuild): hard-gate declared-fully-prebuilt grammars on 6/6 coverage

The strict 6/6 prebuild assertion was dormant whenever a grammar vendors source
(binding.gyp) — which is every grammar — so a dropped prebuild passed CI
silently. Add a FULLY_PREBUILT allowlist of grammars GitNexus has committed 6/6
for (today: swift); those must keep all six even with a source fallback, so
losing one now fails CI. Grammars graduate into the set as the
build-tree-sitter-prebuilds workflow lands their binaries. (The static-import
degradation smoke is covered by the registry-import-closure regression test
extended in the C lazy-load commit.)

* chore(deps): promote node-gyp-build/node-addon-api to regular dependencies

Every vendored grammar's index.js does `require("node-gyp-build")` at runtime
to load even a prebuilt .node, so node-gyp-build is runtime-load-critical (and
node-addon-api is needed for the source-build fallback). They were
optionalDependencies, surviving `--omit=optional` only via the required
tree-sitter's transitive edge — correct today but fragile. Promote both to
regular dependencies so the contract is explicit (optionalDependencies is now
empty and removed). Lock the contract with a cli-commands assertion.

* chore(vendor): add Windows cflags parity block to tree-sitter-c/binding.gyp

c's binding.gyp used an unconditional `cflags_c: ["-std=c11"]`, while
kotlin/swift gate MSVC flags behind an `OS=='win'` condition (/std:c11 /utf-8).
Inert today (no non-ASCII bytes in c's parser.c, and node-gyp ignores cflags_c
on MSVC anyway), but align the three so a future source-build fallback on
Windows behaves consistently.

* docs(agents): correct stale optional-grammar / postinstall notes

AGENTS.md still said postinstall "patches tree-sitter-swift, builds
tree-sitter-proto" and that only kotlin/swift are "optional". Update to the
vendored-uniform model: postinstall materializes the vendored grammars and
prefers a committed prebuild (source-build only when none matches); c is
required while dart/proto/swift/kotlin are optional + skippable via
GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1, with non-fatal warnings only on a
toolchain-less host with no matching prebuild.

* fix(install): preserve the backup and warn loudly on a failed materialize rollback

If renameSync(partial, dest) failed AND the rollback renameSync(backup, dest)
also failed, the grammar was left unmaterialized (node_modules/<name> missing)
with only a generic "could not materialize" warning — the recoverable backup at
<dest>.materialize-bak was unmentioned. Emit a CRITICAL warning naming the
backup path and the recovery command on that double-failure, and document that
the fail-soft catch removes only the scratch `partial`, never the `backup`
(which may be the sole recoverable copy). Never-throw / exit-0 contract intact.

* fix(publish): make the coverage guard's npm-pack inspection script-safe

The prepack guard shelled out to `npm pack --dry-run --ignore-scripts --json`,
but the `--ignore-scripts` flag is not reliably honored by npm pack's
prepare/prepack lifecycle on the CI npm — so build.js ran, polluted the --json
stdout with `[build] …`, and the guard's JSON.parse threw. That broke every
`npm pack` (packaged-install-smoke on ubuntu+windows) and failed the guard's own
real-repo unit test (the only coverage-job failure). Force script-skipping via
the reliable `npm_config_ignore_scripts` env config (also removes the prepack
re-entry/recursion risk) and parse defensively from the JSON-array start.

* fix(publish): make the coverage guard deterministic — read `files`, not `npm pack`

The npm-pack-based guard timed out in CI: `npm pack`'s prepare/prepack lifecycle
is not skipped by `--ignore-scripts` (flag or env config) on the CI npm, so the
inner pack ran the full build (~20s+) — fine for the slow smoke job, but it blew
past vitest's 30s test timeout in the coverage job (and risked re-entering this
prepack guard).

Replace it with a deterministic, fast (~0.1s) check that needs no subprocess:
since `files: ["vendor"]` OVERRIDES `.npmignore` for the vendored subtree (so
`.npmignore` can never drop vendored source — verified), the ONLY lever that can
exclude source is narrowing the package.json `files` field. The guard now reads
`files` directly: a grammar "ships source" iff `files` includes the vendor
subtree AND the grammar carries a buildable source set on disk. A lean publish
that narrows `files` while a grammar lacks 6/6 prebuilds still fails the gate.

* feat(ci): vendored tree-sitter grammar update monitor

Adds a weekly (+ dispatchable) workflow that checks each vendored grammar against
its source-of-origin (npm for swift/kotlin, the GitHub default branch for
dart/proto; c is excluded — held at 0.21.4 for ABI safety) and opens a PR
re-vendoring any update that is ABI-COMPATIBLE with the pinned tree-sitter@0.21.1
(LANGUAGE_VERSION 13-14).

ABI awareness is the point: most upstreams have moved to ABI 15 (newer
tree-sitter), so a blind "bump to latest" would open PRs that can't build. The
monitor fetches the candidate source, reads its parser.c LANGUAGE_VERSION, and
only re-vendors 13/14 — incompatible updates are reported (notice + job summary),
never applied. (Confirmed live: dart/proto upstreams are ABI 15 today and are
correctly held; swift/kotlin are current.)

The re-vendor refreshes only the source-build inputs + runtime entrypoints,
preserving the GitNexus-hardened binding.gyp / README / prebuilds; the version
bump then triggers build-tree-sitter-prebuilds.yml, whose ABI-validation is the
final safety net so a subtly-wrong re-vendor can't silently ship. PR creation is
gated on the RELEASE_APP secret (skips with a notice if absent), mirroring the
build aggregate. Unit test locks the ABI gate; the script is import-safe.

* feat(ci): monitor tree-sitter-c too (report-only, ABI-pinned)

c was excluded from the update monitor, so an upstream c update went unnoticed.
Include it, but as report-only via a `hold`: c is ABI-pinned at 0.21.4
(#1242/#858) and must not auto-bump without a tree-sitter runtime upgrade, so an
available c update is detected + surfaced (notice + job summary) but never
auto-PR'd — even if it were ABI-13/14. `--apply c` refuses defensively. (Live:
upstream c is 0.24.1 / ABI 15 today, so c is doubly held — reported, not applied.)

* fix(ci): drop the shell in the grammar monitor's github fetch (CodeQL)

CodeQL flagged the GitHub-tarball fetch — it used `bash -c "gh api …/tarball/$ref
> src.tgz && tar xzf src.tgz"`, interpolating the API-derived ref into a shell
command (the shell-command-injection family: "this shell command depends on an
uncontrolled file name"). Replace it with a shell-free path: capture `gh api`'s
binary tarball as a Buffer via execFileSync, write it to a fixed file, and
extract with execFileSync('tar', …). No shell, no injection surface. Verified the
dart/proto fetch + ABI read still work.

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 18:16:24 +01:00
Nilotpal Kashyap
1716bf7c1e
feat(cli): add gitnexus uninstall to reverse setup (#2060) (#2062)
* feat(cli): add `gitnexus uninstall` to reverse setup (#2060)

`gitnexus uninstall` was documented in #168 but never implemented, so the
CLI rejected it with "error: unknown command 'uninstall'" (#2060).

Add an `uninstall` command that reverses `gitnexus setup` target-by-target:
removes the GitNexus MCP server entries (Cursor, Claude Code, Antigravity,
OpenCode, Codex), the installed skill directories, and the Claude Code /
Antigravity hook entries plus their bundled hook scripts. Edits are surgical
and idempotent — only gitnexus-owned keys/entries/dirs are touched, and JSONC
comments/indentation are preserved. Defaults to a dry-run preview; `--force`
applies. Per-repo indexes and the global npm package are left alone with
printed hints, since both are destructive in ways setup never caused.

Adds i18n entries (en + zh-CN), help wiring, README/CHANGELOG docs, and unit
tests covering MCP/hook/skill/Codex-TOML removal, dry-run, corrupt-file
safety, and the no-op case.

* changelog changes

* changelog changes

* fix(cli): harden uninstall against data-loss edge cases (review #2062)

Address review findings on the uninstall command:

- Empty derived skill name no longer wipes the whole skills dir: a bare
  '.md' source file would make basename() return '', resolving to the
  skills dir itself. Skip empty names in derivation and reject
  empty/'.'/'..'/separator names in removeSkillsFrom.
- Corrupt settings.json no longer orphans the hook: gate the hook-script
  dir removal on status !== 'corrupt' so we don't delete a script while a
  still-registered entry points at it (Claude + Antigravity blocks).
- Hook removal is now element-granular: delete only the gitnexus command
  inside an entry's hooks[], removing the whole entry only when it becomes
  empty. Preserves a user command co-located in the same entry.
- Fallback TOML stripper: also remove descendant sub-tables
  ([mcp_servers.gitnexus.env]), track multiline strings so a bracketed
  line inside a value isn't treated as a header, and stop reflowing
  unrelated blank lines.
- Set process.exitCode=1 on partial failure; add a 10s timeout to
  'codex mcp remove'.

