GitNexus/gitnexus/test/integration
Gergő Magyar 14397dd4aa
feat(taint): intra-procedural taint analysis (#2083) (#2164)
* feat(taint): harvest occurrence-tagged call/member sites on StatementFacts (#2083 U1)

Worker-side site harvest in TsHarvester: call/new/member-read records with
dotted callee paths, receiver slots, per-argument occurrence tagging with
nested-site links, per-declarator resultDefs, spread/template/require-literal
markers. hasTaintSafeSites validation seam. The pdg parse-cache chunk-key
namespace is versioned (pdg:1 -> pdg:2) instead of a global SCHEMA_BUMP so
flag-off users keep warm caches; bench fingerprints re-baselined for the
three call-bearing scenarios (straight-line/dense-bindings byte-unchanged).

* feat(taint): built-in TS/JS source/sink/sanitizer model + site matcher (#2083 U2)

Typed spec (kind taxonomy; sanitizers carry neutralizes-kinds), the canonical
Express/Node model, and matchFunctionSites: ESM alias/namespace + require-
literal callee resolution, bare-name fallback restricted to true globals,
sanitizers module-or-global only (never user-shadowable by name), spread/
template arg-position rules, deterministic taintModelVersion.

* feat(taint): pure intra-procedural taint propagation engine (#2083 U3)

Two-rule model (statement-local + du-fact worklist) with per-taint
neutralized-kind exclusion sets: sanitizers exclude only the sink kinds
they neutralize (escape(req.body) suppresses res.send but still fires
db.query; exec(path.basename(t)) fires), intersection-over-paths so a
bypass occurrence keeps the taint live, kill locality on resultDefs,
propagate-through args+receiver with viaCall hops, one path per finding,
deterministic caps, coverage-gap statuses. Test-first: 38 scenarios on
real harvested CFGs.

* feat(taint): thread taint caps + model version through pdg config/meta (#2083 U5)

resolvePdgConfig gains maxTaintFindingsPerFunction (200), maxTaintHops (32),
and the taintModelVersion digest; RepoMeta.pdg + RunScopeResolutionInput
surfaces added. The key-union comparator trips full writeback on M2->M3
upgrade and on model-version change without --force (mode-flip tested).
No CLI flags or rc keys (programmatic parity with the other caps).

* feat(taint): in-phase taint emit with sparse TAINTED/SANITIZES edges (#2083 U4)

run.ts pdg window: match-first fast path (solver only when a function has
both a matched source and sink) -> computeReachingDefs with the shared RD
fact derivation -> computeTaintFlows -> per-finding TAINTED (versioned
hop-encoded reason via the shared path codec, statement-level occurrence
identity) + per-kill SANITIZES, dedup-before-budget, truncate-and-warn.
All emit counters surfaced (aggregate warn for gaps/drops, debug for
volume); PROF gains taint=. Flag-off golden untouched.

* feat(mcp): explain tool for persisted taint findings (#2083 U6)

Anchorless calls enumerate the sparse TAINTED table (bounded, deterministic,
limit-clamped); anchored calls (file or symbol via resolveSymbolCandidates)
return full decoded hop detail. sinkKind rides a version-1 codec header
(1;<kind>|hops — no other persisted channel exists; U4/U6 ship together).
RepoMeta.pdg probe yields a no-taint-layer note instead of an error.
TAINTED/SANITIZES pinned OUT of VALID_RELATION_TYPES (KTD9a negative-
membership tests); generators + canonical skill docs + mirrors updated.

* test(taint): acceptance fixture battery, snapshots, and bench gates (#2083 U7)

pdg-repo taint-cases fixtures complete the six plan shapes; committed
findings/kills snapshot via a shared pure-path harness that also feeds the
AE2 exact-equality assertion (stored TAINTED == pure-path findings, the
no-explosion gate). New taint-dense bench scenario with four --check gates:
per-function findings pinned AT the cap, absolute reason-byte + site-bytes
disk ceilings (the load-bearing R10 gate), zero-match pass < 0.5x match-
dense, N-linearity. Pre-existing scenario baselines untouched.

