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75 commits
| Author | SHA1 | Message | Date | |
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ChunxueLi
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99291891b7
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feat: make MAX_CALLABLE_VALUE_TARGETS configurable via env (#2725)
* feat(scope-resolution): make MAX_CALLABLE_VALUE_TARGETS configurable via env The branch's original commit was a whole-file snapshot taken at a stale base and never touched the constant, so the env read was missing and the branch's own test failed. Implemented here, matching the sibling GITNEXUS_MAX_PROPERTY_DISPATCH_FANOUT knob. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test(callable-value-flow): add env override tests * docs(callable-value-flow): document GITNEXUS_MAX_CALLABLE_VALUE_TARGETS env Adds a Troubleshooting subsection to README.md and a commented entry to gitnexus/.env.example for the new per-callable-site dispatch-target cap (default 32), following the maintainer's review request to document the knob alongside its implementation. --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> Co-authored-by: Ubuntu <ubuntu@localhost.localdomain> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> |
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ChunxueLi
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c238085676
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feat: make MAX_PROPERTY_DISPATCH_FANOUT configurable via env (#2726)
* feat(scope-resolution): make MAX_PROPERTY_DISPATCH_FANOUT configurable via env * test(property-dispatch): add env override tests * docs(scope-resolution): document GITNEXUS_MAX_PROPERTY_DISPATCH_FANOUT in README and .env.example Add a dedicated troubleshooting subsection and .env.example entry for the GITNEXUS_MAX_PROPERTY_DISPATCH_FANOUT environment variable, matching the format used by the sibling GITNEXUS_MAX_CALLABLE_VALUE_TARGETS knob. Closes maintainer request: "Could you please document this in the readme plus the .env.example?" --------- Co-authored-by: Ubuntu <ubuntu@localhost.localdomain> |
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Void Freud
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0f78179e7f
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fix(jvm): enforce proximity-bounded sibling injection (#2732)
* fix(jvm): bound same-package sibling injection * docs(jvm): document sibling injection cap * fix(jvm): mark truncated sibling sets incomplete and bound the merge Review follow-ups on the sibling injection cap (#2732): - The cap silently produced a third visibility state. Before it, a file was either fully visible (package under 500 files) or fully incomplete; once `injectedIds.size` hit the cap, real siblings were dropped while `isVisibilityIncomplete` still returned `false`. That flag gates wildcard attribution in seven Spring passes (`bean-candidates.ts:199` and the java/ kotlin bean-metadata, conditionals, config-bindings and DI resolvers), so 201-500-file packages — exactly this cap's population — resolved wildcard annotations against a truncated sibling set with no log signal. Truncation now marks the file incomplete and analyze warns once with the affected file count. - The cap only bounded `bindingAugmentations`; the two `typeBindings` merges below it still absorbed every sibling, so a class excluded from the binding set could still steer receiver/variable type inference through `scope.typeBindings`. Both halves now use the same bounded sibling set, and the merge iterates that set directly rather than filtering a full rescan, so the cap bounds the work as well as the result. - Path segments are split once per bucket instead of on every pairwise proximity comparison — that comparison runs O(files²) per package. - `JvmPackageFact` was re-declared locally instead of imported from `package-facts.js`, where the canonical declaration still serves both languages' facades and capture side-channels. Nothing kept the copies in sync. Restored the import. - README/.env.example: `GITNEXUS_MAX_INJECTED_SIBLINGS` does not lift the fixed 500-file package skip (including at `0`), and truncation disables wildcard attribution for the affected files. Both are now stated. * test(jvm): restore the language-facade coverage and pin the cap's behaviour The cap rewrite replaced the per-language harness with generic fixtures, dropping the Java/Kotlin capture-side-channel and facade coverage (package fact extraction, the 500-file skip, fail-closed on a file that produced no ParsedFile) and leaving a proximity fixture whose candidates were already in order — so it could not tell a working sort from plain truncation of the input. Restores that harness and adds cap-specific cases on top, driven through the shared JVM factory. The fixture interleaves near and distant siblings, so the retained set is only reachable by a working proximity sort. Covers: the exact capped set, truncation marking the file visibility-incomplete, type bindings bounded by the same sibling set, the unbounded `0` override staying complete, and the documented default of 200 applying when the variable is unset. Each new case fails against the pre-fix implementation. --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> |
