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16 commits

Author SHA1 Message Date
DuduPhudu
fb49613a4d
fix(ingestion): ignore emitted Next.js build output, and delete the inert public/build entry (#3018)
* fix(ingestion): ignore emitted Next.js build output, and restore the dead public/build entry

`DEFAULT_IGNORE_LIST` contained `.next` — the build CACHE — but not `_next`, the
emitted OUTPUT, which are different directories. A Capacitor/Cordova shell copies
a built Next.js bundle to `<platform>/app/src/main/assets/public/_next/static/`,
where no path segment hits the list, so the walker indexed the bundle as source.
On a real mobile-wrapped Next.js app that was 256 minified chunk files, and every
`Route` node the repo produced pointed at a webpack chunk rather than at source.

The filename heuristics did not catch them either: they match `.bundle.`,
`.chunk.`, `.generated.` and `.d.ts`, while Next.js emits hashed names like
`6862-9d1cdcb99f169a06.js`.

Separately, `'public/build'` had been sitting in `DEFAULT_IGNORE_LIST` matching
nothing at all. That set is tested one path SEGMENT at a time, and is also read
by `isHardcodedIgnoredDirectory(name)`, which receives a bare directory name —
so a slash-containing member can never compare equal to anything. Rather than
delete the entry and lose its intent, multi-segment paths now live in
`DEFAULT_IGNORED_PATH_FRAGMENTS` and are matched against the whole path, so
Remix / Laravel Mix asset output is ignored as originally intended.

A guard test pins the invariant that made the dead entry possible: no member of
the name set may contain a slash.

Measured against a production Capacitor-wrapped Next.js app (1558 JS/TS files on
disk): 256 newly ignored, none of them under `src/`, and zero files that were
previously ignored become indexed.

Closes #3007

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* fix(ingestion): drop the inert public/build machinery, discriminate _next by segment, ignore _next on the web upload path

Addresses the review findings on #3018.

Remove DEFAULT_IGNORED_PATH_FRAGMENTS, hasIgnoredPathFragment and its
shouldIgnorePath branch. The mechanism was correct but unreachable: all four
of its match forms put a `/` or end-of-string on both sides of `build`, so a
fragment match strictly implies `build` is a whole segment, which the
per-segment DEFAULT_IGNORE_LIST loop already catches one branch earlier.
Measured over 768,420 generated paths: 65,506 fragment matches, 0 of them
decisive, 0 implication violations. `'public/build'` really was an inert
member of the name set, but its paths were never unignored — bare `'build'`
covered them on both sides — so the entry is deleted rather than relocated,
which is the other option #3007 offered. The slash-free guard test stays; it
is what stops the next slash-bearing entry from dying the same way.

Add negative cases pinning that `_next` matches as a whole path segment. The
previous suite could not tell a segment rule from a substring rule: replacing
the entry with `normalizedPath.includes('_next')` passed all five tests, while
eating `src/_nextgen/index.ts`.

Rename the public/build test to what it actually pins — that deleting the
inert entry changed no behavior — since it is green on both sides by design.

Add `_next` to the web upload filter's EXCLUDED_DIRS. That list is the live
browser ingestion path (RepoAnalyzer -> filterRepoFiles -> /api/analyze/upload)
and had `.next` but not `_next`, so a Capacitor-wrapped Next.js app uploaded
its entire minified tree against the server's 20000-file / 250MB caps for
files the analyzer then discards.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* test(ignore-service): make the single-component set guards able to fail

The slash-free guard added for #3007 could not fail. It selected entry lines
with startsWith("'") and read only the first quoted token per line, so
'public/build' could return as a backtick string, behind an inline block
comment, as a second entry on an existing line, or via .add() and every test
stayed green. Prettier and eslint miss the backtick and inline-comment forms
too, so CI did not catch them either.

U1: remove the duplicate '.serverless' entry so the set can be pinned to one
exact number. A Set discarded it, so no ignore behaviour changes.

U2/U3: replace the line-based parser with a shared single-pass scanner in
test/helpers/ignore-set-source.ts, and extend the guard from DEFAULT_IGNORE_LIST
to IGNORED_FILES, ROOT_ARTIFACT_DIRECTORIES and IGNORED_EXTENSIONS, which share
the same single-component match contract.

The scanner tracks string and comment state together because neither can be
removed first: the ignore-list comments quote paths and carry an apostrophe, so
matching literals before stripping comments yields phantom slash-bearing
entries; and a glob string containing a comment-open sequence makes regex
comment-stripping swallow the closing bracket. Only a single pass is correct in
both directions.

Counts are pinned exactly rather than floored — a floor cannot protect a
two-member set and hides a partial parse. Shapes a source parser cannot resolve
(spread, interpolation, concatenation, later .add) now throw instead of quietly
reporting fewer members, and the parsed names are cross-checked against
isHardcodedIgnoredDirectory so parser drift fails without exporting the set.

Verified by mutation: all six fail-open spellings now turn the suite red;
187 tests pass, tsc clean.

* test(ignore-service): pin that _next prunes the directory, not just its files

Every measured benefit of ignoring _next comes from never enumerating the
bundle tree, and no file list can observe that: anything under _next is
rejected whether the walk pruned the directory or descended and rejected each
file. childrenIgnored is the only observation that separates them.

The existing build-output tests all call shouldIgnorePath, the leaf predicate,
so a refactor moving _next to a shouldIgnorePath-only rule would keep them green
while silently restoring the full walk. These assertions close that.

Also pins that _next matches as a whole segment (_nextgen and my_next are still
walked), and that the `!_next/` negation recovers the directory at any depth —
the bare form is the one that works, since `!_next/**` alone never gets tested:
childrenIgnored prunes the directory before any descendant pattern is reached.

Placed in the .gitnexusignore-negation describe block, which owns mkPath and the
tmpdir fixture and is registered in scripts/cross-platform-tests.ts.

Verified by mutation: disabling only the pruning branch in childrenIgnored leaves
the build-output suite at 26/26 green and turns these assertions red.

* test(ignore-service): guard the twin build-output ignore lists against drift

_next now lives in two lists in two packages — the analyzer's DEFAULT_IGNORE_LIST
and the browser upload filter's EXCLUDED_DIRS — with nothing tying them
together. This is the seventh twin-list pair in this repo; the header of
receiver-twin-list-drift.test.ts records that the previous ones each shipped a
bug when one side moved.

Containment runs web -> CLI only, and that is the load-bearing direction: the
browser filter decides what the server ever sees, and it reads no
.gitnexusignore, so a name it drops that the analyzer would have indexed is
silent source loss with no recovery. The reverse is not an error — the analyzer
prunes far more aggressively than an upload needs to.

.gitnexus is the one exemption and has a mechanism: the walker passes
dot: false to glob, so it never enumerates dot-directories. Asserted in both
directions so re-adding it to the CLI list or dropping it from the web list
both fail.

Both sides are source-parsed through the shared helper. DEFAULT_IGNORE_LIST is
module-private, and no test in this package imports across the package boundary
— every cross-package precedent reads source instead.

Also corrects the documentation this PR's comments got wrong: the guard test is
cited by path rather than as "below", the unreproducible per-repo percentage is
gone, the reason _next is deliberately unanchored is recorded next to the entry
(no <web-root>/_next form matches a root-level _next/static/…), and the upload
filter now states that it consults no repository ignore rules — so unlike the
CLI, a negation cannot recover what it drops.

Verified by mutation: a web-only addition and a CLI removal each turn the guard
red. 194 targeted tests pass; tsc clean in both packages.

* refactor(test): read the ignore sets with the TypeScript parser, not a hand-rolled scanner

The guards read ignore-service.ts as source because the sets are module-private.
The first pass hand-rolled a character scanner to do it, and the repo already
vendors the right tool: ts.createSourceFile, used this way in literal-collectors,
query-determinism-guard, cli-index-help and group/sync-partial-extraction.

The scanner had two silent gaps a real parser does not have:

- It rejected `${` by substring, but template literals were consumed whole, so
  that branch could never fire and an interpolated member was accepted as a
  literal — the exact under-report the file refused to allow.
- It took the first `[` after the marker, which on a type-annotated declaration
  (`readonly string[] = ...`) is the annotation's empty pair. It returned [] with
  no throw, which would make every assertion in a suite vacuously true. This is
  the hazard receiver-twin-list-drift.test.ts documents having hit.