* refactor(taint): share one pointKey helper across propagate + emit (#2083 review)

Extract pointKey(ProgramPoint) to cfg/reaching-defs.ts (colon-separated,
matching the codebase block:stmt id convention) and import it in both
propagate.ts and emit.ts, replacing the two divergent locals (':' vs '.').
Edge-id material now uses the colon form; ids are in-memory only and no
test asserts the pointKey segment shape.

* fix(taint): discriminate taint state by source occurrence (#2083 review)

Two distinct sources flowing into one variable at one def point no longer
collapse to a single TAINTED edge: the taint-state key gains a root
source-occurrence discriminator ({point, siteIndex} — the same fields
recordFinding's identity uses, excluding kind). Def->use fact lookup keys
on the source-independent (binding, def-point) portion. Same-source
multi-path flows still share one state so their exclusion sets intersect
(the raw arm soundly wins); termination holds (finite keys, monotone
shrink, no cross-source ping-pong). Restores the KTD6 identity contract.

* fix(mcp): route dotted symbol names in explain to symbol resolution (#2083 review)

The fileish classifier matched any dotted name (UserController.create)
as a file via its extension-like suffix, so symbol resolution never ran
and the tool returned a silent empty file-anchored result. Tighten the
classifier to require a path separator or a real source extension (derived
from the resolver's EXTENSIONS list, multi-language), so dotted/bare names
route to resolveSymbolCandidates (found / ambiguous / not-found).

* fix(mcp): gate explain no-taint-layer note on taintModelVersion (#2083 review)

An M1/M2-era --pdg index has meta.pdg defined (BasicBlock/REACHING_DEF
recorded) but no taintModelVersion and zero TAINTED rows. The probe keyed
on generic meta.pdg presence, so explain returned the generic empty note
instead of the actionable 'no taint layer — run analyze' hint. Gate on
meta.pdg?.taintModelVersion (the field M3 stamps) so an M2-era index gets
the layer hint; a taint-stamped index with no findings still gets the
generic note.

* fix(taint): sequence-expression value flows only the final operand (#2083 review)

A comma expression in value position (exec((log(x), 'safe'))) default-
descended, fanning every operand's occurrences into the enclosing sink
argument — over-tainting exec's arg 0 with x. Add an explicit walkValue
case that records earlier operands' uses with occurrence fan-out suppressed
(new FactAccumulator.suppressOccurrences) and routes only the last operand
through the value path. Sites-layer only; defs/uses/mayDefs byte-identical
(cfg + reaching-defs snapshots unchanged).

* perf(taint): FIFO head-cursor worklist + dedup before chainHops (#2083 review)

Replace queue.shift() (O(N) dequeue) with a strict-FIFO head cursor plus
order-preserving prefix reclamation; FIFO is load-bearing because chainHops
reads the live taints map whose parent/source/viaCall are rewritten
order-sensitively on monotone shrink, so hop determinism is dequeue-order
contingent. Extract findingKey() and dedup-check before chainHops in the
justify branch — already-recorded identities discard their hop chain
(first write wins), so the ancestry walk was pure waste. The else kill
branch is untouched. Findings + hops byte-identical (snapshot unchanged).

* perf(taint): O(1) member-read dedup via composite-key set (#2083 review)

addMemberRead rescanned the whole per-statement sites array per call to
dedup by (object, property, parent) — O(n^2) on member-read-dense
statements. Track a composite-key Set alongside sites for O(1) dedup.
(The require-literal join is already O(sites) with a no-op body on
non-require sites, so no early-exit is needed there.) Behavior identical:
harvest + model-match + taint snapshots unchanged.

* refactor(taint): drop test-only export; source taint caps via emit.ts (#2083 review)

Remove the sanitizerNeutralizes export (its only consumers were two test
assertions — inlined to entry.neutralizes membership). Re-export the
DEFAULT_PDG_MAX_TAINT_* caps from emit.ts and point run.ts at emit.ts, so
the pipeline's taint dependency surface is the single orchestration module
rather than reaching into propagate.ts.