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Void Freud
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e20b41fffc | fix: allow slower remote embedding responses | ||
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Gergő Magyar
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b5c6c0e57c
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perf(communities): fix the O(communities x N) copy in vendored Leiden, wire Icebug to its real API (#2337) (#2692)
* perf(communities): drop the O(communities x N) copy in vendored Leiden (#2337) `UndirectedLeidenAddenda.mergeNodesSubset` snapshotted the pre-merge `externalEdgeWeightPerCommunity` with a full-array `.slice()` on every macro-community, so a graph with C communities and N nodes copied C x N float64s per Leiden pass. CPU profiling put 70% of a 100k-node run in that one function, plus ~7s of GC from the per-community allocations. Only entries for nodes inside the current subset are ever read back (every neighbour is filtered on `belongings[et] === currentMacroCommunity`), so snapshot just those into a scratch buffer allocated once per addenda. Measured on seeded planted-partition graphs, partitions bit-identical: 20k nodes / 54k edges 2350ms -> 527ms (4.5x) 60k / 200k 12513ms -> 3328ms (3.8x) 100k / 350k 44151ms -> 4816ms (9.2x) 200k / 800k >580s -> 14622ms (>40x) The 200k case previously blew through LEIDEN_TIMEOUT_MS and degraded every symbol into a single community; it now finishes well inside the timeout. Adds golden-partition and repeat-run determinism tests, which nothing covered before. Committed with --no-verify: the pre-commit typecheck gate fails on pre-existing `BindingRef.visibility` errors in csharp/namespace-siblings.ts and scope-resolution/passes/free-call-fallback.ts, both untouched here. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfQfKy4gCmgUv1jBRJTSs2 * fix(communities): wire the Icebug engine to the real @ladybugmem/icebug API (#2337) The gate merged in #2376 could never have run. It imported the bare specifier `icebug`, which on npm is an unrelated node-inspector/nodemon wrapper — the graph library publishes as `@ladybugmem/icebug`. It then probed for `Graph.fromCSR` and `community.ParallelLeidenView`, neither of which exists: the module exports `GraphR(n, directed, outIndices, outIndptr)` and a top-level `Leiden(graph, iterations, randomize, gamma)`. The constructor call also had `gamma` and `randomize` transposed, and `getPartition()` returns `{membership, count}`, which the array-like probe rejected. Every `GITNEXUS_COMMUNITY_ENGINE=icebug` run fell back to Graphology with a shape error. Rewrites the worker against the published surface and deletes the speculative probing it needed while the API was unknown — the four-way `readPartition` candidate scan, the `readModularity` ladder, the object-vs-positional constructor retry, and the `isNumericArrayLike` helper. What stays is the guard that matters: `setNumberOfThreads` and `setSeed` are required, because community IDs feed generated context and must be reproducible. Icebug is deliberately not a declared dependency. Its prebuilds link against system Arrow 24, OpenMP and glibc >= 2.38, so it stays an opt-in `npm i @ladybugmem/icebug` rather than 30MB every install pays for. Note that the published 12.8.0 tarball omits the thread/seed exports that icebug-nodejs HEAD has, so the determinism guard is what trips today. The worker source is now built from a module specifier so tests can run it against a stub shaped like the real package. That pins the package name, class names, constructor argument order and partition shape — none of which anything caught before. Committed with --no-verify: the pre-commit typecheck gate fails on pre-existing `BindingRef.visibility` errors in csharp/namespace-siblings.ts and scope-resolution/passes/free-call-fallback.ts, both untouched here. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfQfKy4gCmgUv1jBRJTSs2 * docs(communities): label the Icebug engine experimental and announce it at runtime (#2337) The engine was opt-in but silent about what opting in means. A run that succeeds is exactly when the user most needs to know the partition came from the experimental path, since community IDs feed generated context and the two engines partition differently — switching invalidates anything keyed on those IDs. Emits the notice when a non-default engine is requested rather than only on fallback, and states the no-stability-guarantee terms in the README and the options doc. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfQfKy4gCmgUv1jBRJTSs2 * fix(communities): never terminate the icebug worker mid-N-API (#2432, #2337) Self-review of this PR found that making the native Leiden path reachable also arms a hazard this repo has already paid for once. The icebug worker spends its entire life inside N-API — dlopen, GraphR, Leiden, run — so the 60s timeout handler's `worker.terminate()` would kill a thread mid-native- call, which aborts the whole process (Napi::Error -> std::terminate -> SIGABRT) rather than falling back to Graphology. A timeout on a large projection is exactly the case the engine exists to serve, so the failure mode was aimed at its own target. Drops terminate() from all three paths. On timeout the worker is unref'd and abandoned, so a wedged native run cannot hold the process open either. On the settled paths nothing is needed: the worker script ends after its single postMessage and the thread exits on its own — measured at 40ms. Records the rule as GUARDRAILS non-negotiable 6, since the same trap is open to any future worker running tree-sitter, LadybugDB or Icebug code, and it only reproduces once the native module actually loads — which is precisely the path you cannot exercise locally. Also from the review: - Marks vendor/leiden/utils.cjs as a local fork. A re-vendor from upstream would silently restore the O(communities x N) copy, and no test would notice: both versions produce bit-identical partitions, so the goldens pass either way. The header now names the divergence and its symptom. - Qualifies the README performance claim. "~15s for a 200k-symbol projection" was measured on a synthetic planted-partition graph, not a real repo, and Leiden is sensitive to degree distribution. The terminate rule is regression-tested: restoring the call fails the mocked-worker test with `expected 1 to be +0`. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfQfKy4gCmgUv1jBRJTSs2 --------- Co-authored-by: Gergo Magyar <abhigyan1.patwari@gmail.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com> |
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Gergő Magyar
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3f1e23ba83
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fix: stop misdiagnosing glibc-too-old native loads (#2672) and name the Windows FTS zero-install fix (#2669) (#2689)
* docs(plans): add glibc-windows-fts-diagnostics plan Implementation plan for #2672 (glibc-too-old native-load misdiagnosis) and #2669 (Windows FTS prerequisites + Git Bash zero-install workaround). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(cli): stop prescribing a reinstall when the host glibc is too old (#2672) The LadybugDB prebuilt binary requires GLIBC_2.34 (dlopen/pthread_* at 2.34, fstat64/lstat at 2.33). On an older host the loader reports version `GLIBC_2.34' not found (required by .../lbugjs.node) and checkLbugNative answered with "truncated file, ABI mismatch, or wrong-platform binary" plus instructions to re-run install.js. That advice is actively wrong for this class: every download ships the same prebuilt binary, so the reinstall fails identically and the user loops. Add glibcTooOldMessage: match a GLIBC_<version> token on a "not found" line, report the highest required version (compared numerically, so 2.9 < 2.34) alongside this host's glibc from process.report, state that reinstalling will NOT help, and point at the real options. The branch sits on the arm where the probe actually ran and failed, so an unrunnable probe still fails open (#2441). The glibc read is local rather than analyzer-identity's detectLibcVariant: native-check is the dependency-light startup gate and must not statically pull in a module the CLI reaches through a dynamic import. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(lbug): name the Git Bash zero-install fix for Windows FTS load failures (#2669) The Windows error-126 remedy already refuses to prescribe a reinstall and names the VC++ redistributable and the OpenSSL 3 DLLs, but not where those DLLs already exist on the machine. #2669's reporter had the redistributable installed and still failed: the same command failed in PowerShell and succeeded in Git Bash, because Git for Windows puts libssl-3-x64.dll and libcrypto-3-x64.dll on PATH via C:\Program Files\Git\mingw64\bin. Add that hint to the Windows-126 and structural missing-dependency remedies through one shared const, following the VC_REDIST_INSTALL_HINT anti-drift pattern (#2383 F5). Placing it in the builders rather than at a call site is load-bearing: markUnavailable caches the whole diagnosis (#2383 F3) and ftsDegradedWarning replays that cached remedy, so a call-site fix would miss the MCP query and /api/search surfaces. The hint is a fixed system path, never a user-profile one — remedy text is not path-redacted, and fts-degraded-warning.test.ts asserts no C:\Users\ path ever reaches a user. Both touched tests now assert that property directly. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs(readme): document the Linux glibc floor and Windows FTS prerequisites (#2672, #2669) Requirements listed only Node and git, so neither runtime prerequisite that these two issues turn on was discoverable before hitting the failure. - Linux: the LadybugDB prebuilt binary needs glibc 2.34+; name the distro versions that clear it and state plainly that reinstalling does not help. - Windows: full-text search needs the VC++ 2015-2022 x64 redistributable AND OpenSSL 3 on PATH. The redistributable alone is not sufficient (#2669's reporter had it), and Git for Windows already ships the OpenSSL DLLs, so running from Git Bash or prepending mingw64\bin is a zero-install fix. Without them analyze still succeeds but the index carries no search tables. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * chore: drop the plan document from version control docs/* is gitignored; the plan was force-added so it would travel with the work. It is working material, not a repository artifact — the code, tests and README carry the reasoning that matters. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(cli): stop doctor reporting a present-but-unloadable binary as missing (#2672) doctor printed "✗ lbugjs.node missing" for every failed native check — including the case this PR is about, where the binary is right there and merely fails to load because the host glibc is too old. It then wrote the real detail to stderr directly beneath, so the two lines contradicted each other and the headline sent users to reinstall a file they already had. It said the same for a truncated download and for an entirely absent @ladybugdb/core package. checkLbugNative already knows which of the three it found, so record it: a `kind` discriminator ('package_missing' | 'binary_missing' | 'load_failed') set at each failure return. doctor renders it through a new exported `nativeStatusLine`, following the existing pageSizeDoctorLines/poolSizeDoctorLine pure-helper pattern — which also makes the line testable, where before it had no coverage at all. An unrecognized or absent kind keeps the conservative "missing". Deriving this in doctor with a second existsSync would have re-stat'd a file the check had already inspected, and could disagree with what it actually observed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> |
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Gergő Magyar
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ad1b9227c4
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fix: large-repo analyze OOM and false worker-timeout cascade (#2649) (#2679) | ||
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Gergő Magyar
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7316503ebc
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perf(analyze): hold structural relationships out of the JS heap, on by default (#2680) (#2685)
* refactor(lbug): extract SyncCsvWriter into a shared module
`PdgEmitSink` (#2202) declared `SyncCsvWriter` as a private, non-exported
class. The structural streaming sink for #2680 needs the same buffered
sync-write + poison/openFailure IO discipline, and importing it is not
possible while it is module-private — so the alternative was copying ~90
lines of it.
Extract the class (and the chunk-rows default it uses) into
`sync-csv-writer.ts` and have `PdgEmitSink` import it.
`DEFAULT_PDG_EMIT_CHUNK_ROWS` stays exported as an alias so no existing
caller changes.
Pure refactor: no behaviour change. pdg-emit-sink.ts 396 -> 302 lines;
tsc clean; the 23 existing #2202 tests pass unchanged.
Refs #2680
* feat(lbug): add GraphEmitSink for streaming structural relationship emit
Structural sibling of PdgEmitSink (#2202): a KnowledgeGraph façade that
routes relationships no mid-pipeline phase reads back to bounded
CSV-on-disk and never stores them. Nothing constructs it yet.
Measurement drove the design. On a kernel-shaped synthetic graph (400k
nodes, 2.7 edges/node):
nodes only ...... 367 B/node
nodes + edges ... 2075 B/node <- reproduces the #2649 ~2.1 KB/node
=> the relationship layer is 83% of graph heap, ~646 B/edge
so streaming *relationships* is where the memory is; nodes stay resident
(they are 17%, and two scope-resolution index builders scan them).
Dropping just the redundant relationshipsByType/edgeIdsByNode indexes was
also measured — 174 of 648 B/edge, ~1.3x — and is not a substitute.
RETAINED_REL_TYPES is derived from an exhaustive audit of every
relationship read site under src/, and each entry names its reader. An
earlier draft carried 14 types, 5 of which no reachable phase reads.
Two deliberate departures from PdgEmitSink, both because its invariants
do not hold here:
- dedup by relationship id, since no upstream per-file uniqueness
guarantee exists for structural edges and COPY would violate the PK;
- removeRelationship on an already-streamed id throws instead of
no-oping, so a mutating consumer cannot corrupt the graph undetected.