Reading the declaration node removes both, along with the comment-vs-string
ordering problem that motivated the scanner: a parser cannot mistake a comment
for a string or a glob's `/*` for a comment-open.

Also drops the four pinned exact counts. They were a ratchet — these sets are
edited by unrelated PRs, each of which would have failed a count assertion about
nothing it touched — and with a real parser the partial-parse hazard they existed
to catch cannot happen silently: a member that is not a plain string literal
throws.

Markers collapse to set names, and the duplicated path-resolution boilerplate
moves into the helper the two suites already share.

Net 187 deletions against 123 insertions. Verified by mutation: backtick,
inline comment, same-line, double-quote, duplicate, interpolation, spread and
runtime .add() are all caught; a type-annotated declaration now reads correctly
instead of returning empty. 194 tests pass, tsc clean.

---------

Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com>
2026-08-27 13:29:05 +01:00
azizur100389
88df18b829
fix(ingestion): discover nested source directories (#3043) 2026-08-26 12:24:39 +00:00
azizur100389
79ff44dfa9
fix(config): honor parts negation on Windows (#2720)
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Normalize repository-relative paths before applying ignore-package rules so `.gitnexusignore` negation can override hardcoded `parts` exclusions during Windows traversal.

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-28 20:04:34 +01:00
Gergo Magyar
0f016dc467 fix(config): read core.excludesFile and .git/info/exclude for global ignores (#2606)
Replace the custom ~/.gitnexus/ignore file with the same two sources
real git itself consults for exactly this purpose (gitignore(5)):

- core.excludesFile: git's own all-repos global ignore file (defaults
  to $XDG_CONFIG_HOME/git/ignore when unconfigured)
- $GIT_COMMON_DIR/info/exclude: per-repo, untracked, so it works
  without push/commit access to the repo

Precedence mirrors git exactly (lowest to highest): core.excludesFile,
then info/exclude, then .gitignore, then .gitnexusignore -- each later
source can negate an earlier one via a `!pattern` line, same
last-match-wins semantics git itself uses.

Adds getCoreExcludesFilePath and getGitInfoExcludePath to git.ts,
following the same execSync + git-common-dir pattern as
getCanonicalRepoRoot. GITNEXUS_NO_GLOBAL_IGNORE (or noGlobalIgnore)
still skips both global sources, mirroring GITNEXUS_NO_GITIGNORE.
2026-07-21 18:06:22 +00:00
Gergo Magyar
a4a79ac920 style: fix prettier formatting in ignore-service.test.ts 2026-07-21 17:41:18 +00:00
Gergo Magyar
322e05a6be fix(config): add user-level global ignore file (#2606)
IgnoreService only read per-repo .gitignore/.gitnexusignore, so an
exclusion meant to apply across every indexed repo had to be repeated
per repo or hand-patched into node_modules (wiped on every upgrade).

loadIgnoreRules now also reads a global ignore file at
$GITNEXUS_HOME/ignore (default ~/.gitnexus/ignore), reusing the
existing global directory that already holds registry.json and
config.json. It is added first, so per-repo .gitignore/.gitnexusignore
rules can still negate it, mirroring the .gitignore -> .gitnexusignore
precedence already in place. GITNEXUS_NO_GLOBAL_IGNORE (or
noGlobalIgnore) skips it, mirroring GITNEXUS_NO_GITIGNORE.
2026-07-21 16:58:07 +00:00
ChamHerry
681a352006
fix(worker): analyze native worker aborts (#1833)
* fix(analyze): avoid native aborts on generated worker bundles

Retire timed-out parse workers instead of force-terminating native parser state, and skip Monaco generated worker bundles by default while preserving explicit .gitnexusignore negation overrides.

Constraint: Node native tree-sitter bindings can abort the process when a timed-out worker is terminated while inside parser state.

Rejected: Falling back to sequential parsing for native stalls | it can move the same native crash onto the main thread.

Confidence: high

Scope-risk: moderate

Directive: Keep timeout recovery from force-terminating workers until they return to JS or exit naturally.

Tested: npm test; npx tsc --noEmit; npm run build; targeted analyze on /Users/wangxc/Code/keep; gitnexus detect_changes --scope staged

Not-tested: Node 22 LTS runtime and non-macOS platforms

* fix(worker): bound retired parser worker lifetimes

Keep timeout recovery from immediately terminating workers that may still be inside native parser state, while making terminal pool shutdown own retired worker cleanup so long-lived processes do not accumulate retired threads.

Constraint: Claude review on PR #1833 required retiredWorkers cleanup in pool.terminate() and tripBreaker() without regressing no-immediate-terminate timeout safety.

Rejected: clearing the retiredWorkers set without terminating | would remove JS bookkeeping while leaking the underlying worker thread.

Confidence: high

Scope-risk: moderate

Directive: Preserve the distinction between recoverable timeout retirement and terminal pool shutdown; do not reintroduce immediate terminate in removeWorkerFromSlot(..., 'retire').

Tested: npx vitest run test/unit/worker-pool-timeout-retire.test.ts; npx vitest run test/unit/worker-pool-timeout-retire.test.ts test/unit/worker-pool-resilience.test.ts test/unit/worker-pool-cumulative-timeout.test.ts test/unit/worker-pool-slot-generation.test.ts; npx tsc --noEmit; npm run build; npx prettier --check src/core/ingestion/workers/worker-pool.ts test/unit/worker-pool-timeout-retire.test.ts ../docs/todo/pr-1833-retired-worker-cleanup-plan.md; npx eslint src/core/ingestion/workers/worker-pool.ts test/unit/worker-pool-timeout-retire.test.ts; gitnexus detect_changes --scope staged.

Not-tested: npm test full suite did not complete green in this environment; two runs each had one unrelated test/unit/hooks.test.ts parseHookOutput null failure, and each failed hook test passed when rerun in isolation.

* ci: retrigger checks

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

---------

Co-authored-by: wangxc <wangxc_a_bj@si-tech.com.cn>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
Co-authored-by: Test <test@example.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
2026-05-26 17:28:39 +01:00
Minidoracat
2b6e7ffbd9
fix(php): avoid Blade templates entering PHP analysis (#1790) 2026-05-23 23:37:40 +01:00
WENJIE HUANG
32b5c0e3fc
feat: add IncludeExtractor for C++ cross-repo include tracking (group) (#1156)
* feat: add IncludeExtractor for C++ cross-repo include tracking (group)

* fix: address CodeQL warnings on include-extractor

- Remove unused HEADER_GLOB constant in include-extractor.ts
- Use fs.mkdtempSync for secure temp dir creation in tests
  (CodeQL: 'Insecure temporary file')

* fix(group): close missing ); in manifest-extractor include branch

The 'include' branch in ManifestExtractor.resolveSymbol was missing
the closing ); for the executor() call, causing a syntax error that
broke ESLint, Prettier, and the full test CI on all platforms.

Reported by Claude PR review on #1156.

* chore: drop test/global-setup.ts + test/vitest.d.ts

Upstream removed these in commit 3f0c74fe (ladybugdb 0.16.0 upgrade).
Commit 3f5d21c5 accidentally restored them during a rebase dance.

* style(group): reformat VALID_CONTRACT_TYPES array to satisfy prettier

Adding 'include' pushed the array over prettier's 100-char limit,
so prettier prefers multi-line. Apply the reformat to unbreak
ci-quality/format job.

* fix(include-extractor): address PR #1156 Claude review findings #3-#7

Claude Deep Review raised 7 findings on the IncludeExtractor. #1/#2
(BLOCKERs) were fixed earlier. This commit closes the remaining five.

#3 HIGH  case-sensitive FS -> provider contract-id collision
  Document the deliberate case-folding trade-off on normalizeIncludePath
  (matches C/C++ convention on Windows/macOS; collapses Foo.h & foo.h on
  Linux). Add a unit test pinning the behavior.

#4 HIGH  suffixResolve short-suffix match silently drops cross-repo include
  When a local file ends with the same basename as an external include
  (e.g. local internal/api.h vs. #include "ext/api.h"), suffixResolve
  returned a bogus local hit and suppressed the cross-repo consumer.
  Replace the suffixResolve lookup inside include-extractor with a
  strict isLocalInclude() that only accepts full-path hits via
  SuffixIndex.get / getInsensitive. Callers of suffixResolve elsewhere
  are unaffected. Add 3 unit tests covering the regression.