* test(taint): extract the shared TS CFG/taint test harness (#2083 review)

The parse/collectFunctions/cfgOf/cfgsOf/importsFor harness was copied
byte-for-byte across four suites (harvest, model-match, propagate,
taint-emit). Promote it to test/helpers/ts-cfg-harness.ts and import it.
site-safety/reaching-defs carry a structurally different inlined builder
and are left as-is. Pure extraction, no assertion changes.

* test(mcp): harden explain limit-rejection battery (#2083 review)

Add NaN, Infinity, -Infinity, and a numeric string to the out-of-bounds
limit cases — a regression fence over the interpolated LIMIT, confirming
the Number.isInteger guard rejects every non-integer/non-finite/string
input before it reaches the query.
2026-06-12 07:35:09 +01:00
..
cfg feat(taint): intra-procedural taint analysis (#2083) (#2164) 2026-06-12 07:35:09 +01:00
cli feat(core): adopt pino structured logger (#1336) 2026-05-07 20:56:25 +01:00
group feat: add IncludeExtractor for C++ cross-repo include tracking (group) (#1156) 2026-05-09 09:31:59 +01:00
mcp feat(mcp): paginate list_repos to avoid client token truncation (#2119) (#2120) 2026-06-09 19:59:54 +01:00
optional-grammars feat(install): toolchain-free tree-sitter via vendored prebuilds (#2113) 2026-06-09 18:16:24 +01:00
resolvers fix(cpp): suppress deleted overload winners (#2094) 2026-06-10 18:41:30 +01:00
analyze-heap-oom-e2e.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
analyze-wal-checkpoint-failure.test.ts fix(lbug): add WAL checkpoint-threshold control (#1772) 2026-05-22 14:46:49 +01:00
antigravity-hook-e2e.test.ts fix(hooks): silence MCP-owned-DB augment skip for strict hook runners (#1913) (#2134) 2026-06-10 09:09:41 +01:00
api-impact-e2e.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
api-query.test.ts fix: Use Ladybug native read-only enforcement and prepared statement execution for Cypher query paths (#1655) 2026-05-18 06:54:24 +01:00
ast-helpers-object-literal-binding.test.ts feat(ingestion): Link object literal methods to exported bindings (#1718) 2026-05-21 17:18:27 +01:00
augmentation.test.ts fix(augment): add CONTAINS fallback when FTS indexes unavailable (#1476) 2026-05-11 16:39:10 +01:00
basicblock-roundtrip.test.ts feat(ingestion): M0 — taint/PDG substrate (schema + seams + spikes) (#2080) (#2092) 2026-06-08 18:56:10 +01:00
c-cpp-typedef-legacy-parse.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
class-impact-all-languages.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
cli-e2e.test.ts test(cli): make cli-e2e read-only + eval-server tests robust under load (#2000) 2026-06-03 21:50:22 +01:00
cobol-pipeline-benchmark.test.ts refactor(ingestion): delete legacy call-resolution DAG + heritage processor (RING4-1, #942) (#2023) 2026-06-04 11:07:37 +01:00
context-typed-property.test.ts fix(csharp): include generic typed properties in context and impact (#1399) 2026-05-09 09:07:24 +01:00
cpp-adl-benchmark.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
cpp-pipeline-benchmark.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
cross-file-binding.test.ts fix(ingestion): classify Python class methods as Method (#1102) 2026-04-27 09:04:50 +01:00
csharp-pipeline-benchmark.test.ts fix(csharp): eliminate global-namespace typeBindings O(files²) OOM (#1871) (#1954) 2026-05-31 18:21:07 +01:00
csharp-scope-capture-tripwire.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
csv-pipeline.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
enrichment.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
expo-routes.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
fastapi-prefix-pipeline.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
filesystem-walker.test.ts fix(analyze): prevent cache-hit native workers from aborting (#1751) 2026-05-21 16:17:02 +01:00