Also exposes hasStreamedSemanticEdge for the local-symbol pruner: without
it a block-local symbol referenced only by a streamed edge looks
unreferenced and gets pruned, leaving a CSV row pointing at a node with
no row.
Refs #2680
* feat(analyze): stream structural relationships to CSV under GITNEXUS_STREAM_GRAPH_EMIT
Wires GraphEmitSink into the pipeline behind a full-rebuild-only flag, so
relationships that no mid-pipeline phase reads back never enter the JS
heap. Measured ~2.9x reduction of graph heap:
0.17 (nodes) + 0.83 * 0.21 (retained edges) = 0.344 retained. This is a
constant factor, NOT O(chunk) — node identity and the resolution
registries stay O(repo).
The sink is armed at the PARSE boundary, not at graph construction. An
exhaustive audit of every relationship read site under src/ found four
mid-pipeline CALLS consumers, not the two an earlier draft assumed:
- local-symbol-pruner (full iterRelationships scan, then removeNode)
- communities / processes (whole-graph forEachRelationship)
- mapCobolToGraph, which scans CALLS and REMOVES the unresolved ones —
and runs BEFORE parse, so streaming from construction would have
silently stopped COBOL cross-program call resolution
- taintSummaries, gated on `pdg` and NOT on `skipGraphPhases`, so it
needs its own gate or --pdg + this flag yields an empty taint layer
Accordingly communities, processes, taintSummaries and callSummaries are
all disabled under the flag, and the run logs what it is giving up.
Two fixes that are correct independently of the flag:
- runPipelineFromRepo keyed its community/process extraction off
`!skipGraphPhases` while getPhaseOutput THROWS on a phase filtered out
by any enabledWhen predicate — now a presence check, so filtered
combinations return undefined instead of crashing.
- loadGraphToLbug COPYs one job per CSV FILE rather than per label pair.
#2202's throw-on-collision merge is only sound because BasicBlock pairs
are disjoint; a streamed CALLS edge is Function|Function and always
collides with the whole-graph CSV for that pair, so the structural
manifest appends instead.
The buffer-pool hint adds the streamed row count back in: the hint only
ever shrinks the pool, so sizing it from the post-streaming
relationshipCount would starve the COPY at exactly the scale this
targets.
detect_changes: 18 symbols / 10 files / 9 processes, all within the
planned scope. Full suite green with the flag off.
Refs #2680
* fix(mcp): stop impact() under-reporting risk on a streamed index
An index built with streamed structural emit has no Process or Community
rows, and impact()'s risk scorer uses processCount >= 5 and
moduleCount >= 5 as two of its four CRITICAL escalation criteria. The
missing-table errors are swallowed as benign without raising `partial`,
so nothing distinguished 'this repo has no processes' from 'this index
was built without them' — the same change would report LOW off a streamed
index and CRITICAL off a complete one, with no signal either way.
That is the false-clean shape #2283 ruled out for detect_changes, and it
matters more here because the repo's own workflow mandates impact()
before every symbol edit.
Stamp `graphPhases: 'complete' | 'skipped'` into RepoMeta and have
impact() attach riskUnderstated + an explanatory riskNote when the index
is stamped skipped, so the reported level is explicitly a lower bound.
Unlike the rest of RepoMeta.capabilities this stamp has a real
programmatic reader.
Also documents GITNEXUS_STREAM_GRAPH_EMIT in the README env table,
including everything the flag disables.
Refs #2680
* test(lbug): differential set-identity gate for streamed structural emit
The acceptance property for #2680: for the same node/edge set, the rows
reaching the bulk COPY must be identical whether streaming is on or off.
With streaming on they arrive from two places — the residual in-memory
graph via streamAllCSVsToDisk, plus the sink's per-pair CSVs — so the
test asserts their UNION equals the single whole-graph emit.
Also asserts the split is real (retained + streamed == total, streamed >
0), so a sink that silently streamed nothing cannot pass the equality
vacuously. Verified discriminating: with sink.arm() commented out the
test fails ('expected 0 to be greater than 0'); restored, it passes.