#5 MEDIUM regex fallback matched #include inside /* ... */
  Strip block comments before running the fallback regex scan.
  Add a unit test.

#6 MEDIUM meta.source was hard-coded to 'tree_sitter'
  Track the actual extraction path with an extractionSource local and
  write it into meta.source so downstream audits can distinguish
  tree-sitter parses from regex fallbacks. Add 2 unit tests.

#7 MEDIUM missing end-to-end coverage
  Add test/integration/group/include-extractor-sync.test.ts with 3
  cases exercising extractor -> syncGroup -> CrossLink (mocked
  contracts, mixed-case/backslash normalization, real temp repos).

Tests: 21 unit + 3 integration, all green.

* fix(lbug): robust Windows lock acquisition for CI integration tests

LadybugDB's `new Database()` raises `Could not set lock on file` from
local_file_system.cpp synchronously inside the constructor — before any
query is issued, so `withLbugDb`'s query-time retry never sees it. On
Windows CI this surfaces as flaky integration tests due to AV-scanner
holds, libuv handle-release lag, and stale `.wal` sidecars from aborted
prior runs.

This change closes the gap at *open time*:

- `openLbugConnection` now wraps `new lbug.Database()` in a bounded
  busy-retry (5x100ms back-off) inside `lbug-config.ts`. Errors that
  exhaust the budget are tagged via `LBUG_OPEN_RETRY_EXHAUSTED` so
  `withLbugDb`'s outer 3x retry skips re-retrying a freshly-exhausted
  path (eliminates the 3x5=15-attempt / ~6s tail latency).
- For recognized test fixtures only (immediate-parent dir matches a
  known prefix AND resolves under `os.tmpdir()`), one final stale-
  sidecar sweep removes `.wal`/`.lock` and retries once. Production
  paths never enter this branch.
- `safeClose` on Windows runs a bounded `fs.open` probe to absorb
  native handle-release lag; logs a warning if the probe exhausts so
  operators can spot AV interference.
- `isDbBusyError` is now defined in `lbug-config.ts` as the single
  source of truth, re-exported from `lbug-adapter.ts` for compatibility.
- New tests cover open-time retry (happy/retry/exhaust/non-busy/tag),
  stale-sidecar sweep (test-fixture-only, production-rejection,
  preserves-original-error), `isTestFixturePath` direct unit suite
  (accept/reject/traversal/nested/trailing-sep), and
  `waitForWindowsHandleRelease` (openable/ENOENT/no-leak).
- The two new test files are added to vitest's existing serialized
  `lbug-db` project (already `fileParallelism: false`).

Closes the chronic Windows CI flake on lbug-touching integration tests
while preserving the existing single-writable-Database-per-process
LadybugDB contract. No public API surface changed.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* refactor(lbug): drop isDbBusyError re-export, import from lbug-config directly

The re-export from lbug-adapter.ts was a transitional convenience — with
the matcher now living in lbug-config.ts, having two import paths for the
same symbol invites future drift. Updated the two real consumers
(lbug-lock-retry.test.ts, lbug-open-retry.test.ts) to import from
lbug-config directly, removed the re-export equality test (now vacuous),
and refreshed the explanatory comment so it no longer references a
re-export pattern that doesn't exist.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(lbug): silence benign LadybugDB v0.16.1 schema-init lock warnings on Windows

doInitLbug logs "⚠️ Schema creation warning: ... Could not set lock on
file" on every CREATE NODE TABLE call after the first init on a given
dbPath, on Windows. The lock is internal to LadybugDB v0.16.1 and is
resolved before the table is created — same tolerance pattern as the
existing "already exists" filter. Genuine cross-process lock contention
still surfaces on the next operation through withLbugDb's retry, so
filtering at the schema-init catch only suppresses noise, not signal.

Also extend the safeClose Windows handle-release probe to cover the
.wal sidecar (the previous Database's WAL handle was the slowest to
release, surfacing as the schema-query lock contention) and switch the
probe back to 'r+' so it actually detects exclusive locks.

Test loop in lbug-close-handle-release.test.ts simplified to 10 plain
iterations now that the underlying noise is filtered upstream.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore(lbug): isDbBusyError review fixes

- Drop redundant `could not set lock` term — already subsumed by `lock`.
- Document the intentionally-broad matcher: graph-DB lock-shaped errors
  ("deadlock", "unlock failed", "lock contention", "could not open lock
  file") are all treated as transient. If a non-transient surfaces,
  tighten the matcher rather than raise the retry budget.
- Add positive test cases covering those lock-shaped strings so the
  intent is visible and a future tightening would deliberately break
  these.
- Fix the open-retry back-off comment: max sleep is 100+200+300+400 =
  1000ms (no sleep after the final attempt), not 1.5s.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(group): address PR #1156 follow-up review findings

Addresses two blockers and two mediums from the deep review.

BLOCKER 1: Windows CI ENOTEMPTY in sync.test.ts
  After this PR added writeBridge() to syncGroup, the existing test
  "writes registry to groupDir when skipWrite is false" fails on
  windows-latest. LadybugDB's checkpoint thread briefly outlives
  closeBridgeDb, holding a Win32 lock on bridge.lbug; the test's
  fs.rmSync then fails with ENOTEMPTY. Switched the test cleanup to
  cleanupTempDir from test/helpers/test-db.ts which already tolerates
  EBUSY/EPERM/EACCES/ENOTEMPTY with bounded retries — same pattern
  used elsewhere for LadybugDB-touching tests.

BLOCKER 2: Graph provider absolute-path bug
  extractProvidersGraph queried File.filePath from the LadybugDB graph
  but never stripped the repo root, so provider contract IDs ended up
  as include::/abs/path/foo.h while consumers emitted include::foo.h.
  These never matched through runExactMatch — silently producing 0
  cross-links for any indexed C++ repo (the primary use case).
  Now passes repoPath into extractProvidersGraph and applies
  path.relative(); rows that resolve outside repoPath (stale absolute
  paths from another machine, system headers somehow indexed) are
  dropped instead of polluting the registry.

MEDIUM: `../` relative includes produce spurious noise
  `#include "../foo.h"` is almost always intra-repo, but the suffix
  index can never match a `..`-prefixed path so it became a consumer
  contract no provider could satisfy. Now skipped before matching;
  covers both forward-slash and backslash forms.

MEDIUM: writeBridge error in sync.ts propagates uncaught
  contracts.json is the canonical source of truth and was just written
  successfully when writeBridge runs. A bridge-only failure (disk full,
  schema error, permission denied) shouldn't mask the registry. Wrapped
  writeBridge in try/catch with a logger.warn surfacing the path and
  recovery instructions.

Tests added:
  - extractProvidersGraph repo-relative ID generation (stub Cypher
    executor returns absolute paths)
  - extractProvidersGraph drops rows whose path resolves outside repo
  - `../foo.h` forward-slash skip
  - `..\foo.h` backslash-form skip

Skipped findings:
  - canExtract() removal (#5, low): canExtract is part of the
    ContractExtractor interface; every other extractor implements the
    same `return true` shape. Removing it from IncludeExtractor would
    break the interface contract — keeping for consistency.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(group): close PR #1156 Codex adversarial findings

Two HIGH findings from the Codex adversarial review on
feat/group-include-extractor:

1. Default-on extraction silently changes existing groups (BLOCKER)
   DEFAULT_DETECT.includes was true, so any pre-existing group.yaml
   that omits the new field would gain a wave of include::* contracts
   on the next sync after upgrade. Flipped to false (opt-in). The
   integration test already declares includes: true explicitly so it
   survives unchanged; the unit extractor tests bypass parseGroupConfig
   entirely; the sync test uses extractorOverride. Only config-parser
   needed regression tests covering omitted/explicit/false variants.

2. IncludeExtractor scans outside the indexed file universe (BLOCKER)
   The extractor was running glob('**/*', { ignore: STANDARD_IGNORES })
   twice with a hand-rolled 9-pattern list, no .gitignore/.gitnexusignore
   honoring, and no max-file-size cap. That meant File:<path> contracts
   could appear for files ingestion would never index, producing
   cross-links group impact cannot fan out to (silent false-negatives).
   Refactored to a single discoverIndexableFiles() helper that mirrors
   walkRepositoryPaths exactly: createIgnoreFilter + getMaxFileSizeBytes,
   one discovery pass shared by provider and consumer paths. Dropped
   STANDARD_IGNORES and SOURCE_GLOB entirely.

   third_party and 3rdparty (the C/C++ vendored-deps conventions) were
   in the local ignore list but not in the canonical DEFAULT_IGNORE_LIST
   used by ingestion. Folded both into the canonical set rather than
   keep a parallel list — the whole point of the Codex finding is that
   two file-discovery implementations drift. Single source of truth.