Tests expanded 7 -> 17: empty-skill guard, corrupt-settings hook
preservation, shared-entry hook removal, OpenCode MCP keyPath,
Antigravity MCP + AfterTool hooks, codex-remove success path, TOML
sub-table + multiline-string cases, dry-run for hooks/skills, and the
directory-layout skill branch.

* refactor(cli): share setup/uninstall target map + harden TOML fallback (review #2062)

Maintainer review follow-ups:

- Extract editor target identities into editor-targets.ts (MCP paths/keyPaths,
  Codex TOML section, skill dirs, hook settings/events/needles/script dirs,
  shared detectIndentation). Both setup.ts and uninstall.ts consume it, so a
  target change updates both sides — killing the silent drift hazard.
- Add a setup -> uninstall round-trip integration test that iterates
  getEditorTargets(): setup writes every target, uninstall removes all of them,
  and a co-located user MCP server + user hook survive. Drift tripwire in both
  directions.
- Preview now prints the exact paths it would remove; command output + README
  state skills are matched by bundled gitnexus skill name. (Provenance marker
  deferred to a tracked follow-up.)

Hardening of the hand-rolled Codex TOML fallback (found in code review):
- Strip a section header that has a trailing inline comment (was matched as a
  header but failed the exact classify check -> section left behind while
  reported removed).
- Preserve CRLF line endings instead of rewriting the whole file to LF.
- Fix multiline-string scan: a line with an odd count of BOTH """ and '''
  no longer mis-picks the delimiter and desyncs the scanner (left->right scan).
- removeSkillsFrom guard also rejects absolute names.

Regression tests added for each. Full setup/uninstall suite green.

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-09 10:50:18 +01:00
Gergő Magyar
895c16f35b
Merge branch 'main' into feat/cfg-layer-m1 2026-06-09 09:04:12 +01:00
Gergő Magyar
f1151660b9
fix(install): graceful Kotlin optional-grammar install + accurate toolchain docs (#2110)
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* fix(install): document Kotlin optional-grammar toolchain behavior + graceful install probe

tree-sitter-kotlin is a third-party npm optionalDependency that ships
source-only (no upstream prebuilds) and compiles its native binding via
node-gyp at install. It was the only optional grammar without a GitNexus
install-time probe, and the README's GITNEXUS_SKIP_OPTIONAL_GRAMMARS
"no toolchain needed" note omitted Kotlin entirely. This adds a fail-soft
probe (mirroring the Swift one) that warns clearly and always exits 0 so
install never breaks, wires it into postinstall, and corrects the
optional-grammar docs in README.md and .devcontainer/README.md. Shipping
prebuilt .node binaries (the literal request) needs an upstream/CI build
matrix and is intentionally left as follow-up.

Refs #2107

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

* fix: address PR #2110 tri-review findings (Kotlin optional-grammar install)

Addresses the four P2 findings from the PR #2110 tri-review:

- F1: docs no longer imply GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 skips Kotlin's
  toolchain. npm compiles tree-sitter-kotlin via its own node-gyp-build step
  regardless of that variable; point to `npm install --omit=optional` as the
  real lever (README.md + .devcontainer/README.md).
- F2: the install probe now surfaces its "Kotlin unavailable" guidance on the
  dir-absent branch — the dominant toolchain-less case, where npm prunes the
  failed optional dependency so the package dir is gone at postinstall. Gated on
  npm_config_omit so a deliberate `--omit=optional` stays silent. Still never
  throws or exits non-zero.
- F3: add a behavioral test that executes the probe across its skip /
  dir-absent-warn / dir-absent-omit-silent paths and asserts exit code 0
  (guards the postinstall "never exit non-zero" invariant a static assertion
  cannot).
- F4: reframe prebuilt Kotlin as deferred Swift-parity follow-up — GitNexus
  already vendors its own self-built Swift prebuilds and could do the same for
  Kotlin — tracked in #2107, not an upstream-only blocker.

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

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 09:04:01 +01:00
Gergő Magyar
cf62aa7fa2
Merge branch 'main' into feat/cfg-layer-m1 2026-06-09 08:47:20 +01:00
Gergő Magyar
288b96f3e5
fix: batch query enrichment, bake FTS extension into CLI image, add FTS memory repro (#2108)
* perf(query): batch per-symbol process/cohesion/content lookups (N+1 -> 2-3)

Port of the local-backend query-batching from gitnexus-enterprise PR #222
into the OSS local MCP backend. The query tool traced each matched symbol
to its processes + cohesion (+ content) with up to 3N sequential pool
round-trips; batch them into 2-3 'WHERE n.id IN $nodeIds' queries keyed
back to each symbol by a prepended 'n.id AS nodeId' column. Output is
identical: the aggregation loop is unchanged, iterates merged in the same
order, and reads pre-fetched maps instead of issuing a query per symbol.

Adaptations over a blind cherry-pick (would otherwise change output):
- per-nodeId first-row community pick replaces the per-symbol LIMIT 1, so
  each symbol keeps its own community (not one for the whole batch);
- batched rows regrouped to the originating merged item by nodeId so the
  JS-side RRF item.score still drives process ranking;
- positional fallbacks shift +1 (process row[1..6], cohesion [1]/[2],
  content [1]); CodeRelation{type:...} relation form kept; IN-list chunked
  at 100 like the impact path.

Adds a regression test asserting per-node community/content association
(func:login keeps comm:auth; func:validate inherits no community).

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

* fix(docker): bake LadybugDB FTS extension into the CLI/serve image

The container runs `serve` under the default `load-only` extension policy
(the read pool pins {policy:'load-only'}), so a runtime LOAD EXTENSION fts
never INSTALLs. Dockerfile.cli copied the extension installer but never ran
it, so the runtime user's HOME had no FTS extension: keyword search
silently degraded (no FTS indexes written, ranking falls back to
vector-only with only a warning field). Same class of footgun fixed for
the Hub image in gitnexus-enterprise PR #222.

Run install-duckdb-extension.mjs as the `node` user with the runtime HOME
so INSTALL fts materializes the extension under $HOME/.lbdb/extension where
the runtime LOAD resolves it offline. Pin ENV HOME=/home/node because
Docker does not derive HOME from USER — without it the build-install and
runtime-load would resolve different paths. Verified locally: INSTALL lands
in $HOME/.lbdb/extension/0.17.0 and a fresh offline load-only
`LOAD EXTENSION fts` resolves it. Dockerfile.web is unaffected (static
frontend, no @ladybugdb backend).

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

* test(lbug): FTS evict->reload RSS repro + inert pool RSS tracing

Settles the gitnexus-enterprise PR #222 root-cause hypothesis for OSS:
does re-running LOAD EXTENSION fts on every pool evict->reload strand the
native FTS arena (unbounded RSS growth in long-lived MCP serve), or does
db.close() reclaim it (bounded by MAX_POOL_SIZE)? Static read could not
decide — the native lbugjs.node binary documents no close->extension-unload
contract.

Adds gitnexus/scripts/bench/fts-evict-reload-rss.mjs: a NATIVE mode that
reproduces the exact native sequence doInitLbug()+closeOne() perform
(open Database -> Connection -> LOAD EXTENSION fts -> QUERY_FTS_INDEX ->
close) across K self-built FTS fixtures, and a --via-pool mode that drives
the real compiled pool (initLbug/executeParameterized/closeLbug) against an
existing analyzed repo. Plus a behavior-neutral GITNEXUS_POOL_RSS_TRACE=1
stderr trace on pool init/close (stdout reserved for MCP JSON-RPC; single
env read when disabled).

RESULT (native, 24 and 40 cycles x 6 fixtures, --expose-gc): PLATEAU. RSS
warms up to ~400 MB then flattens (40-cycle: +36 MB over cycles 1-10, +3 MB
over 30-40; decelerating), not the linear climb a per-reload arena leak
would produce (240 reloads x stranded arena = multi-GB). db.close()
reclaims the FTS arena. The unbounded-leak hypothesis is NOT reproduced for
the OSS path: the pool's LRU eviction + close-on-evict BOUNDS the footprint,
which is exactly the protection the enterprise Hub supervisor lacked (it
opened bridge DBs in-process without eviction -> 15 GB). => plan U4
(worker/process isolation) is NOT justified by this evidence; U1 + U2 are
the only OSS-shared changes. Caveat: small fixtures + awaited close; a
--via-pool run against a large analyzed repo over a long session is the
production-faithful follow-up (instrumentation is in place for it).