go-multi-name-worker-metadata.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
go-pipeline-benchmark.test.ts fix(go): generic composite literal constructor inference (F33) (#1976) 2026-06-03 05:24:31 +01:00
grammar-introspection.test.ts feat(ingestion): tree-sitter node-type/field validation gate + remove dead literals (#1937) 2026-05-31 10:29:41 +01:00
grammar-literal-validation.test.ts feat(ingestion): tree-sitter node-type/field validation gate + remove dead literals (#1937) 2026-05-31 10:29:41 +01:00
has-method.test.ts feat(cpp): C/C++ MethodExtractor config with pure virtual detection (#617) 2026-04-01 18:07:11 +01:00
hooks-e2e.test.ts fix(hooks): resolve gitnexus on PATH with a pure-Node scan, all-OS (#1938) (#1980) 2026-06-03 03:19:49 +01:00
ignore-and-skip-e2e.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
impact-ambiguous-blast-radius.test.ts fix: stop impact()/route_map under-reporting blast radius (#2129, #1858, #1589/#1852) (#2136) 2026-06-10 11:25:48 +01:00
impact-epistemic-lower-bound.test.ts fix: stop impact()/route_map under-reporting blast radius (#2129, #1858, #1589/#1852) (#2136) 2026-06-10 11:25:48 +01:00
java-class-impact.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
js-array-method-callback-attribution.test.ts refactor(ingestion): delete legacy call-resolution DAG + heritage processor (RING4-1, #942) (#2023) 2026-06-04 11:07:37 +01:00
lbug-close-handle-release.test.ts fix(lbug): drain checkpoint result before close (#1506) 2026-05-12 14:03:45 +01:00
lbug-core-adapter.test.ts fix: make extension installs offline-first (#1161) 2026-05-29 20:04:41 +01:00
lbug-lock-retry.test.ts fix(lbug): robust Windows lock acquisition for CI integration tests (#1430) 2026-05-08 11:58:01 +01:00
lbug-non-ascii-path.test.ts fix(lbug): resolve non-ASCII paths for KuzuDB on Windows (#1811) (#1817) 2026-05-25 21:28:12 +01:00
lbug-open-retry.test.ts fix(lbug): robust Windows lock acquisition for CI integration tests (#1430) 2026-05-08 11:58:01 +01:00
lbug-orphan-sidecar-recovery.test.ts fix(lbug): Recover gitnexus analyze from orphan LadybugDB sidecars when main DB file is missing (#1622) 2026-05-16 11:45:32 +01:00
lbug-pool-stability.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
lbug-pool.test.ts fix(parse): correct worker-pool docs drift + surface worker-side stack on crash (#2068) (#2070) 2026-06-08 07:20:12 +01:00
lbug-readonly-init.test.ts fix(lbug): skip init lock and filesystem mutations for read-only opens (#1783) (#1784) 2026-05-24 08:05:27 +01:00
lbug-vector-extension.test.ts fix(embeddings): create VECTOR index via conn.query, not the prepared path (#2114) 2026-06-10 07:59:37 +01:00
literal-collectors.test.ts feat(ingestion): tree-sitter node-type/field validation gate + remove dead literals (#1937) 2026-05-31 10:29:41 +01:00
local-backend-calltool.test.ts fix: batch query enrichment, bake FTS extension into CLI image, add FTS memory repro (#2108) 2026-06-09 08:46:46 +01:00
local-backend.test.ts fix: Use Ladybug native read-only enforcement and prepared statement execution for Cypher query paths (#1655) 2026-05-18 06:54:24 +01:00
local-symbol-pruner-pipeline.test.ts perf(ingestion): prune inert local value symbols (#2065) 2026-06-07 14:47:51 +01:00
markdown-processor-crlf.test.ts fix(markdown): handle CRLF line endings in section heading parser (#1469) 2026-05-14 08:58:58 +01:00
multi-branch-analyze.test.ts feat: multi-branch indexing and branch-scoped querying (#2106) (#2137) 2026-06-10 10:24:40 +01:00
object-literal-method-exports.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
object-literal-owner-resolution.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
orm-dataflow.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