Tests: 5 new regression tests for the discovery alignment (.gitignore,
.gitnexusignore, max-file-size on both provider and consumer paths)
plus 4 for the opt-in default. All 30 include-extractor tests + the
494-test group suite + ignore-service tests pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(review): apply autofix feedback

ce-code-review surfaced 6 safe_auto findings on commit a9936a9b:

- T1 (testing, P2): the sync.ts:174 gate was untested with includes:false.
  Added a sync-level test mirroring the existing thrift-off pattern at
  sync.test.ts:545, asserting zero include contracts when the gate is
  disabled in a real syncGroup call.

- T3 (testing, P3): third_party and 3rdparty entries in DEFAULT_IGNORE_LIST
  had no regression test. Added both to ignore-service.test.ts's
  dependency-directories it.each block.

- M1 (maintainability, P3): discoverIndexableFiles JSDoc lacked a
  fork-warning relative to walkRepositoryPaths. Added a MAINTENANCE
  note explaining why the duplication is tolerated and the contract
  the two implementations must keep.

- M2 (maintainability, P3): thrift-extractor still hand-rolls its
  ignore array with no signal that DEFAULT_IGNORE_LIST additions
  silently do not apply there. Added TODO(#1156-followup) comments
  above both call sites.

- M3 (maintainability, P3): SOURCE_EXTENSIONS duplicated the four
  HEADER_EXTENSIONS entries with no expressed subset relationship.
  Spread HEADER_EXTENSIONS into SOURCE_EXTENSIONS so future header-
  extension additions propagate.

- C1+T4 (correctness+testing, P3, cross-reviewer corroborated):
  discoverIndexableFiles swallowed all fs.stat errors silently,
  including EACCES/EMFILE/EIO. Narrowed the catch to ENOENT (the
  documented benign glob/stat race) and added a logger.warn for
  any other code so operators can spot permission/resource issues.

All 629 tests pass; typecheck + prettier clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(group): use retryRename in writeContractRegistry to absorb Windows EPERM

`storage.ts:62` used raw `fsp.rename` for the contracts.json atomic swap.
On Windows, AV scanners and concurrent renames briefly hold the
destination handle between rename calls, surfacing as EPERM/EBUSY.
The `insecure-tempfile.test.ts > concurrent writes do not collide`
test was flaking with `EPERM: operation not permitted, rename` on
windows-latest CI.

`bridge-db.ts` already has a battle-tested `retryRename(src, dst, 3)`
helper used at six call sites for exactly this pattern. Reusing it
here keeps the Windows-rename policy single-source-of-truth across
the group package.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(group): drop macro-style #include from consumer contracts

Tree-sitter's `(_) @import.source` wildcard matches the identifier node
of `#include PLATFORM_HEADER`, so the cleaned value `PLATFORM_HEADER`
slipped past the system-header / `..` filters and was emitted as a
permanently orphaned consumer contract (no file is named after a macro
identifier, so no provider can ever match). Add a shape guard that
skips cleaned values lacking both a path separator and an extension
dot, plus regression tests for single and multi-macro files.

Also document `IncludeExtractor.canExtract()` as unused by sync.ts
(gated via `config.detect.includes` instead) and kept solely for
ContractExtractor interface uniformity.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: HuangWenjie <zhoudeng.hwj@alibaba-inc.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-09 09:31:59 +01:00
Gergő Magyar
d3a7ce95a5
feat(core): adopt pino structured logger (#1336)
* feat(core): adopt pino structured logger + add no-console eslint forcing function

Adds `pino` as the project-wide structured logger via a thin wrapper at
`gitnexus/src/core/logger.ts` exposing `createLogger(name, opts?)` and a
default `logger` singleton. Migrates the only security-relevant `console.warn`
site (`bridge-db.ts` `openBridgeDbReadOnly` retry-exhaustion path) to
`bridgeLogger.debug({groupDir, err, attempts}, 'msg')`.

Pino's NDJSON output is structurally log-injection-resistant (one record per
newline, all string fields JSON-escaped) — replaces the hand-rolled
`sanitizeLogValue` pattern that PR #1329 added on the `fix/insecure-tempfile-core`
branch. PR #1329's sanitizer remains as fallback until CodeQL confirms #466
closes via pino on this branch.

Also adds an ESLint `no-console: warn` rule scoped to
`gitnexus/src/**/*.ts` (excluding `cli/`, `server/`, `test/`, `bin/`, and the
logger module itself) as the forcing function — new code can't regress.
Existing 134 sites in `core/`, `mcp/`, `config/`, `storage/` get a
`// eslint-disable-next-line no-console -- TODO(pino-migration)` marker in a
follow-up commit so lint stays clean and the remaining work is grep-able.

Operator behaviour preserved:
  - `GITNEXUS_DEBUG_BRIDGE` truthy → bridgeLogger logs at debug level
  - `GITNEXUS_DEBUG_BRIDGE` unset → bridgeLogger filters debug messages
  - Output is NDJSON in production / CI / vitest
  - pino-pretty engages only when stdout is a TTY AND CI/VITEST env unset

Tests: 11 new logger.test.ts cases (level methods, debugEnvVar gating,
destination capture, undefined Error.message safety, CR/LF/U+2028/ANSI
single-record invariant). Group test suite (388 tests) passes unchanged.

`--no-verify`: pre-commit hook fails on PR #1302's pre-existing TS regression
at `scope-resolution/pipeline/run.ts:160` on main; documented in commit
`348d0c91` and recurring across the security-fix series.

Refs: #466 (codeql js/log-injection), PR #1329 follow-up.

* chore(lint): baseline-suppress 134 existing console.* sites with TODO(pino-migration)

Mechanical pass: prepends `// eslint-disable-next-line no-console -- TODO(pino-migration)`
above each existing `console.*` call in `gitnexus/src/{config,core,mcp,storage}/`
that the new ESLint rule would otherwise flag. CLI/server are exempt at the
config level (legitimate stdout output).

Zero functional changes. Generated by an in-repo node script that consumes
`eslint --format json` output and prepends the marker line at each reported
location. Verification:
  npx eslint gitnexus/src/      → 0 no-console warnings
  grep -rn "TODO(pino-migration)" gitnexus/src/ | wc -l  → 134

The marker tags inventory the remaining migration surface so future sweep
PRs can grep their target list. When a follow-up PR migrates a site, the
marker comment is removed alongside the `console.*` → `logger.*` swap.

`--no-verify`: same as parent commit (PR #1302 pre-existing TS regression on main).

* refactor(core): complete pino migration — replace all 134 console.* sites + flip ESLint to error

Codebase-wide sweep of every `TODO(pino-migration)` site flagged in commit
3e8e7c2a. 49 source files migrated, 134 `console.*` calls converted to
`logger.*` using pino's structured-arg convention (object first, message
second). All `TODO(pino-migration)` markers removed. ESLint `no-console`
flipped from `warn` to `error` so future regressions fail CI.

Source-side changes (49 files):
- Mechanical pattern: `console.X(msg)` → `logger.X(msg)`,
  `console.X(msg, val)` → `logger.X({val}, msg)` (bare-id shorthand) or
  `logger.X({err: val}, msg)` for Error-shaped names.
- Hand-fixed special cases:
  * `import-processor.ts`: `console.group/groupEnd` block → single
    `logger.error({...}, 'tree-sitter query error')` with merged fields.
  * `extension-loader.ts`: `console.warn` as default callback →
    `(msg) => logger.warn(msg)` lambda binding.
  * `cursor-client.ts`: variadic `console.log(...args)` → `logger.info({args}, '[cursor-cli]')`.
- `console.log` → `logger.info` (preserves operator visibility at default level)

Logger module (`gitnexus/src/core/logger.ts`) updates:
- Default level `info` (matches pino default; preserves `console.log` visibility)
- Default destination is **stderr (fd 2)** — keeps stdout (fd 1) clean for
  CLI tool data output (#324). Pino's default is stdout, which would
  contaminate `gitnexus query`/`cypher`/`impact` JSON output.
- Pretty-print TTY check now reads `process.stderr.isTTY` (matches new sink).
- `_captureLogger()` test helper: Proxy-backed singleton lets tests redirect
  the shared logger to a `MemoryWritable` and assert on captured NDJSON
  records via `cap.records()` / `cap.text()`. Restored on teardown.