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

* fix(review): apply ce-code-review autofix feedback (#222 migration)

Adversarial review found the U3 bench PLATEAU->no-leak conclusion was
over-claimed from a 600-row fixture: a size-proportional FTS-arena leak
would be sub-threshold at that scale. Strengthen the bench and make its
verdict honest:
- scale the fixture (--rows, UNWIND batch insert), probe ALL 5 FTS indexes
  in --via-pool (not 2 of 5), add a --no-await-close variant (the pool
  fire-and-forget close shape), and replace the absolute-delta gate with a
  SLOPE-DECELERATION 3-way verdict (PLATEAU / CLIMB / INCONCLUSIVE) plus
  step-discontinuity detection. At production-representative scale the
  synthetic runs are noisy/INCONCLUSIVE (deceleration argues against an
  UNBOUNDED leak but does not prove bounded), so plan U4 stays GATED on a
  --via-pool run against a real large analyzed repo -- not closed.
- Dockerfile.cli: source the scratch-DB size from ENV GITNEXUS_LBUG_MAX_DB_SIZE
  (single source of truth) and add a build-time verify-only LOAD gate
  that fails the build on a HOME/extension-dir mismatch instead of silently
  degrading runtime keyword search.
- install-duckdb-extension.mjs: additive verify-only mode (LOAD-only in a
  fresh process) + robust size parse; back-compatible with the runtime
  positional-size caller (validated).
- tests: wire func:validate into a second process (proc:beta-flow) so the
  batched STEP_IN_PROCESS row[1..6] positional shift is exercised by a
  genuine multi-process symbol, and assert process ranking. No blast radius
  (75 seed-consuming tests pass).
- pool-adapter.ts: trim the traceRss narrated-code comment (DoD 2.3).

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

* fix(bench): classify a sustained sub-floor RSS slope as INCONCLUSIVE, not PLATEAU

Tri-review P2: the FTS evict->reload verdict short-circuited to PLATEAU
whenever secondHalfSlope < SUSTAIN_FLOOR, BEFORE the deceleration check —
so a sustained (non-decelerating) linear leak below 0.5 MB/cycle was
labeled PLATEAU ("no leak"), the label that would wrongly close plan U4.

Extract median/slopeMbPerCycle/classifyVerdict into a pure, side-effect-free
fts-rss-verdict.mjs (zero imports) so it is unit-testable without loading the
native addon or running the bench, and fix the classifier:
- epsilon-first gate: a truly flat tail (< 0.1 MB/cycle) is PLATEAU regardless
  of decelRatio (guards against over-correcting a real negative into
  INCONCLUSIVE);
- a sustained sub-floor positive slope (>= epsilon, < floor, decelRatio >= 0.6)
  is INCONCLUSIVE — a slow creep RSS cannot distinguish from noise at this
  scale, so the honest label is "not resolved", never a clean PLATEAU;
- the noise floor now scales with the WORKING-SET growth (peak-baseline), not
  the pre-DB baseline RSS (which is interpreter/addon overhead, larger in
  --via-pool mode, and would inflate the floor and HIDE leaks).

Reconcile the stale "per-row-relative delta floor" docstring; add floor +
decelRatio to the MACHINE line. New fts-rss-verdict.test.ts pins all label
boundaries (flat->PLATEAU, sustained-sub-floor->INCONCLUSIVE,
decelerated->PLATEAU, sustained-linear->CLIMB, step->INCONCLUSIVE,
working-set floor, no import side effects). U1 does NOT add detection power
for sub-floor leaks (RSS cannot attribute that magnitude) — it stops the
false PLATEAU and routes that regime to the --via-pool run.

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

* fix(query): signal partial/warning on a real enrichment failure (not benign missing-table)

Tri-review P2: when a batched enrichment query (process/cohesion/content)
threw, it was caught + logged and the chunk's symbols silently fell back to
`definitions` with no signal — the caller could not tell "genuinely
standalone" from "enrichment failed".

Track an `enrichmentDegraded` flag in the three enrichment catch blocks and,
at response build, compose a single `warning` (FTS-missing and/or the
enrichment message, so neither overwrites the other) plus `partial: true`.
Both fields are omitted on the clean path, so the success-path response shape
is byte-identical.

Crucially, the flag fires ONLY for a REAL failure (timeout / lock / native
fault), NOT the benign "no Process/Community table" prepare error — a repo
analyzed without processes/communities is a normal config, and firing
`partial` on every such query would desensitize callers
(isBenignMissingTableError gates it).

New unit test test/unit/query-degraded-signal.test.ts (vi.mock pool-adapter,
override hybrid search to feed one matched symbol, route STEP_IN_PROCESS ->
throw): real failure -> warning+partial+symbol still returned; benign
missing-table -> no signal; FTS-missing + enrichment failure -> both messages
in one warning. Plus a success-path no-warning/no-partial assertion in the
calltool integration test.

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

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 08:46:46 +01:00
Gergő Magyar
7a45df0ab9
Merge branch 'main' into feat/cfg-layer-m1 2026-06-09 07:23:12 +01:00
Gergo Magyar
b51152c05d fix(ingestion): address tri-review + CFG-expert findings (#2081)
Corroborated findings from the tri-review (Codex + CE personas + GitNexus swarm
+ a CFG/program-analysis domain-expert lane). The OFF-path stays byte-identical;
all fixes are within the --pdg path or the benchmark.

- [Codex+CFG-expert] Exceptional `throw` edges now wire EVERY block in a try's
  protected region to the handler, not just the body ENTRY. A branched try body
  (`try { if (x) { use(t); } } catch`) previously left interior blocks with no
  path to `catch` — a taint false-negative into the handler for the M2 PDG pass.
- [Codex+CFG-expert] An unresolved labeled jump (a stacked outer label or a
  labeled non-loop block) now routes to the function EXIT instead of leaving a
  dangling sink — restores the single-exit invariant post-dominator/PDG
  computation needs.
- [Codex] computeChunkHash now folds pdgMaxFunctionLines/pdgMaxEdgesPerFunction
  into the chunk key (not just the pdg boolean), so a warm cache built under one
  cap is never served to a run with a different cap (#2038 class, extended to
  the budgets). Adds PdgCacheKey; boolean form kept for back-compat.
- [perf] visitTry resolves catch/finally in a single namedChild pass (the double
  `namedChildren.find` allocated two throwaway arrays).
- [adversarial] The bench `straight-line` scenario now runs at 2000->8000:
  output is a constant 4 blocks so disk/heap can't see the concat path, and at
  the old N a genuine O(n²) was masked by V8 cons-strings. Verified at the new N:
  the array-join impl ~1.0, a rope-optimized `+=` ~1.0 (correctly not flagged),
  a real O(n²) (re-join-every-append) ~3.8 — budget tightened 2.0->1.5.
- [adversarial+Codex] The bench `--check` now FAILS LOUDLY when run without
  `--expose-gc` instead of silently skipping the retained-heap gate.
- Doc: re-labeled the finally-bypass as a SOUNDNESS (false-negative) limitation
  tracked for M2, not mere "precision."

3 new regression tests (branched-try interior→handler, stacked-label→EXIT,
cap-fold key). 99 CFG tests pass; build clean; bench gate green.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 06:11:26 +00:00
azizur100389
3a4247ec36
feat(cpp): resolve inheritance-lattice member lookup (#2077)
* feat(cpp): resolve inheritance-lattice member lookup

* fix(cpp): harden inheritance-lattice lookup

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-09 06:53:11 +01:00
Gergo Magyar
ebfb62c1a9 perf(ingestion): add memory + disk growth gates to the CFG benchmark (#2081)
Extend bench/cfg/measure.mjs beyond wall-time to the two other scalability
dimensions that matter at kernel scale:

- DISK growth: utf8 byte size of the serialized cfgSideChannel — exactly what a
  --pdg run writes onto every ParsedFile shard (durable store + parse cache).
- MEMORY growth: retained JS heap of the cfgSideChannel payload, measured by the
  release-delta method (heap held minus heap after dropping it) — robust to
  pre-existing garbage and dead-stable run-to-run. Needs `node --expose-gc`;
  without it the heap metric is null and its gate is skipped (local runs still
  work). ci-tests.yml now passes --expose-gc so the heap gate runs in CI.

Both gated on linear scaling in baselines.json (disk_bytes_budget / heap_budget
1.2-1.3). Measured: disk ~1.0-1.04, retained heap ~0.87-1.0 — both linear
(~1KB/function each; ~2MB heap / 1.6MB disk at 2000 functions, --pdg only).
Bumped REPS 7->15 to stabilize the noisier time signal and widened the coarse
time tripwire budgets (the disk/heap gates carry the tight regression detection).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 05:28:17 +00:00
Gergő Magyar
e6f04fae7b
Merge branch 'main' into feat/cfg-layer-m1 2026-06-09 06:14:01 +01:00
dependabot[bot]
774cd4d568
chore(deps)(deps): bump @ladybugdb/core in /gitnexus (#2098) 2026-06-09 05:59:57 +01:00
Gergo Magyar
f427a6dff8 perf(ingestion): benchmark CFG construction + O(n) block-text accumulation (#2081)
Closes the M1 review's requires_verification perf gap ("no benchmark for
collectFunctionCfgs; a wall-time + cfgSideChannel byte-size regression gate
would catch the extendBlock concatenation before kernel scale").