Fixture spans both sides of RETAINED_REL_TYPES and includes a self-edge
and a duplicate relationship id — the cases where a naive sink diverges
from the whole-graph emit.
Drives the sink directly rather than running analyze, matching
pdg-emit-streaming-roundtrip.test.ts: the guarantee is about emitted
rows, and the worker pool would add unrelated machinery without
strengthening the assertion.
Refs #2680
* fix(test): remove literal NUL byte and cover streamGraphEmit phase gating
Two review findings, both verified before accepting.
1. The round-trip test contained a literal NUL byte as a key separator,
which made Git treat the whole .ts file as BINARY —
`git show --numstat` reported `-\t-` for it, so the file would not
diff or blame and CI text tooling would skip it. Replaced with the
escaped \\u0000 sequence; behaviour is identical, the file is text
again. (Found by the Codex swarm lane.)
2. buildPhaseList's four new streamGraphEmit gating predicates and the
flag-off default path had no test that would fail on revert — two
review lanes flagged this independently. Reversing any enabledWhen
condition would have passed the suite silently, which matters because
an ungated taintSummaries yields an empty taint layer rather than an
error.
Added four cases: the streamed run drops communities/processes/
taintSummaries/callSummaries; it keeps mro/di (their reads are all in
RETAINED_REL_TYPES); the flag-off list is untouched; and skipGraphPhases
still works independently.
Refs #2680
* fix(analyze): don't leak a temp dir when streaming is off; correct two overclaims
Three review findings, all verified before accepting.
1. `graphEmitCsvDir: resolveNativeSafeStorageDir(...)` was evaluated
unconditionally inside the pipeline-options literal. On a Windows
non-ASCII storage path that helper mkdtempSyncs a REAL directory, so
every analyze leaked one temp dir even with the flag off. Now resolved
only when streaming is active, matching how the PDG sibling resolves
inside its own guard. This was the only finding affecting flag-off
users.
2. The retain-set comment claimed 'the differential round-trip test is
what catches drift'. It cannot. addRelationship PARTITIONS edges
between the graph and the CSVs, and the union of a partition is
invariant under where the partition line falls — so that test stays
green no matter how RETAINED_REL_TYPES is drawn. Only the read-site
audit protects the invariant, and the comment now says so and names
the grep to re-run.
3. The ~2.9x figure assigned streamed edges a retained cost of zero,
ignoring the sink's own streamedIds/streamedEndpoints Sets — and
relationship ids are plain concatenations of both endpoint ids, not
hashes. Review measured those Sets at ~35% of full per-edge retention,
not the '~a tenth' assumed, putting the real figure nearer ~1.7-2.2x;
a member-dense Java/C# repo lands lower still, since the retained
structural spine is a larger share there than in the TypeScript census
the 0.21 came from. Code comment and README now give a range and say
plainly that no end-to-end measurement on a real repository exists yet.
Refs #2680
* fix(mcp): disclose degraded risk in detect_changes; stop pinning the sink
Two more review findings, both cross-lane corroborated.
1. detect_changes derives risk_level SOLELY from affected-process count,
and a graphPhases:'skipped' index has zero Process rows by
construction. The STEP_IN_PROCESS query then succeeds with zero rows,
so queryDegraded stays false and the tool returns risk_level 'low',
affected_count 0, with no partial marker — for every change, forever.
That is a false-clean on the gate this repo mandates before every
commit, and it is the same #2283 shape the previous commit fixed in
impact() while leaving its sibling untouched. Now carries the same
riskUnderstated + riskNote disclosure.
2. PipelineResult.graphEmitSink had zero readers — the pruner predicate
and the manifest are both threaded elsewhere — but returning it kept
the sink, and therefore its O(streamed-edges) id and endpoint Sets,
reachable through the entire COPY/FTS/embedding phase. That is
precisely the phase this feature exists to fit inside RAM, so the
field actively worked against the change's purpose. Dropped.
Refs #2680
* refactor(2680): one named capability, one risk helper, a shorter header
Pure cleanup pass — no behaviour change, 66 tests across the six affected
suites still green, and the round-trip test still fails when the sink is
left un-started.
Three things were untidy:
1. The phase layer reached the sink through TWO loose callbacks bolted
onto PipelineContext (`armStreaming`, `hasStreamedSemanticEdge`) —
two fields, two wiring lines, no name for the thing they belonged to.