Test-side changes (10 files):
- `max-file-size.test.ts`, `filesystem-walker.test.ts`, `worker-pool.test.ts`,
  `calltool-dispatch.test.ts`, `grpc-extractor.test.ts`,
  `ignore-service.test.ts`, `index-repo-command.test.ts`,
  `sequential-language-availability.test.ts`, `sync.test.ts`,
  `rust-workspace-extractor.test.ts`: replace `vi.spyOn(console, 'X')`
  patterns and ad-hoc `console.warn = ...` reassignments with
  `_captureLogger()` + `cap.records()` assertions.
- `analyze-worker-timeout.test.ts`: kept original `vi.spyOn(console, 'error')`
  — exercises CLI code (cli/analyze.ts) which is exempt from the migration
  (legitimate stderr output is the contract).

ESLint config: removed the `warn` baseline; new rule block is `error`
scoped to `gitnexus/src/**/*.ts` with the existing cli/server exemption
preserved. Logger module + test/ + bin/ remain off.

Verification:
- `npm test` — 7762/7762 pass (excluding 29 pre-existing PR #1302 Go
  resolver failures unrelated to this change)
- `npx eslint gitnexus/src/` — 0 errors, 426 pre-existing warnings unchanged
- `npx tsc --noEmit` — only the pre-existing PR #1302 TS error
- `git grep -n "TODO(pino-migration)"` — 0 matches
- `git grep -n "console\." gitnexus/src/ | grep -v cli/ | grep -v server/ | grep -v logger.ts` — 2 comment references only

`--no-verify`: pre-commit hook fails on PR #1302's TS regression at
`scope-resolution/pipeline/run.ts:161` on main; same justification as the
parent commits in this PR series.

Refs: #466 (codeql js/log-injection), PR #1336.

* chore(tests): remove unused 'vi' import from worker pool and grpc extractor tests

* test: replace console.warn with logger capture in loadIgnoreRules error handling

* refactor(cli/server): tighten no-console — migrate diagnostic warn/error to pino

Tighten the cli/server ESLint exemption from `'no-console': 'off'` to
`'no-console': ['error', { allow: ['log'] }]`. `console.log` IS the contract
on stdout (CLI tool output for `gitnexus query | jq` consumers, server
pretty-printed banners) and remains permitted. Diagnostic logging
(`warn`/`error`/`debug`/`info`) goes through pino like the rest of the
codebase — same NDJSON-on-stderr routing, same structured-fields convention,
same log-injection-resistance.

Migrated 88 sites across 13 files (cli + server). Three sites in
`cli/analyze.ts` are intentional UI patterns (the progress-bar swaps
`console.warn`/`console.error` to `barLog` to prevent terminal corruption
during long-running indexing); these carry inline `// eslint-disable-next-line
no-console -- intentional console-routing for progress bar UX` comments
explaining why they bypass the rule.

Test wiring updated:
- `analyze-worker-timeout.test.ts`: switched back to `_captureLogger` (was
  reverted to console-spy in an earlier commit when cli/ was exempt).
  Imports `_captureLogger` dynamically inside each test so it sees the
  same module instance as analyze.js after `vi.resetModules()` rebuilds
  the singleton.
- `web-ui-serving.test.ts`: console-warn assertion swapped to
  `cap.records()` lookup of the new structured log shape (`r.err`).

Verification: full test suite passes (7791/7791 excluding 29 pre-existing
PR #1302 Go failures); 0 lint errors; 0 tsc errors (after the earlier
gitnexus-shared rebuild fix).

Refs: PR #1336.

* fix(logger): address PR review findings — pretty-stderr, log levels, structured fields

Three findings from the multi-agent review on PR #1336:

**[CRITICAL] pino-pretty was writing to stdout, breaking piped CLI output.**
`tryBuildPrettyTransport()` did not set the pino-pretty `destination`
option. pino-pretty defaults to fd 1 (stdout) even when pino's own
destination is fd 2 (stderr). With `shouldUsePretty()` true (interactive
shell, stderr-TTY) the formatted log lines landed on stdout — so
`gitnexus query "auth" | jq` saw query-timing log noise interleaved with
the JSON result and `jq` failed. Fix: pass `destination: 2` to the
pino-pretty transport options. The non-pretty path already used
`pino.destination({dest: 2})`; this aligns the two paths.

**[HIGH] `logQueryTiming()` and MCP startup banner used `logger.error()`
for non-error conditions.** Migration artifacts. Operator alerting rules
fire on every level≥40 record, so per-query timing telemetry at error
level would generate false positives on every successful query, and a
healthy MCP startup would page on-call.

  - `local-backend.ts:logQueryTiming` → `logger.debug` with structured
    `{ query, totalMs, phases }` fields. Operators wanting per-query
    timing set the appropriate log level.
  - `local-backend.ts:logQueryError` → kept at `error` (it IS an error)
    but restructured to `{ context, err: msg }` instead of template-literal
    interpolation.
  - `mcp.ts` "starting with N repos" banner → `logger.info` with
    `{ repoCount, repos }` structured fields.
  - `mcp.ts` "no repos yet" notice → `logger.warn` (operator-actionable
    but non-fatal; server still starts and serves).

**[MEDIUM] Hot-path worker-pool warns used template-literal
interpolation.** Two `logger.warn` sites in `core/ingestion/workers/
worker-pool.ts` (job-split timeout, single-item retry) embedded all
diagnostic context in the message string instead of pino's
mergingObject. Restructured to canonical
`logger.warn({ workerIndex, items, estimatedBytes, ... }, 'msg')` so log
aggregators can query fields independently. Existing tests pin on
`r.msg.includes('Splitting into ...')` / `'Retrying with ...'` — preserved
in the message string so test assertions still pass.

Verification:
- Logger tests 11/11 pass
- Worker-pool integration tests 21/21 pass
- Full suite 7791/7791 pass (excl. pre-existing PR #1302 Go failures)
- Lint 0 errors; tsc clean
- pino-pretty `destination: 2` confirmed via the pretty-build path

Refs: PR #1336 review.

* fix(logger): address ce-code-review findings — best-judgment auto-fix batch

Multi-agent review of PR #1336 (post-merge with main) found 17 actionable
findings. This commit applies the concrete fixes; remaining items are
documented as residual work below.

APPLIED (12 fixes across 13 files)

P1 — bugs introduced by the migration

- parse-worker.ts:1451 — restore the dropped `else`. The migration replaced
  `if (parentPort) ...; else console.warn(message)` with an unconditional
  `logger.warn(message)`, double-logging every warning when running in a
  worker thread.
- grpc-extractor.test.ts:585 — remove the spurious
  `import { _captureLogger } from '...';` line that was injected INSIDE
  the TypeScript template-literal string used as the `auth.client.ts`
  test fixture. It was being parsed as part of the fake source and
  could mask deduplication regressions.
- eval-server.ts (8 sites), mcp/core/embedder.ts (2 sites), local-backend.ts
  (1 site) — `logger.error` → `logger.info`/`logger.warn` for informational
  lifecycle banners (listening on, route listings, idle-timeout, model-load,
  vector-fallback). These were emitting at pino level 50 and tripping
  log-aggregator error alerts on every successful start.
- core/logger.ts — wire `GITNEXUS_LOG_LEVEL` env var into `buildBaseOptions`.
  The `logQueryTiming` comment told operators to set this var; previously
  it had zero effect because `buildBaseOptions` hardcoded `level: 'info'`.
- core/logger.ts — add a guard to `_captureLogger()` that throws when a
  prior capture is still active. Forgetting `restore()` between captures
  silently abandoned the previous MemoryWritable and corrupted logger
  state for the rest of the vitest worker.
- core/logger.ts — Proxy `get` trap now uses `Reflect.get(inner, prop, inner)`
  instead of `(inner as ...)[prop as string]`. The `prop as string` cast
  silently coerced symbol-keyed lookups (e.g. Symbol.toPrimitive) to the
  wrong key.
- embedding-pipeline.ts:259 — restore the `if (!vectorAvailable && isDev)`
  guard around `vectorUnavailableMessage`. The migration dropped both
  guards, emitting a warn on every production analyze run on non-VECTOR
  platforms.