- bench/cfg/measure.mjs (new): build-free tsx harness timing collectFunctionCfgs
  (parse once, reuse the tree) across three scaling scenarios — straight-line
  (extendBlock path), many-functions (collect walk), branchy (block/edge growth)
  — at 500→2000. Reports a wall-time scaling ratio AND a cfgSideChannel
  byte-size ratio, plus an order-independent sha256 over the emitted blocks/edges
  as the behavior gate. `--check` compares both ratios + the fingerprint against
  bench/cfg/baselines.json; mirrors the scope-capture / python-scope harnesses.
- .github/workflows/ci-tests.yml: run the gate on every test job (build-free,
  alongside the existing scope-capture guards) so an O(n^2) re-regression fails CI.
- cfg-builder.ts: structural fix for the one real hotspot the bench surfaced —
  accumulate basic-block text as fragments joined once in finish(), instead of
  concatenating onto a growing string per coalesced statement (O(n^2) → O(n)).
  Behavior-identical (the CFG fingerprint + the AC1 snapshot are unchanged).

Measured (post-fix): time ratios straight-line ~1.3, many-functions ~1.0,
branchy ~1.1 (all sub-quadratic; a true O(n^2) would be ~4.0). cfgSideChannel
bytes scale linearly (~1.0-1.04). 60 CFG tests green; build clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-09 04:19:06 +00:00
Gergő Magyar
4de4d205dd
fix(ingestion): lazy-load optional grammars so analyze never crashes when one is missing (#2091, #2093) (#2101) 2026-06-09 04:58:01 +01:00
Gergo Magyar
e3d4cb6a87 fix(review): apply ce-code-review autofix feedback (#2081)
Review (10 reviewers) confirmed OFF-path byte-identity (adversarial + golden)
and found defects all within the --pdg path. Fixes:

- P1 same-line BasicBlock id collision: add a start-column disambiguator to
  FunctionCfg + the id (`BasicBlock:<file>:<line>:<col>:<idx>`) so two functions
  sharing a start line no longer collide under first-writer-wins addNode.
- P1 worker crash-cascade: per-file try/catch around collectFunctionCfgs so a
  CFG-build throw cannot escape to the language-group catch and silently drop
  every remaining file in the group.
- P2 edge-cap drop now logs unconditionally (input.onWarn is validator-gated/
  silent in prod) — upholds the no-silent-truncation guarantee.
- P2 Array.isArray guard before the cfgSideChannel cast in run.ts.
- P2 maxFunctionLines default: worker applies DEFAULT_PDG_MAX_FUNCTION_LINES=2000
  when unset; caps forwarded through run-analyze AnalyzeOptions (closes the
  server-path drop).
- P3 README duplicate paragraph removed; `0`-vs-default docstrings corrected;
  CLI --pdg flag made language-neutral; reachableBlocks JSDoc corrected.
- Documented the break-through-finally + stacked-label CFG limitations.
- Tests: same-line id-collision regression, standalone throw→EXIT, dead-code-
  after-return, async/generator/method coverage, strengthened labeled-continue.

Refuted: the HTTP-500 getNodeQuery finding — M0 already shipped the BasicBlock
branch + name-floor (R12/web-safety handled).

CFG + analyze-config suites: 95 tests green; golden parity (AC4) byte-identical.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 20:18:02 +00:00
Gergo Magyar
c57bbb05a0 test(ingestion): drop unused helper in cfg-snapshot test (#2081)
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:55:05 +00:00
Gergo Magyar
d19b4ca639 test(ingestion): U7 — CFG acceptance fixtures, parity, end-to-end + docs (#2081)
Acceptance criteria for the M1 CFG layer:
- AC1: a 10-function TS fixture's CFG node/edge set matches a committed snapshot
  (cfg-snapshot.test.ts).
- AC2: every BasicBlock is reachable from its function ENTRY (property test over
  the emitted graph; the fixture has no dead code).
- AC3: hazard fixtures lock the classic-bug coverage — try/throw/finally
  post-domination + labeled break/continue resolution.
- AC4: the existing pipeline-graph-golden test stays byte-identical with --pdg
  off (verified; no UPDATE_GOLDEN), proving the opt-in adds zero default-run
  drift.
- End-to-end (pipeline-pdg.test.ts): runPipelineFromRepo({ pdg: true }) on a
  tiny repo emits BasicBlock nodes + CFG edges with both endpoints present —
  the true both-sinks proof (worker builds → store → scope-resolution emits);
  the default run emits zero.

Docs: CHANGELOG M1 entry, ARCHITECTURE "Optional CFG/PDG emission" subsection
(why emit is in-phase, not post-mro), README CFG language-support note.

Full CFG suite (U1–U7): 56 tests green.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:53:53 +00:00
Gergo Magyar
416bbcbbae feat(cli): U5 — --pdg opt-in plumbing (CLI + .gitnexusrc → both sinks) (#2081)
Expose the CFG/PDG substrate as an opt-in and thread it from CLI/.gitnexusrc to
the single source of truth (PipelineOptions.pdg), which fans out to BOTH sinks
already wired in U3/U4: the worker build gate (workerData.pdg) and the
scope-resolution emit gate. Off by default (R7).

- cli/index.ts: `--pdg` commander flag.
- cli/analyze.ts: AnalyzeOptions.pdg + pass `pdg` into runFullAnalysis options.
- cli/analyze-config.ts: KEY_SPECS `pdg` (boolean) so `.gitnexusrc { "pdg": true }`
  normalizes and a non-boolean value fails closed with GitNexusRcError.
- core/run-analyze.ts: AnalyzeOptions.pdg → runPipelineFromRepo({ pdg }).

(The internal PipelineOptions/WorkerPoolOptions/workerData fields + the
parse-cache key fold landed in U3/U4; this unit adds the user-facing surface.
The budget knobs stay at internal defaults for M1.)

Tests: analyze-config pdg normalization + non-boolean rejection; opt-in.test.ts
covers the CLI/file merge precedence and that pdg perturbs the chunk-dispatch
key. The full worker-build + main-emit round-trip is the U7 integration test.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:43:10 +00:00
Gergo Magyar
d8b14cfa7f feat(ingestion): U4 — emit BasicBlock + CFG within scope-resolution (#2081)
Emit persisted BasicBlock nodes + CFG edges from each ParsedFile's worker-built
cfgSideChannel, INSIDE scope-resolution's Phase-4 graph emission — the last
point where the worker-built CFGs are loaded (emitParsedFiles carries the
channel; the disk store is cleared right after the orchestrator returns). This
is the architecture the doc-review corrected to: a standalone post-`mro` phase
(the issue's literal subtask) provably reads empty data (KTD1).

- cfg/emit.ts (new): pure emitFileCfgs(graph, cfgs, maxEdgesPerFunction, onWarn).
  BasicBlock id = `BasicBlock:<filePath>:<functionStartLine>:<blockIndex>`
  (KTD3 — funcStart disambiguates blocks across functions in one file; no
  `name` column). CFG edge = CodeRelation type 'CFG' with the edge KIND
  (seq/cond-true/…) in `reason` (kinds can't be their own edge type). Per-
  function edge cap stops at the cap and warns with the dropped count — no
  silent truncation (R6/KTD6).
- run.ts: pdg-gated emit pass over emitParsedFiles after emitPostResolutionEdges
  (store still live); RunScopeResolutionInput gains pdg + pdgMaxEdgesPerFunction.
- phase.ts: thread ctx.options.pdg / pdgMaxEdgesPerFunction into the call.
- pipeline.ts: PipelineOptions.pdgMaxEdgesPerFunction.

6 tests: node/edge shape (KTD3 id, no name, type='CFG', kind in reason),
cross-function id uniqueness, AC2 reachability-from-ENTRY property, the edge
cap's no-silent-truncation contract, and empty-input no-op. Flag-off
byte-identity + full runPipelineFromRepo round-trip land in U7. Build clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:37:48 +00:00
Gergo Magyar
15bb02abbc feat(ingestion): U3 — worker CFG build + cfgSideChannel + cache coherence (#2081)
Run the CFG visitor in the parse worker (where the AST lives), serialize the
per-function CFG onto a new ParsedFile.cfgSideChannel, and keep it coherent
across the disk-backed store and the warm/durable parse cache (R3, R4).