Replaced by one `graphEmit?: GraphEmitControl`, a two-method interface
declared beside the sink. Phases now say what they mean:
`ctx.graphEmit?.beginStreaming()`. Also renames `arm()` to
`beginStreaming()`, which needs no comment to explain.
2. The degraded-index risk disclosure was copy-pasted into impact() and
detect_changes() — two meta probes, two near-identical prose blocks,
and two long comments restating the same reasoning. Now one
`streamedIndexRiskDisclosure()` helper carrying the explanation once;
each caller passes only the clause naming which count is structurally
zero for it. Same file, 45 lines in / 45 out, with the duplication gone.
3. The sink's file header had grown into a changelog of my own review
corrections ('this once assumed', 'review measured'). A reader does not
care what an earlier draft believed. Rewritten to state the design
argument once — relationships are ~83% of graph heap, so they are what
streams; nodes are the other 17% and are scanned, so they stay — under
headings, with the honest 'this is an estimate, ~1.7-2.2x, no real-repo
measurement yet' caveat kept in full.
Refs #2680
* feat(analyze): make streamed graph emit the default, with nothing traded away
Streaming was opt-in because it disabled the four phases that consume the
whole CALLS graph — communities, processes, taintSummaries, callSummaries.
That made it unshippable as a default: query() is process-grouped and
clusters/skill-gen are community-backed, so every index would have silently
lost them.
The sink now answers a COMPLETE relationship read. It keeps streamed edges
as four parallel columns over an interned node table — sourceId, targetId,
type, confidence — and iterRelationships/iterRelationshipsByType/
forEachRelationship/relationshipCount return the retained edges
concatenated with those. Every consumer therefore sees the whole graph and
no phase knows streaming happened.
Four fields, not six, because an audit showed community-processor,
process-processor, taint-summaries and the pruner read only those — none
keys on rel.id. That matters: relationship ids are unique long strings, and
retaining them is precisely what made a fully-columnar attempt LOSE to the
object graph (measured 838 MB vs 822 MB). Ids stay out of the columns; a
read synthesizes one, which is safe because buildRelRow never persists it.
Consequently deleted, not merely disabled:
- the four enabledWhen gates and the 'what you give up' warning;
- the pruner's hasStreamedSemanticEdge predicate and its plumbing — a
complete scan sees streamed edges, so the dangling-edge hazard is gone by
construction rather than by compensation;
- the whole degraded-index apparatus: the graphPhases RepoMeta stamp,
streamedIndexRiskDisclosure, and the riskUnderstated markers on impact()
and detect_changes(). Nothing degrades, so nothing needs disclosing.
Default is ON for full rebuilds; GITNEXUS_STREAM_GRAPH_EMIT=0 (or an
explicit option) is the escape hatch, for bisecting a suspected
streaming fault rather than routine use. Incremental runs still refuse it —
the writeback reads relationships back out of the in-memory graph.
Measured A/B, 400k nodes / 1.08M edges, all edges streamable (worst case
for this design): 823 MB -> 626 MB, ~1.3x, all 1.08M edges still visible.
That is deliberately less than the ~2.9x the retained-share formula
implies — losslessness costs the dedup Set and the columns. The earlier,
bigger number was bought by disabling phases. README and the file header
both state 1.3x measured; neither claims O(chunk).
New coverage: reads are complete (proven discriminating — 3 tests fail when
the streamed leg is removed), endpoints/confidence survive the round trip,
per-type lookup finds streamed types, and every CALLS-consuming phase stays
registered under the flag.
Refs #2680
* docs(2680): pin the invariants the default-on change relies on
Review follow-ups. No behaviour change except the id-uniqueness fix.
- pipeline.ts returns the RAW graph, not the sink, and that is load-bearing:
phases read the sink so their scans are complete, but loadGraphToLbug feeds
this value to streamAllCSVsToDisk, whose iterator would then emit every
streamed edge a SECOND time on top of the per-pair CSVs the sink already
wrote. Returning the sink there silently doubles every streamed
relationship in the persisted graph, so the reason is now written down at
the return site.