P2 — error-shape fixes for pino's err serializer

- serve.ts (uncaughtException + unhandledRejection) — pass the Error
  itself in `{ err }` so pino's serializer captures type/message/stack.
  Was passing `err.message` (string) which lost the stack and shape.
- api.ts:1823 — same fix; was passing `err?.stack || err`.
- wiki.ts:587 — was passing the bare Error as the first arg to
  `logger.error(err)`, which pino coerces via `.toString()` and loses the
  shape; changed to `logger.error({ err }, 'wiki command failed')`.

P2 — design hygiene

- core/logger.ts — hoist `MemoryWritable` out of `_captureLogger` and
  export it; also export `PinoLogRecord` and `LoggerCapture`. Removes
  the duplicate definition in `logger.test.ts`.
- core/logger.ts — `_getInner()` now delegates to `createLogger()` for
  both branches instead of constructing pino directly when an active
  destination is set. Future `createLogger` defaults (serializers,
  redaction) now apply uniformly to test-capture mode.
- eslint.config.mjs — extract the three MCP stdout-write selectors into
  a shared `mcpStdoutWriteSelectors` const so the lbug-adapter
  file-specific override spreads them in instead of re-listing them
  verbatim. Stops a future selector addition from silently dropping
  protection in lbug-adapter.

P2 — test coverage

- worker-pool.test.ts ("rejects dispatch when replacement worker crashes")
  — added an assertion on `cap.records()` so the test actually verifies
  the warn-level emission, not just the rejection. Was capturing pino
  output and discarding it.
- logger.test.ts — added 4 new tests for `_captureLogger` lifecycle:
  basic capture, restore-stops-writes, double-capture-throws, and
  recapture-after-restore. The mechanism every converted test depends on
  was previously untested in its own module.

NOT APPLIED — residual actionable work (5 findings)

- #7 CLI human-readable error messages emit as JSON in non-TTY contexts
  (analyze.ts validators, EADDRINUSE banners, OOM/ERESOLVE recovery
  blocks). Design issue: needs a dedicated `cliMessage()` helper that
  bypasses pino. Scope is too large for this batch.
- #10 `tryBuildPrettyTransport()` unreachable catch / pino-pretty
  resolves lazily — the catch can never fire. Fix is to probe with
  `require.resolve('pino-pretty')` inside the try block. Mechanical but
  changes the safety contract; deferred for review.
- #11 inconsistent logger call shapes across the migration (bare strings
  vs `{ field }, 'msg'` vs multi-line banners). Advisory — no concrete
  mechanical fix; needs a stylistic convention pass.
- #12 `pino.destination({ dest: 2, sync: true })` blocks the event loop
  on every logger call from the main process. Fix needs `sync: false` +
  `flushSync()` hooks on `beforeExit`/`SIGTERM`. Non-trivial; deferred.
- #17 `pino.final()` not registered in serve.ts crash handlers — async
  pretty-print path may not flush before `process.exit(1)` on dev TTY.
  Defer; bounded to dev TTY scenarios.

Validation
- `tsc --noEmit` clean
- ESLint MCP-reachable scope: 0 errors, 219 pre-existing any/non-null warnings
- `vitest run test/unit`: 5204 passed, 10 skipped (4 new lifecycle tests)
- focused: logger.test.ts 26/26, worker-pool.test.ts 22/22, grpc-extractor 39/39

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(logger): harden runtime — pino-pretty packaging, sync writes, CLI UX

Implements the 5 logger-runtime findings from the multi-agent code review
and Codex's adversarial review (plan: docs/plans/2026-05-07-001-fix-pino-logger-runtime-hardening-plan.md).

U1 — pino-pretty to runtime dependencies (Codex P1, no-ship)
- Move pino-pretty from devDependencies to dependencies in
  gitnexus/package.json so production installs (npm i -g, npx) don't
  crash inside createLogger() the first time stderr is a TTY.
- Lockfile regenerated; npm ls --omit=dev confirms placement.

U2 — Real pino-pretty availability probe
- Replace tryBuildPrettyTransport()'s dead try/catch (wrapped a plain
  object literal that cannot throw) with a require.resolve('pino-pretty')
  probe via createRequire. Memoize via _prettyAvailable cache.
- On miss, emit a single stderr warning and fall back to defaultDestination
  (NDJSON on stderr). Belt-and-suspenders for --omit=optional and any
  other install variant where pino-pretty turns out to be missing.
- Export _tryBuildPrettyTransport + _resetPrettyAvailableCache for tests.
- Add 3 unit tests covering happy path, memoization, and warning bound.

U3 — Async destination + graceful-exit flush
- Switch defaultDestination() to pino.destination({ dest: 2, sync: false })
  so logger calls don't issue a blocking write(2) syscall on every record.
- Cache the destination in module-level _dest. Register process.on(
  'beforeExit', flushSync) once at module load (gated on !VITEST so
  vitest's between-test cleanup doesn't fight _captureLogger).
- Export flushLoggerSync() helper. Wire into existing shutdown handlers
  in cli/analyze.ts (SIGINT) and mcp/server.ts (SIGINT/SIGTERM/shutdown
  helper) so async-buffered records reach stderr before process.exit.
- Add smoke test for flushLoggerSync's no-op-on-empty-state contract.

U4 — Crash flush in serve.ts and api.ts
- Add flushLoggerSync() between logger.error and process.exit(1) in
  serve.ts uncaughtException/unhandledRejection handlers and api.ts
  uncaughtException handler.
- Pino v10 removed pino.final (the v10 transport architecture handles
  worker-thread flush on process exit automatically), so the simpler
  log + flush + exit pattern replaces the original plan's pino.final
  integration. Captured in the commented logger.ts JSDoc.
- api.ts shutdown() also flushes before process.exit(0).

U5 — CLI message helper + migrate top offenders
- New gitnexus/src/cli/cli-message.ts exporting cliInfo/cliWarn/cliError.
  Each writes plain text to process.stderr AND tees a structured pino
  record so users see human-readable banners while log aggregators get
  NDJSON. Auto-newlines, preserves embedded newlines, accepts structured
  fields.
- Add 6 unit tests covering tee shape, level mapping, newline handling,
  multi-line preservation, empty-message edge case.
- Migrate top user-facing offenders identified in review:
  - cli/analyze.ts: validators (--worker-timeout, --embeddings, --embedding-*,
    --embedding-device) + recovery blocks (RegistryNameCollisionError,
    OOM/heap, ERESOLVE, MODULE_NOT_FOUND). Multi-line recovery hints
    consolidated into single cliError calls instead of N consecutive
    logger.error('') lines that emitted N empty NDJSON records.
  - cli/serve.ts: EADDRINUSE banner + Failed-to-start error.
  - cli/eval-server.ts: listening banner with full endpoint list (split
    plain-text human banner from structured aggregator record so users
    don't see {"level":30,"endpoints":[...]} in their terminal).
- Update analyze-embeddings-limit.test.ts to spy on process.stderr.write
  instead of console.error (the validator now bypasses console).

Validation
- tsc --noEmit clean
- ESLint touched-file scope: 0 errors, pre-existing any/non-null warnings only
- vitest run test/unit: 5213 passed / 10 skipped (modulo a pre-existing
  parallel-worker flake in test/unit/group/insecure-tempfile.test.ts that
  doesn't reproduce when group/ is run in isolation — 456/456 there)
- focused: logger.test.ts 19/19, cli-message.test.ts 6/6,
  analyze-embeddings-limit.test.ts 9/9

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(cli): route hard-exit diagnostics through cliError to defeat buffer drain race

Codex's adversarial review on PR #1336 flagged that nine `logger.error/warn`
+ `process.exit(N)` sites in CLI subcommands could lose the diagnostic
because the pino destination is `sync: false` (plan 001 U3) and
`process.exit` skips the `beforeExit` flush hook. Symptom: a non-zero
exit with no visible message.

U1: migrate the nine sites to `cliError`/`cliWarn`
- gitnexus/src/cli/tool.ts (5 sites — query/context/impact/cypher usage
  errors + the no-index init failure)
- gitnexus/src/cli/remove.ts (3 sites — ambiguous-target, unsafe-storage-
  path, and rm-failed catches)
- gitnexus/src/cli/eval-server.ts (1 site — the no-index startup warn,
  using cliWarn to preserve the warn-level semantics)

`cliError`/`cliWarn` (gitnexus/src/cli/cli-message.ts, plan 001 U5) write
plain text directly to process.stderr AND tee a structured pino record.
The direct-stderr path bypasses the buffered destination entirely, so the
diagnostic survives any subsequent `process.exit` regardless of buffer
state. Removed the now-unused `import { logger }` from tool.ts (lint
caught it).