- gitnexus-shared parsed-file.ts: add `cfgSideChannel?: unknown` as a DISTINCT
  field from captureSideChannel (different producer/consumer/lifecycle; plain
  JSON data — blocks/edges deliberately lack the `nodeId` the store's interning
  reviver keys on, so no mis-interning).
- cfg/types.ts + visitors/typescript.ts: add CfgVisitor.isFunction so the worker
  enumerates functions (and applies the line budget) by a cheap node-type test.
- cfg/collect.ts (new): collectFunctionCfgs walks the tree, builds one CFG per
  function (nested included), applies maxFunctionLines (over-cap = skipped).
- language-provider.ts: add `cfgVisitor?: CfgVisitor<SyntaxNode>` hook;
  typescript.ts attaches it to both the TS and JS providers (shared grammar).
- parse-worker.ts: read pdg + pdgMaxFunctionLines from workerData (read once at
  init — the worker never sees PipelineOptions), gate the build, attach
  cfgSideChannel alongside captureSideChannel.
- parse-cache.ts: bump SCHEMA_BUMP 4→5 (ParsedFile shape changed) and fold the
  pdg flag into computeChunkHash so a pdg-off cached chunk is NOT reused on a
  --pdg run (the #2038-class warm-cache trap). Default path keeps its keys.
- worker-pool.ts + parse-impl.ts + pipeline.ts: thread pdg/pdgMaxFunctionLines
  PipelineOptions → WorkerPoolOptions → workerData, and into the chunk-hash key.

9 boundary tests: collect contract, JSON round-trip identity (no AST leakage),
the pdg cache-key guard, the line-cap skip, and the no-visitor gate. Full CFG
suite (U1+U2+U3) green; build clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:26:58 +00:00
Gergo Magyar
d33c69f799 feat(ingestion): U2 — TS/JS CFG visitor over tree-sitter AST (#2081)
Add the TS/JS CfgVisitor that walks a function's tree-sitter AST and drives
the U1 CfgBuilder to produce a serializable FunctionCfg. One visitor covers
both languages (shared grammar family).

Handles the classic CFG hazards explicitly (R2, R10):
- loops allocate a dedicated loop-exit block so `break` has a concrete target
  before the loop's successor is known; `continue`/back-edge close the loop
  (while, do-while, C-for with init-once + increment-as-continue-target,
  for-in, for-of)
- switch fallthrough falls out naturally: a non-breaking case yields exits we
  wire to the next case as `fallthrough`; a breaking case wires to the switch
  exit via ControlFlowContext
- try/catch/finally: normal completion AND exceptional flow both route through
  finally (post-domination); a conservative exceptional edge models that the
  protected region may raise to its handler (not just explicit `throw`)
- labeled break/continue resolve against the labeled loop's frame
- early return/throw wire to EXIT/handler and terminate their block

19 hazard tests (one per construct) + AC1 10-function fixture; all green.
No change to the committed U1 core or ControlFlowContext.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 19:16:48 +00:00
Gergo Magyar
6e0c1e1e7f feat(cfg): language-agnostic CFG construction core (#2081)
U1 of M1 (CFG layer). Plain JSON-serializable CFG data model (BasicBlockData/
CfgEdgeData/FunctionCfg — must survive the worker→main boundary + ParsedFile
store), a CfgBuilder accumulator (leaders→blocks→edges, synthetic ENTRY/EXIT,
idempotent edges), a ControlFlowContext (break/continue/switch + labeled-jump
target stacks), and a TraversalResult ({entry, dangling exits}). AST-agnostic
and unit-tested on the classic control-flow topologies (if/else, while back-edge,
mid-block return, labeled break/continue) the S2 spike validated; reachability
helper backs the R9 property test.
2026-06-08 18:36:40 +00:00
Gergő Magyar
f2c9e69792
feat(ingestion): M0 — taint/PDG substrate (schema + seams + spikes) (#2080) (#2092) 2026-06-08 18:56:10 +01:00
Copilot
689e6ef1f8
chore: Sync Claude plugin manifests with the 1.6.6 release (#2090)
* Initial plan

* fix: sync Claude plugin manifest versions

* test: fold manifest sync check into existing node suite

* chore(autofix): apply prettier + eslint fixes via /autofix command

* test: run manifest sync guard in always-on suite

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2026-06-08 16:50:09 +01:00
Gergő Magyar
2cf7e7fa88
chore: release v1.6.6 (#2075)
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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>
2026-06-08 09:44:28 +01:00
xianzuyang9-blip
1ca4f15267
fix: declare onnxruntime-common runtime dependency (#2074)
* Declare onnxruntime-common runtime dependency

* Declare onnxruntime-common runtime dependency

* Declare onnxruntime-common runtime dependency

* Declare onnxruntime-common runtime dependency

* Declare onnxruntime-common runtime dependency

* Remove package metadata unit test

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-08 08:44:05 +01:00
Gergő Magyar
df5ce1f49b
fix(ingestion): close remaining open language parsing-layer coverage gaps (#1919) (#2072)
* fix(c): skip computed #include MACRO instead of emitting a garbage import source (F5)

* fix(cpp): emit a Variable per name for structured-binding declarations (F9)

* fix(dart): extract static const/final class fields (F26)

* fix(dart): capture old-style function typedefs (F28)

* fix(dart): read real top-level variable shape instead of a dead type field (F29)

* fix(kotlin): capture callable references (F47)

* fix(kotlin): anchor infix-call capture to the operator only (F49)

* fix(kotlin): extract secondary constructors as members (F48)

* fix(kotlin): capture destructuring declarations (F51)

* fix(kotlin): index companion-object properties as fields (F52)

* test(kotlin): assert callable-reference coverage runs on the worker path (F47)

* fix(swift): extract protocol property requirements (F75)

* fix(swift): recognize enum_class_body as a method body node (F79)

* test(ingestion): rebaseline swift captures-golden + scope-capture fingerprints (#1919)

* fix(kotlin): attribute secondary-constructor body calls to the Constructor node (#1919 review CF1)

A Kotlin secondary constructor's body executes statements like a method body,
but the registry-primary scope-resolution path had no Function scope or
Constructor def for it. A call inside the body resolved its caller anchor up to
the enclosing Class scope, mis-attributing the CALLS edge to the class rather
than the Constructor.

Add `(secondary_constructor) @scope.function` to the Kotlin scope query so the
body becomes its own scope, and synthesize a `@declaration.constructor` (named
`constructor`, qualified `<Class>.constructor`, with parameter metadata) so the
scope owns a Constructor def that bridges to the structure-phase Constructor node.

Also add an arity-disambiguating lookup key for overloadable callables: two
same-name secondary constructors of different arity (e.g. a zero-arg vs a 2-arg)
share the qualified key whose first-write-wins assignment is source-order-
dependent — so a zero-arg overload could resolve to a sibling. The structure
node id encodes `#<arity>`; mirror that in the bridge keyspace and match by the
def's parameterCount. Same-arity overloads collapse onto one arity key exactly
as before, so no regression there.

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

* fix(kotlin): do not own function-local property bindings under the enclosing class (#1919 review CF3)

Kotlin emits destructuring / loop bindings (`val (a,b) = pair`,
`for ((k,v) in m)`) as `@definition.property` to dodge the block-scope
local-symbol pruner. When such a binding sits inside a method body of a class,
the structure-phase owner walk found the enclosing class and emitted a spurious
HAS_PROPERTY edge (e.g. `C -> k`), treating a function-local as a class member.

Guard the Property owner resolution: if a function-like ancestor is reached
before any class container, the property is function-local and gets no owner
edge (it falls back to a File DEFINES edge). Language-agnostic — genuine class
fields sit directly in the class body with no intervening function, so they
keep their HAS_PROPERTY owner edge.

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

* test(kotlin): guard non-companion property isStatic=false (#1919 review CF4)

Add a field-extraction case for a plain non-companion class
`class C { val x: Int = 1 }` asserting the property `x` has isStatic=false,
guarding the `isInsideKotlinCompanion` walk against false-positives.

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

* refactor(kotlin): dedup type_identifier lookup in extractOwnerName (#1919 review CF5)

The `node.namedChildren.find(c => c.type === 'type_identifier')?.text` lookup was
duplicated across the companion and non-companion branches of the Kotlin
field-extractor's extractOwnerName. Hoist it into a single local, preserving the
existing behavior (anonymous companion falls back to "Companion"; other nodes
prefer the `name` field, else the type_identifier text, else undefined).

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

* fix(dart): capture generic old-style function typedefs (#1919 review CF2)

* test(dart): guard multi-name field count and top-level-var labels (#1919 review CF4)

* docs(swift): correct isStatic comment re multi-modifier hasKeyword (#1919 review CF5)

* test(ingestion): rebaseline dart+kotlin scope-capture fingerprints after review remediation (#1919)

* fix(ingestion): correct CF3 owner-strip boundary set for accessor/init bodies and Dart signatures (#1919 review)

The CF3 property-ownership guard used FUNCTION_NODE_TYPES, which (a) includes
Dart bare signatures (function_signature/method_signature) — over-stripping
every Dart class getter/setter's HAS_PROPERTY owner — and (b) omits Kotlin
anonymous_initializer/getter/setter and Swift computed accessors — under-
stripping destructuring/locals inside init{} and accessor bodies, emitting
spurious Class->local HAS_PROPERTY edges. Introduces a guard-specific
LOCAL_SCOPE_BODY_NODE_TYPES set (signatures excluded, accessor/init bodies
included). Adds Dart accessor-ownership + Kotlin init/accessor destructuring
regression fixtures. Both confirmed on the worker pipeline; no cross-language
regression (1597 cross-language tests green).