parse-impl-chunk-concurrency.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
parse-impl-clone-skip.test.ts fix(parse): survive non-cloneable worker results so large-repo analyze doesn't crash (#2112) (#2135) 2026-06-10 13:47:22 +01:00
parse-impl-env-reads.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
parse-impl-large-fixture.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
parse-impl-progress-monotonic.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
parse-impl-quarantine-cache-skip.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
parsing.test.ts feat(ingestion): tree-sitter node-type/field validation gate + remove dead literals (#1937) 2026-05-31 10:29:41 +01:00
php-pipeline-benchmark.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
php-scope-capture-tripwire.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
pipeline-graph-golden.test.ts fix(test): isolate cli-e2e from shared mini-repo fixture (#954) 2026-04-18 12:54:59 +01:00
pipeline.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
python-import-index-reuse.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
python-scope-capture-tripwire.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
qualified-class-lookups.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
query-compilation.test.ts [dart] Add call patterns for await, cascade, lambda, and widget-tree contexts (#801) 2026-04-13 11:21:11 +01:00
ruby-pipeline-benchmark.test.ts perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038) 2026-06-06 22:46:34 +01:00
ruby-scope-capture-tripwire.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
rust-pipeline-benchmark.test.ts feat(rust): Migrate Rust to scope-based resolution (RFC #909 Ring 3) (#1639) 2026-05-25 13:20:08 +01:00
rust-scope-capture-tripwire.test.ts perf(ingestion): linearize scope-capture across all languages + Python import resolution (O(n²)→O(n)) (#1918) 2026-05-30 19:44:22 +01:00
search-core.test.ts fix: Use Ladybug native read-only enforcement and prepared statement execution for Cypher query paths (#1655) 2026-05-18 06:54:24 +01:00
search-pool.test.ts fix(search): surface warning when FTS indexes are missing (#1418) 2026-05-08 17:05:18 +01:00
server-analyze.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
server-http-startup.test.ts fix(server): restore gitnexus serve startup under Express 5 (#1749) 2026-05-21 10:18:09 +01:00
setup-antigravity.test.ts feat(setup): implement antigravity integration setup and hook adapter… (#1730) 2026-05-25 14:46:17 +01:00
setup-skills.test.ts fix(setup): correct OpenCode skills install path in status message (#1386) 2026-05-07 14:27:49 +01:00
setup-uninstall-roundtrip.test.ts feat(cli): add gitnexus uninstall to reverse setup (#2060) (#2062) 2026-06-09 10:50:18 +01:00
shape-check-regression.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
skills-e2e.test.ts feat(csharp): migrate C# to registry-primary scope-resolution (Closes #934) (#1019) 2026-04-23 12:38:13 +01:00
spring-route-pipeline.test.ts feat(ingestion): Java Spring route annotation → Route node extraction (#2078) 2026-06-10 09:44:56 +01:00
staleness-and-stability.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
swift-scope-capture-tripwire.test.ts feat(swift): migrate Swift to scope-based registry resolution (#937) (#1948) 2026-05-31 16:56:47 +01:00
taint-explain.test.ts feat(taint): intra-procedural taint analysis (#2083) (#2164) 2026-06-12 07:35:09 +01:00
tree-sitter-languages.test.ts fix(go): capture multi-name declarations (#2032) 2026-06-06 04:47:17 +01:00
vue-pipeline-benchmark.test.ts feat(vue): migrate Vue SFC to scope-based resolution (RFC #909 Ring 3, closes #940) (#1950) 2026-06-03 21:48:38 +01:00
worker-pool.test.ts fix(analyze): prevent cache-hit native workers from aborting (#1751) 2026-05-21 16:17:02 +01:00