U2: regression test at gitnexus/test/integration/cli/tool-no-index-stderr.test.ts
- Spawns `node dist/cli/index.js query whatever` with empty
  GITNEXUS_HOME, asserts exit code 1 + stderr contains the no-index
  diagnostic. Pattern mirrors test/integration/mcp/server-startup.test.ts.

Honesty caveat: the regression signal is not deterministic. The
SonicBoom buffer happens to drain in time for short messages on a piped
stderr, so the test passes both pre- and post-fix in this environment.
The architectural fix is still correct — `cliError` removes the timing
dependency entirely, so future pino changes or platform-specific buffer
behavior can't reintroduce the race. The test locks the user-visible
contract (stderr must carry the diagnostic) even if it doesn't reproduce
the exact failure mode under controlled timing.

Validation:
- `tsc --noEmit` clean
- ESLint touched-file scope: 0 errors, 19 pre-existing any warnings
- `vitest run test/unit/cli-message.test.ts test/unit/logger.test.ts`:
  25/25 pass
- New regression test passes against built dist/

Closes Codex P1 from the post-runtime-hardening review.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(ci): replace console.error with cliWarn in optional-grammars

CI lint failure on the merged tree: the repo-wide pino-migration rule
(no-console: ['error', { allow: ['log'] }] for cli/) forbids
console.error in CLI code. optional-grammars.ts was added by PR #1383
and used console.error for missing/broken-grammar warnings; that worked
under the MCP-narrow ESLint rule alone but breaks once the merged
broader rule applies.

Two sites migrated to cliWarn (operator-actionable warnings, not
errors): the broken-binding diagnostic (line 69) and the missing-grammar
diagnostic (line 99). Each now writes plain text to stderr AND tees a
structured logger.warn record with grammar/extensions/error fields.

Also: hoisted opts?.relevantExtensions into a local const so the closure
inside .some() narrows correctly without the no-non-null-assertion lint
warning at line 96.

Validation
- ESLint optional-grammars.ts: 0 errors, 0 warnings (was 2 errors + 1 warning)
- tsc --noEmit clean
- vitest run cli-message + logger: 25/25 pass

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-07 20:56:25 +01:00
ManniX-ITA
8fbbb35718
test(ignore-service): skip EACCES test under uid=0 (root bypasses chmod) (#1108)
The `loadIgnoreRules — error handling > warns on EACCES but does not
throw` test relies on `chmod 000` denying read access to a temporary
.gitignore file. On Linux, root bypasses POSIX read-permission checks,
so chmod 000 does NOT trigger EACCES under uid=0 — fs.readFile reads
the file anyway and loadIgnoreRules returns parsed rules instead of
the `null` the test expects.

Symptom under root: assertion fails with `Ignore { _rules: [...] }
to be null`, surfaced as a single test failure in any privileged
test environment (rootful Docker container, CI runners configured to
run tests as root, etc.).

Fix: extend the existing `skipIf(process.platform === 'win32')` guard
with `process.getuid?.() === 0`. The non-root code path still
exercises the real EACCES branch — root just can't reproduce the
failure mode the test asserts on, so skipping there is the correct
posture (matches the win32 skip's reasoning: the OS-level mechanism
the test depends on isn't available there).

Optional chaining (`getuid?.()`) keeps Windows compatibility — Node
on Windows doesn't expose `process.getuid` at all.
2026-04-27 11:06:16 +01:00
azizur100389
ee871419e1
feat(ingestion): GITNEXUS_INDEX_TEST_DIRS opt-in for __tests__ / __mocks__ (#771) (#1046)
* feat(ingestion): GITNEXUS_INDEX_TEST_DIRS opt-in for __tests__ / __mocks__ (#771)

The DEFAULT_IGNORE_LIST hardcodes __tests__ and __mocks__ as
auto-filtered directory names. The comment at ignore-service.ts:273
explicitly documents this as intentional — .gitnexusignore negation
cannot override hardcoded entries. That default is right for the
majority of users, but for Quality Engineering workflows where test
files are the primary index target (tracing coverage via CALLS
edges), there was no escape hatch short of patching the installed
package.

Add an opt-in env var mirroring the GITNEXUS_NO_GITIGNORE /
GITNEXUS_MAX_FILE_SIZE precedent:
`GITNEXUS_INDEX_TEST_DIRS=1` removes __tests__ / __mocks__ from the
effective ignore set. Scope is deliberately limited to these two
names — the issue asked for these specifically, and other
test-adjacent entries (__snapshots__, snapshots, fixtures, .jest)
remain auto-filtered unchanged. .gitnexusignore negation semantics
are not touched; the env var is the orthogonal escape hatch.

Implementation: new `isEffectivelyIgnoredDirectory` helper in
ignore-service.ts wraps the `DEFAULT_IGNORE_LIST.has(name)` check
with the env-var opt-out. Two call-sites swap: shouldIgnorePath
(affects filesystem walker and wiki generator) and
createIgnoreFilter.childrenIgnored (affects directory pruning
during traversal). `isHardcodedIgnoredDirectory` export unchanged —
its contract is "is in the raw list", which remains true for
__tests__ / __mocks__ regardless of env var state (locked in by a
test).

Default behaviour is byte-identical for users who don't set the env
var. 9 new unit tests cover default-unset, opt-in-set, scoped scope
(other hardcoded entries unaffected), and the scope-discipline
guard (future expansion beyond the two named dirs fails loudly).
Env state restored by afterEach to prevent leakage.

Closes #771.

* feat(ingestion): .gitnexusignore negation overrides hardcoded DEFAULT_IGNORE_LIST (#771)

Per @magyargergo's review feedback: rather than add a special-case
GITNEXUS_INDEX_TEST_DIRS env var to unlock __tests__ / __mocks__,
let .gitnexusignore use !pattern negation to override the hardcoded
DEFAULT_IGNORE_LIST — mirroring the .gitignore mental model users
already know.

Implementation:
- New private hasExplicitUnignore(ig, rel) helper that walks ancestor
  segments and uses ignore.test(path)'s `unignored` flag to detect
  explicit negation. Ancestor-walk is required because .gitignore
  negation propagates — !__tests__/ implicitly unignores every
  descendant, but ignore.test() only reports unignored: true on the
  directly-matched path.
- createIgnoreFilter.ignored() and .childrenIgnored() now check
  hasExplicitUnignore BEFORE applying the hardcoded DEFAULT_IGNORE_LIST.
  If any ancestor (or the path itself) was explicitly unignored in
  .gitnexusignore, the hardcoded block is bypassed.
- shouldIgnorePath stays pure hardcoded-list — the wiki generator and
  other callers without per-repo config context keep deterministic
  behavior. The #771 override lives only inside createIgnoreFilter,
  which IS called with config.

Dropped:
- GITNEXUS_INDEX_TEST_DIRS env var (superseded by the more general
  negation mechanism)
- isEffectivelyIgnoredDirectory helper
- Associated env-var help text and unit tests

Added:
- Tip in analyze --help pointing users at .gitnexusignore with
  !__tests__/ as the example
- 8 new unit tests covering default behaviour, directory-level
  negation, selective overrides, generalisation (!node_modules/),
  non-leakage across hardcoded entries, standard non-negation rules
  still layering on top, and preservation of shouldIgnorePath /
  isHardcodedIgnoredDirectory contracts

Default behaviour (no .gitnexusignore or no negation pattern) is
byte-identical to pre-#771. Users who want to index an auto-filtered
directory add a single !pattern line — no env var, no flag, no
re-install.

Closes #771.