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-08 08:09:43 +01:00
Gergő Magyar
3963c497dd
fix(parse): correct worker-pool docs drift + surface worker-side stack on crash (#2068) (#2070) 2026-06-08 07:20:12 +01:00
Gergő Magyar
4fc2ffa5d0
refactor(ingestion): delete shadow-mode parity harness (RING4-3, #944) (#2071)
Ring 4 retires the legacy call-resolution DAG. With the legacy resolver
gone (RING4-1 #942, RING4-2 #943), shadow mode has nothing to dual-run
against, so the remaining shadow-mode artifacts are dead code.

- Delete gitnexus-shared/src/scope-resolution/shadow/{diff,aggregate}.ts
  (pure parity comparison logic) and its gitnexus-shared barrel exports.
- Delete the static parity dashboard (gitnexus/shadow-parity-dashboard/),
  which also removes the last GITNEXUS_SHADOW_MODE reference in the repo.
- Delete the shadow-mode unit tests (gitnexus/test/unit/shadow/).
- Scrub stale doc comments referencing the shadow harness / parity
  dashboard / removed legacy run (csharp/php/python/typescript index.ts,
  evidence.ts, module-scope-index.ts).

Already removed by RING4-1/-2 (verified): the shadow harness source and
GITNEXUS_SHADOW_MODE env handling; no CI job published dashboard artifacts.

Historical parity records preserved per acceptance: the CHANGELOG entry
(#918, #923, #951, #972) and the ci.yml RING4-1 note remain. Last
documented parity state is that historical coverage — no live
.gitnexus/shadow-parity/ run data exists in-tree (runtime output only).

Closes #944.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-07 20:06:42 +01:00
Abhigyan Patwari
f0c292f9e7
perf(ingestion): prune inert local value symbols (#2065) 2026-06-07 14:47:51 +01:00
Gergő Magyar
2dc0cc6398
fix(mcp): prevent sibling-clone repo ID collisions and correct generated MCP tool names (#2067) 2026-06-07 10:57:15 +01:00
dependabot[bot]
2b4d6e742b
chore(deps)(deps): bump @ladybugdb/core in /gitnexus (#2056)
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Bumps [@ladybugdb/core](https://github.com/LadybugDB/ladybug) from 0.16.1 to 0.17.0.
- [Release notes](https://github.com/LadybugDB/ladybug/releases)
- [Commits](https://github.com/LadybugDB/ladybug/compare/v0.16.1...v0.17.0)

---
updated-dependencies:
- dependency-name: "@ladybugdb/core"
  dependency-version: 0.17.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-07 06:31:45 +01:00
Sparsh
baca749e0b
fix(vue): F89 JSDoc fix, F90 dual-script merge, F92 lang plumbing (#1936) (#2050)
* fix(vue): F89 JSDoc fix, F90 dual-script merge, F92 lang plumbing (#1936)

* fix(vue): reviewer fixes — P1 lang routing, P2 lineOffset, P2/P3 pipeline tests

* fix(vue): add jsx to lang routing condition

* fix(vue): update F90/F92 fixtures and test assertions for CI

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-06-07 06:02:30 +01:00
azizur100389
9a40af3d79
fix(java): dedupe inherited RequestMapping prefixes (#2057) 2026-06-07 05:28:10 +01:00
Gergő Magyar
95f87fc12a
perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038)
* fix(ingestion): reduce parse-phase memory for huge repos (#1983)

Stop retaining full parse-cache chunks in RAM alongside the merged graph,
slim on-disk shards, defer worker ParsedFile emission for scope-resolver
languages, and add GITNEXUS_DEBUG_HEAP probes for OOM diagnosis.

Co-authored-by: Cursor <cursoragent@cursor.com>

* fix(ingestion): address #2038 tri-review findings (parse-phase memory)

Resolves the confirmed review findings on PR #2038:

- P1: thread exportedTypeMap through the sequential parse path
  (processParsingSequential) so a no-worker run over a partially-warm
  cache no longer silently drops the sequential-miss files' exported
  types. Cache hits made exportedTypeMap.size > 0, suppressing the
  end-of-loop buildExportedTypeMapFromGraph rebuild, but the sequential
  path never populated the map. Regression test added (fails on the
  pre-fix tree, passes after) plus a fully-sequential differential oracle.
- P2: saveParseCache builds its on-disk index from hashes actually
  written/copied (writtenKeys), never a usedKeys hash whose shard write
  or copy was skipped — no more phantom index entries.
- P2: add a unit test asserting SCOPE_RESOLUTION_LANGUAGES stays in sync
  with SCOPE_RESOLVERS (asymmetric drift would lose a language's ParsedFile).
- Backfill cache coverage: loadParseCacheChunk missing/corrupt -> undefined,
  pruneCache onDiskKeys branch, slim preserves nodes, saveParseCache
  copy-evicted-shard round-trip.
- Cleanups: single-source heap-probe gating via isDebugHeapEnabled();
  hoist the per-chunk mkdir in persistParseCacheChunk behind a
  process-scoped Set; gate COBOL's unused worker-side ParsedFile
  extraction (graph nodes still come from cobolPhase) while keeping
  fileCount/progress unconditional.

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

* refactor(ingestion): remove dead worker-side ParsedFile extraction

After #2038 gated worker `ParsedFile` emission behind `!isScopeResolutionLanguage(language)`, and with all 16 SupportedLanguages registered in SCOPE_RESOLVERS, that gate was structurally always true — the worker already produced no ParsedFiles and scope-resolution re-extracts each file from source on the main thread (run.ts). Remove the now-dead machinery:

- Drop both worker `extractParsedFile` call-sites (tree-sitter processFileGroup + the standalone-provider branch) and the `result.parsedFiles.push`. The standalone branch keeps fileCount/onFileProcessed per file. `result.parsedFiles` stays declared but empty (field removal deferred).
- Remove the now-orphaned `scopeSourceKind` var + `ScopeCaptureSourceKind`/`extractParsedFile`/`isScopeResolutionLanguage` imports.
- Delete the consumerless `migrated-languages.ts` (isScopeResolutionLanguage + SCOPE_RESOLUTION_LANGUAGES) and its drift-guard test — parse-worker was their only importer. Also improves AGENTS.md "shared ingestion code must not name languages" compliance.

`extractParsedFile` and the scope-extractor-bridge stay (scope-resolution/run.ts + Vue resolver use them). Behavior-preserving: worker-sequential-parity passes before and after; tsc/eslint clean; no baseline/golden drift.

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

* refactor(ingestion): worker-pool-only parsing; remove sequential parser (#1983)

Completes the #1983 huge-repo parse-OOM effort by making the worker pool
GitNexus's sole parse path.

Parallel serialization (the perf core): workers serialize their ParsedFiles to
a disk store in parallel and stream them back to scope-resolution, so the main
thread no longer re-parses every file (the tree-sitter native-memory leak that
caused the OOM). Adds chunk merge-pipelining + work-proportional chunk sizing so
the pool stays saturated.

Remove the sequential parser: `--workers 0`, `GITNEXUS_WORKER_POOL_SIZE=0`, and
`skipWorkers` now hard-error (no silent degrade — #1741); the small-repo
threshold no longer selects an in-process path; pool creation stays lazy /
cache-miss-gated so warm all-hit runs never spawn workers.

Worker-path parity fixes — removing sequential surfaced two pre-existing gaps
that tiny-fixture tests had masked by running below the worker threshold, both
fixed by carrying per-file metadata as DATA across the worker boundary (never
re-parsing on the main thread, preserving the OOM fix):
  - C++: templateConstraints wired into worker node identity (SFINAE overload
    disambiguation) + ADL / inline-namespace capture side-channel serialized
    onto the ParsedFile.
  - Kotlin: companion-scope side-channel serialized the same way (companion /
    static dispatch).

Validation: tsc + build clean; full suite green (10,190 pass — the only
deterministic failures were the now-fixed C++/Kotlin worker-path gaps; the 2
remaining full-run failures are pre-existing load flakiness, green in
isolation); cpp-pipeline benchmark stays linear on a 1-worker pool.

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

* fix(ingestion): wire C static-linkage side-channel + ADL O(1) collect + tri-review cleanups (#1983)

Follow-up to the worker-pool-only refactor, from a tri-review of the parse path.

- C static-linkage side-channel (P1): cProvider had no collect/applyCaptureSideChannel,
  so on the now-sole worker path C `static` file-local marks were lost across the worker
  boundary -> false cross-file CALLS edges + over-broad #include wildcard visibility on
  every C analysis (the Linux kernel is C). Mirror the C++/Kotlin wiring: serialize
  `staticNames` per file onto ParsedFile.captureSideChannel and restore it on the main
  thread (no re-parse). + a worker-path regression test (the existing c-static-isolation
  fixture passed vacuously — its collision resolves via #include before the global
  free-call fallback ever consults static-linkage).

- captureSideChannel `kind` discriminant: add `kind:'cpp'`/`kind:'c'` tags + guards
  (Kotlin already had one) now that C/C++/Kotlin share the single generic field.

- Perf: collectCppAdlSideChannel scanned the whole argInfoBySite/noAdlSites maps per file
  (O(F^2) per sub-batch, ~100M parseSiteKey calls at kernel scale). Add per-filePath
  lockstep indexes -> O(1) collect; serialized snapshot byte-identical.

- Cleanups: inline the one-line processParsingWithWorkers wrapper into processParsing;
  drop the always-empty WorkerExtractedData.calls/assignments/constructorBindings fields;
  remove the voided astCache param from processParsing; refresh stale "sequential
  fallback" JSDoc.

Validation: tsc + build clean; cpp 297/297, c 8/8 (incl. the new worker-path
static-linkage guard), typescript + parsedfile-store green; cpp ADL benchmark stays linear.

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

* perf(scope-resolution): index C/C++ #include resolution in finalize (O(n²)→O(n))

Kernel-scale C/C++ analysis ground in finalizeScopeModel because three
per-#include operations each did a full O(F) scan with no index — the
finalize O(n²) that surfaced once the #1983 parse-phase OOM was fixed:

- expand{C,Cpp}WildcardNames: parsedFiles.find() per wildcard edge → O(R·F)
- resolveImportTarget: new Set(allFilePaths) rebuilt per #include
- resolveCImportTarget: suffix-match scanned all workspace paths

Each is replaced with a WeakMap-per-pass index keyed on the stable
parsedFiles/allFilePaths references that scope-resolution run.ts passes
once per pass:

- Map<ScopeId,ParsedFile> for wildcard expansion (c/static-linkage.ts +
  cpp/file-local-linkage.ts)
- memoized augmented header set (c/scope-resolver.ts + cpp/scope-resolver.ts)
- basename-bucketed suffix index in resolveCImportTarget (c/import-target.ts),
  shared by C and C++ since resolveCppImportTarget delegates to it

Collapses the C/C++ finalize from O(R·F) to O(R+F). Pure-perf, byte-identical
edge output: 962 targeted tests green (490 C + 472 C/C++ scope-resolution);
the basename index preserves the exact endsWith('/'+target) match and the
fewest-path-components-then-lexicographic tie-break.

The kernel's ~25-30k .h headers are classified C++, so both providers must
be fixed. Proven on the Linux kernel: the C finalize completed
(sr-post-finalize lang=c → sr-end lang=c), which the pre-fix run never
reached in 16+ min of grinding.

Build-independent follow-ups (separate from this finalize fix), documented
for later: emitFreeCallFallback same-name buckets (emit phase),
buildGraphNodeLookup + precount global setup, the ParsedFile store-load,
the dart/go/ruby expand-wildcards .find siblings, and the ~26GB
scope-resolution memory floor (full kernel completion needs >~40GB RAM).

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

* test(bench): regenerate C scope-capture baseline for the #1983 c-static-linkage-worker fixture

bench/scope-capture/measure.mjs fingerprints emitCScopeCaptures over the
lang-resolution/c-* fixture corpus. The #1983 PR added the
c-static-linkage-worker fixture (caller.c/lib.c/lib.h/local.c — the
worker-path static-linkage side-channel test) but did not regenerate the C
baseline, so `--check` has been red on this branch (main, lacking the
fixture, still matches 0de009b).

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). Regenerated: 0de009b -> 39f3a83. Bench now
PASS (14 languages). Unrelated to the finalize O(n²) fix.

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

* perf(scope-resolution): lower kernel-scale resident memory floor + setup cost

Reduce the scope-resolution resident-memory floor and setup throughput on
huge repos (Linux kernel), the wall that remains after #1983 (parse OOM) and
the finalize O(n^2) fix (b71c77b8). Five units; all preserve byte-identical
edge output (C fixture 177n/255e + c/cpp/cross-file/php/static-linkage suites
green, 619 tests).

U1 (src/cli/analyze.ts): RAM-aware auto heap-cap. Replace the hardcoded
16384MB cap with computeHeapCapMb = max(16384, floor(0.75*effectiveRAM)),
where effectiveRAM = min(os.totalmem(), process.constrainedMemory()) with the
unconstrained-sentinel guard. Add --max-semi-space-size=128 on the respawn.
A user-supplied NODE_OPTIONS heap still wins (no re-exec). Verified: 23973MB
on a 31964MB box, 16384 floor on small machines, cgroup-aware, sentinel safe.

U2 (src/storage/parsedfile-store.ts, .../pipeline/phase.ts): export forceGc()
and call it at the per-language eviction boundary, so a finished language's
ParsedFiles are reclaimed before the next language's store-load instead of
collected lazily under the next pass's allocation pressure (which at cap>=RAM
degrades into swap-thrash). Measured on a real drivers/net/ethernet run:
C 2113->894MB and C++ 1754->1057MB reclaimed at the boundary (no fragmentation
defeat). Answers the plan's Open Question 1.

U3 (src/storage/parsedfile-store.ts): intern def objects by nodeId in the load
reviver so a SymbolDefinition's three serialized copies (localDefs /
scope.ownedDefs / scope.bindings[].def) collapse to one shared object on load.
Per-shard def pool (a def's copies are shard-local). Measured ~42% off the
def-object retained heap (3->1; 1.8M->600k distinct objects on 600k defs).

U4 (.../passes/free-call-fallback.ts): memoize pickUniqueGlobalCallable's
post-filter candidate list per (name, callerFilePath), only when no per-caller
visibility filter applies (the list is then a pure function of name+file), so
repeated free calls of one name from a file reuse the same-name-bucket scan
instead of re-walking a potentially huge bucket per site. The cached array is
read-only-consumed by the .filter()-based arity/overload narrowers. Exported
pickUniqueGlobalCallable + buildGlobalCallableIndex and added an equivalence
test (memoized == un-memoized reference for every (name, file, arity),
including warm-cache repeats and cross-file file-local exclusion).

U5 (.../pipeline/phase.ts): replace the O(L*F) per-language precount + repeated
scannedFiles.filter() with a single O(F) partition-by-language pass; bracket
buildGraphNodeLookup with scope-setup-nodeLookup heap probes so the long setup
is no longer silent.

Plan: docs/plans/2026-06-06-001-perf-kernel-scope-resolution-memory-plan.md
(U6 out-of-core global index deferred). Note: the kernel's full C++ pass floor
(~20k headers + the 8.8GB graph) likely still exceeds 24GB by itself, which is
why U6 remains the only unit that clears the wall.

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

* fix(test): match OOM-guidance e2e assertions to the U1 reworded hint

The analyze-heap-oom-e2e real-child-OOM test still asserted the pre-U1
wording ('...out of memory.' + a hardcoded 24576 cap). U1 reworded the hint
to mention the auto heap-cap and use a <MB> placeholder, so the three
toContain substrings no longer matched (the assertion at line 62 failed on
all platforms). Update them to the current message. The unit twin
(analyze-heap-respawn) was already updated in 85bfc216; this integration
test was missed by the targeted local run.

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

* perf(lbug): U6a — deterministic id-sorted graph output behind GITNEXUS_SORT_GRAPH_OUTPUT

First increment of U6 (out-of-core scope-resolution). Adds an optional
deterministic ordering of node + relationship CSV rows by their unique graph
id, behind GITNEXUS_SORT_GRAPH_OUTPUT (default OFF = today's graph-insertion
order, byte-identical — the iterator is returned untouched). With the flag ON
the CSV becomes a pure function of the node/edge SET rather than of emit order.

This is the structural enabler for the windowed/out-of-core resolve (U6b-U6d):
csv-generator.ts:518 currently iterates graph.iterRelationships() in insertion
order with NO terminal sort, so any deviation from parsedFiles-order emit would
change bytes. With U6a on, a windowed emit need only reproduce the same edge
SET, not the global insertion order — removing the single largest byte-identical
hazard from every later windowing step.

Verified: default off keeps the existing csv-pipeline suite byte-identical; on,
node rows are id-sorted and output is independent of graph insertion order
(set-build) with the same node/edge set.