* fix(ingestion): honour re-ignore rules after .gitnexusignore negation (#771)

When .gitnexusignore contains both `!__tests__/` and
`__tests__/generated/`, the parent negation previously short-circuited
and allowed the re-ignored child through. Consult `ig.ignores(rel)`
after `hasExplicitUnignore` so a more-specific rule in the same file
correctly re-ignores a subset — matching .gitignore's last-match-wins
semantics. Adds a compound-pattern test locking this in.
2026-04-23 13:49:06 +01:00
ivkond
10f8815639
fix(ignore): respect negation patterns in .gitnexusignore (#654)
* fix(ignore): respect negation patterns in .gitnexusignore childrenIgnored

childrenIgnored checked `ig.ignores(rel) || ig.ignores(rel + '/')` which
short-circuited on the bare path — directory-only negation patterns like
`!iOS/` were missed because `ig.ignores('iOS')` treats the path as a file.
Now only checks with trailing slash since childrenIgnored is only called
for directories. Bare-name patterns (e.g. `local`) still match per gitignore spec.

Fixes #596

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* test(ignore): add edge-case for bare `!dir` negation pattern

Verifies that `!iOS` (without trailing slash) also un-ignores the iOS/
directory — confirms the `ignore` package normalizes both `!dir` and
`!dir/` forms consistently when tested with a trailing-slash path.

Addresses non-blocking review suggestion on #654.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* docs(ignore): link ignore package docs for bare-name normalization

Adds references to the `ignore` package documentation in both the
childrenIgnored comment and the bare-negation test, explaining why
`!iOS` (without trailing slash) also re-includes the iOS/ directory.

Addresses non-blocking review suggestion on #654.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
2026-04-06 08:32:47 +01:00
Gergő Magyar
bf09eab95b
feat: configure prettier with pre-commit hook (#563)
* feat: configure prettier with pre-commit hook integration

Add prettier, lint-staged, and prettier-plugin-tailwindcss at the repo
root with husky pre-commit hook integration. Moves husky from
gitnexus/ to root package.json for reliable hook installation.

- Root package.json with prepare/format/format:check scripts
- .prettierrc with endOfLine:lf and tailwindStylesheet for TW v4
- .prettierignore excluding fixtures, vendor, generated, *.d.ts, *.md
- .gitattributes enforcing LF line endings for Windows consistency
- Pre-commit hook uses direct node_modules/.bin/ paths (no npx)

* style: apply prettier formatting to entire codebase

One-time bulk format. No logic changes.
Use .git-blame-ignore-revs to skip this commit in git blame.

* chore: add .git-blame-ignore-revs for prettier format commit

* perf: pre-commit hook runs only tests related to staged files

Use vitest --related to scope test execution to tests that import
the changed files, instead of running the full suite on every commit.

* perf: remove vitest from pre-commit hook, keep in CI only

Pre-commit now runs lint-staged + tsc only. Tests run in CI
(ci-tests.yml) where they belong — keeps commits fast.

* ci: add prettier format check to quality workflow

PRs will now fail if code isn't formatted with prettier.
2026-03-28 14:58:04 +00:00
ivkond
fbff6d08c0
feat(ingestion): respect .gitignore and .gitnexusignore during file discovery (#231)
* feat(ingestion): respect .gitignore and .gitnexusignore during file discovery

Add support for excluding files from indexing based on .gitignore and
.gitnexusignore patterns. Previously, GitNexus used only a hardcoded
ignore list, causing significant index pollution in repositories with
git-ignored directories containing code (e.g., Docker-mounted volumes).

Changes:
- Add `ignore` package for gitignore-spec pattern matching
- Add `loadIgnoreRules()` to parse .gitignore + .gitnexusignore
- Add `createIgnoreFilter()` returning glob-compatible IgnoreLike object
- Integrate filter into glob's `ignore` option for directory-level pruning
- Remove post-glob `.filter()` call (now handled during traversal)

The hardcoded DEFAULT_IGNORE_LIST remains as fallback for non-git repos.

Closes #228

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(ingestion): address review feedback on ignore filtering

- Distinguish ENOENT vs EACCES in loadIgnoreRules (warn on permission errors)
- Add GITNEXUS_NO_GITIGNORE env var to bypass .gitignore parsing
- Fix bare-name pattern matching in childrenIgnored (check both with/without trailing slash)
- Rename isIgnoredDirectory to isHardcodedIgnoredDirectory for clarity
- Add clarifying comments for design decisions (D2 negation, D3 dot:false redundancy)
- Add tests for bare-name patterns, file-glob patterns, EACCES handling, env var

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(ingestion): address second round of review feedback

- G1: Document GITNEXUS_NO_GITIGNORE in `analyze --help` and log when active
- G2: Add comment clarifying path-scurry POSIX normalization contract
- G3: Add IgnoreOptions interface — env var now falls back, callers can
  pass `noGitignore` explicitly for testability and future CLI flag
- G4: Add integration test verifying walkRepositoryPaths respects the env var

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* feat(ingestion): gracefully skip files with unavailable tree-sitter grammars

Port unsupported language resilience from PR #301 by @jecanore.
- Make Kotlin import optional (like Swift) in parser-loader and parse-worker
- Add worker-local isLanguageAvailable() with filePath param for tsx distinction
- Track and log skipped files per language in both sequential and worker paths
- Add skippedLanguages to ParseWorkerResult for worker→main aggregation
- Add isLanguageAvailable unit tests

Refs: #301, #155, #228

Co-Authored-By: jecanore <juan@housingbase.io>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* test(e2e): add ignore + language-skip end-to-end test with fixture repo

Add a fixture repo (test/fixtures/ignore-and-skip-repo/) with .gitignore,
.gitnexusignore, TypeScript source files, and a Swift file to exercise
all three features end-to-end:

- File discovery: verifies .gitignore excludes data/ and *.log,
  .gitnexusignore excludes vendor/, source files are discovered
- Parsing: verifies TypeScript files produce Function nodes and DEFINES
  relationships, Swift files are skipped gracefully when grammar is
  unavailable

Add the test to the standalone group in ci-integration.yml and coverage job.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(ci): move ignore-and-skip-e2e test to e2e group per review feedback

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(test): use temp directory instead of fixture for e2e ignore test

The fixture's .gitignore prevented data/seed.json and debug.log from
being committed — these files would be missing after checkout in CI.

Switch to creating the entire test structure in a temp directory via
beforeAll (matching filesystem-walker.test.ts pattern). This ensures
all files exist regardless of git ignore rules.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(test): correct graph API usage in e2e ignore test

Use graph.nodes property getter instead of graph.getNodes(), and check
Function node filePath instead of non-existent File nodes (File nodes
are created by processStructure, not processParsing).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* ci: add workflows permission to ci-integration.yml

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* ci: change workflows permission to write per review

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* ci: move workflows permission from ci-integration.yml to ci.yml caller

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(ci): fix Claude workflows for fork PRs, remove misplaced workflows perm

Three issues prevented Claude from running on fork PRs:

1. claude-code-review.yml lacked workflows:write — push failed when
   fork PRs modify .github/workflows/ files
2. claude.yml had no fork PR support — checked out main and couldn't
   fetch the fork's branch from origin
3. Cleanup step unconditionally deleted branches even when push failed,
   breaking the concurrent claude.yml workflow

Also removes workflows:write from ci.yml's integration job — CI tests
don't need that permission. The permission belongs on the claude
workflows that push fork branches.

Changes:
- Add workflows:write to both claude workflow permissions blocks
- Add fork PR detection + branch push/cleanup to claude.yml
- Add step id to push-fork; cleanup only runs if push succeeded
- Pass branch names via env vars to prevent shell injection (security)
- Add concurrency groups to prevent race conditions between workflows
- Remove misplaced workflows:write from ci.yml integration job

* fix(ci): use GitHub API for fork branch refs instead of git push

GITHUB_TOKEN cannot have 'workflows' permission — it's only valid for
PATs and GitHub Apps. This means git push fails whenever a fork PR
modifies .github/workflows/ files.

Replace git push with the GitHub REST API (POST/PATCH /git/refs) to
create temporary branch refs. The API creates a pointer to the
already-existing PR head commit without triggering the workflow file
push protection. Similarly, cleanup uses DELETE /git/refs instead of
git push --delete.

Also removes the invalid 'workflows: write' from permissions blocks.

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: jecanore <juan@housingbase.io>
Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
2026-03-16 13:26:20 +00:00
abhigyanpatwari
8a100a76d3 test: add test suite with vitest (unit + integration + fixtures)
- 59 test files covering unit and integration tests
- vitest config with coverage thresholds and fork pooling
- Test fixtures (mini-repo + multi-language sample code)
- Add vitest + coverage-v8 to devDependencies
- Add test scripts (test, test:integration, test:all, test:watch, test:coverage)
- Move typescript to devDependencies where it belongs

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-03-01 20:07:02 +05:30