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

* perf(storage): U6d foundation — disk-backed scope store + lazy ScopeTree

Adds scope-index-store.ts: persistScopeShards (per-file scope shards via the
proven mapReplacer + def-interning reviver) + DiskBackedScopeTree, a lazy
ScopeTree that serves getScope from a bounded LRU of decoded shards plus a small
resident skeleton (scopeId -> {shard, childIds, parent}). Exports
makeInterningReviver from parsedfile-store for reuse.

This is the contained, highest-risk mechanism of U6d (out-of-core scope
resolution): the emit passes reach the heavy per-Scope binding payload
(~17-20GB on the kernel) ONLY through scopeTree.getScope (a point lookup) and
getChildren — they never read parsed.scopes directly — so moving that payload to
disk behind getScope is transparent. Every consumer reads a Scope BY VALUE, so a
value-faithful disk round-trip is byte-identical to resolution.

Proven in isolation: DiskBackedScopeTree is value-identical to buildScopeTree
for getScope/getChildren/getParent/getAncestors/has/size across multiple files
and after LRU eviction, and preserves the def-identity collapse (ownedDefs[i]
=== binding.def). Nothing wires it yet (the resolution-pipeline integration is
the next increment) — zero production impact; default off.

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

* perf(scope-resolution): U6d integration — seal scopeTree to disk before emit (GITNEXUS_DISK_SCOPE_INDEX)

Wires the U6d out-of-core scope index into the live pipeline behind
GITNEXUS_DISK_SCOPE_INDEX (default OFF = byte-identical). When on:

- finalize-orchestrator builds a TransitionalScopeTree (validated, fully
  resident) instead of buildScopeTree, so finalize/propagate/resolve are
  unchanged.
- After resolve, before emit, run.ts seals it: persists the scopes to a
  file-sharded scope-index-store, swaps the model's scopeTree to disk-backed
  serving from the inside (the frozen bundle can't be reassigned, but the
  wrapper nulls its own resident backing), and drops the heavy Scope.bindings
  payload from all THREE holders — the model's tree (seal), the caller's
  preExtractedParsedFiles, and run.ts's own parsedFiles (scope-stripped copies
  for emit). Emit reads scopes only via scopeTree.getScope (a point lookup,
  now disk-backed + LRU) — verified it never reads parsed.scopes.

Purpose: lower the per-language resident PEAK (kernel C pass ~20→~12 GB by
moving the ~8-9 GB scope payload to disk) so the analysis fits on smaller-RAM
machines. At >=24 GB the full kernel already fits with U1-U5 (U2's 8.7 GB
inter-language forceGc reclaim keeps each pass under cap) — empirically
confirmed — so this is the sub-24 GB lever, not needed at 24 GB.

Byte-identical evidence: DiskBackedScopeTree/TransitionalScopeTree return
value-identical scopes vs buildScopeTree (getScope/getChildren/getParent/
getAncestors, across files + after LRU eviction + post-seal); emit reads only
getScope + referenceSites; flag-off (394 tests) and flag-on-resident (91 tests)
resolver suites stay green; an end-to-end A/B on a 212-file C+cpp+rust subset
produced identical 17,444 nodes / 31,343 edges with the seal firing per language
(c: 410→141 MB reclaimed). Kernel-scale peak-drop measurement pending the
in-flight verdict run freeing memory.

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

* perf(scope-resolution): U6d — id-back workspaceIndex so the disk seal can reclaim scopes

The kernel run revealed the contained scopeTree seal didn't lower the heap:
WorkspaceResolutionIndex held Scope OBJECTS (classScopeByDefId / moduleScopeByFile),
built from every ParsedFile and live through emit, so the ~28k module + class
scopes stayed pinned past the seal (sr-seal-pre 17,583 -> sr-seal-post 17,771 MB,
no drop). It was the sole residual Scope-object holder (SemanticModel holds none).

Fix: classScopeByDefId / moduleScopeByFile become id-backed ScopeByKeyView
instances — a ReadonlyMap<K, Scope> facade over a K->ScopeId map + the scopeTree,
whose .get fetches via scopeTree.getScope(id). The index now pins only ids, so
once the tree seals to disk the scopes become collectible. Byte-identical: the
view returns the same Scope the resident tree holds (or a value-identical revived
one in disk mode), and iteration keeps the old insertion order. buildWorkspace
ResolutionIndex takes an optional scopeTree (live pipeline passes it); without it
(unit tests) the legacy direct Scope-object maps are returned unchanged.

Verified byte-identical: 733 tests across workspace-index / imported-return-types
/ c / cpp / cross-file / go / java. Kernel peak-drop re-measurement to follow.

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

* perf(scope-resolution): U6d — precompute exportedCallableByName (fix disk-getScope thrash)

The workspaceIndex id-backing freed the kernel scopes but exposed a throughput
collapse: findExportedDefByName's workspace fallback (walkers.ts:1019) scanned
EVERY module scope's bindings per unresolved free call, and under the U6d
disk-backed scopeTree each module-scope access faulted a shard in from disk —
lib ON went ~1min -> ~7.5min.

Fix: precompute the fallback result once into
WorkspaceResolutionIndex.exportedCallableByName (simpleName -> first module-local
callable def, first-file-wins — the exact semantics the scan returned), built
from the resident module-scope bindings at index-build time. findExportedDefByName
now does an O(1) lookup with zero disk reads.

Result: lib ON ~7.5min -> 21s (cache-warm), byte-identical 17,444/31,343; 758
tests green across workspace-index + c/cpp/cross-file/go/python.

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

* docs: rename cryptic U-unit codes to descriptive names in comments

The plan-unit shorthand (U3/U4/U6a/U6d/...) was meaningless in the code.
Renamed in comments + test descriptions (no behavior change, byte-identical):
  out-of-core scope index   (was U6)
  deterministic output      (was U6a)
  disk-backed scope seal    (was U6d)
  def-object interning      (was U3)
  free-call candidate cache (was U4)
Also renamed throughout the PR title/summary. Pushed commit messages keep
their original U-codes as historical record.

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

* fix(ingestion): durable ParsedFile shards for warm-cache coverage (#2038)

On a warm re-analyze where every chunk is a parse-cache HIT, no parse worker
runs, the run-scoped ParsedFile store is cleared at parse start, and the cached
ParseWorkerResult carries no ParsedFiles (the worker writes them to the store
and empties them from the message). Scope-resolution then found an empty store
and fell back to main-thread extractParsedFile — re-opening the #1983
tree-sitter native-leak OOM the disk store closes (abhigyanpatwari review on
parse-cache.ts).

Fix: workers ALSO write their ParsedFiles to a durable, content-addressed store
(parsedfile-cache/) keyed by chunk hash, mirroring the parse cache's lifecycle
(version-gated by PARSE_CACHE_VERSION, pruned in lockstep to the surviving
keys). On a warm hit the chunk's durable shards are byte-COPIED into the
run-scoped store (no re-parse, no re-serialize -> byte-identical), so
scope-resolution streams them exactly as on a cold run. A coherence gate
re-dispatches the worker whenever a cached chunk's durable shards are missing
(migration / pruned / version-stale) -- never the main-thread extract.

- worker-pool/parse-worker: thread chunkHash through dispatch->job->flush
  (incl. split/requeue) so the worker tags its durable shard by content
- parsedfile-store: durable persist / restore / index / prune API (sibling
  dir, never cleared per run); content-addressing makes stale reuse impossible
- parse-impl: load durable index, gate the cache hit on durable coverage,
  restore on hit, dispatch chunkHash on miss
- run-analyze: prune+save the durable store to the parse cache's surviving keys
- saveParseCache returns its written keys (the durable keepKeys)

Verified on linux/lib: warm preExtractedHits = full coverage (520/207/1, zero
main-thread re-parse), byte-identical cold==warm (17,456n/31,353e), warm 8.5x
faster. New two-run + mixed-mode + coherence-gate regression test.

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

* fix(ingestion): clear stale scope-index-store shards on each seal (#2038)

The disk-backed scope index writes sequential s<n>.json shards into a shared
<storagePath>/scope-index-store/ dir, with the index resetting per
persistScopeShards call. A seal that writes fewer shards than a previous one
(a later language with fewer files, or a re-run of a shrunken repo) left stale
tail shards on disk indefinitely -- never read by the disk-backed tree, but
multi-GB on kernel-scale repos.

Add clearScopeIndexStore() and clear at the start of persistScopeShards: the
previously sealed language has finished emit and been released before the next
seal runs, so its DiskBackedScopeTree never reads those shards again. Unit
tests: a stale prior-run shard is removed, a fewer-files re-seal leaves no tail
shards, and the helper is idempotent.

Addresses abhigyanpatwari review on run.ts (disk hygiene for the
GITNEXUS_DISK_SCOPE_INDEX path).

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

---------

Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-06 22:46:34 +01:00
evolution
3b43eb8b47
fix(go): capture multi-name declarations (#2032)
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