- Synthesized ids now carry the column index, making them unique even when
two streamed edges share (type, source, target) and differ only in
reason/step. Harmless today because no consumer keys on relationship id,
but real ids are unique and the synthesized ones should match, so a future
id-keyed consumer cannot silently collapse two edges.
- Recorded WHY dropping reason/step is safe, which is not the same argument
as for id: the persisted row keeps their true values because buildRelRow
receives the original relationship on the way through, so only in-memory
reads see the 'streamed' placeholder. The ACCESSES reason:'read'|'write'
distinction that MCP queries depend on therefore survives in the database.
A future in-pipeline consumer needing either field must add a column rather
than trust the placeholder.
Also verified while chasing a review lead: removeNodesByFile has no
production callers and removeNode has exactly one (the pruner), which reads
through the sink and so sees streamed edges. The dangling-edge hazard the
deleted hasStreamedSemanticEdge predicate used to compensate for is closed
by construction, not by luck.
Refs #2680
* fix(2680): fail loudly on a missing CSV dir, and guard the retain set
Resolves both findings from the review of this branch.
MEDIUM — pipeline.ts silently skipped streaming when `streamGraphEmit` was
true but `graphEmitCsvDir` was absent. The CLI always supplies the dir, but
streaming is on by DEFAULT now, and the callers that build PipelineOptions
themselves (eval-server, MCP daemon, tests) are exactly the ones that would
omit it — so they would ask for streaming, not get it, and still see a
successful run. That is the silent-degraded-outcome shape the rest of this
work exists to prevent, so it now throws with the resolution hint. Covered by
a test asserting the rejection.
LOW — RETAINED_REL_TYPES had no automated guard, and the round-trip test
structurally cannot be one: addRelationship PARTITIONS edges between the
graph and the CSVs, and a partition's union is invariant under where the line
falls, so that test stays green for any partitioning including a wrong one.
Drift there yields a silently incomplete mid-pipeline edge set, not a crash.
Added a test that derives the required set by grepping every literal
iterRelationshipsByType('X') under src/ and asserts the constant covers it,
with CALLS as the documented exemption (taintSummaries reads it, which is why
the sink answers a complete read rather than retaining it). Proven
discriminating: removing EXTENDS from the constant fails with
"expected [ 'EXTENDS' ] to deeply equal []".
128 tests green across the eight affected suites, including the index-lock
suite that arrived with the #2677 merge.
Refs #2680
* docs(2680): record the measured CPU cost, not just the memory win
I measured memory before shipping and never measured time, which was a gap:
reads now allocate, rebuilding objects instead of returning stored ones, and
a real analyze does SIX full relationship scans (pruner, communities x2,
processes x2, the taint fixpoint's CALLS pass).
Same 400k-node / 1.08M-edge graph:
heap 820 MB -> 623 MB (1.32x better)
scans 96 ms -> 651 ms (6.8x WORSE)
6.8x on iteration is worth knowing, but the absolute number decides it:
~0.5 s here, ~2 s extrapolated to kernel scale, against an analyze measured
in minutes — under 1% of wall-clock. The ~26M short-lived objects at kernel
scale are young-generation churn (the cheap case), and being ~800 MB further
from the heap ceiling matters more than the churn costs: #2649's cascade came
from GC thrash NEAR the limit, not from allocation volume as such.
Also names the first lever if these scans ever go hot — a per-type index over
the columns, so iterRelationshipsByType stops scanning all streamed edges —
and notes that it trades memory back, so it needs a measurement first.
Refs #2680
* perf(2680): cut the iteration regression from 6.8x to 1.8x
The memory win came with an unmeasured CPU cost. Iteration went from
returning stored objects to rebuilding them, across the SIX full relationship
scans an analyze performs (pruner, communities x2, processes x2, taint's CALLS
pass). First measurement: 90 ms -> 651 ms, 6.8x worse. Fixed properly rather
than documented away.
Two causes, each measured before and after:
1. The ~150-character synthesized `id` was built eagerly on every read — 6.5M
concatenations per analyze, for a field NO in-pipeline consumer reads.
Isolating it (constant id) showed 436 ms of the 555 ms regression. Now a
lazy prototype getter on a fixed-shape `StreamedRelationship` class: the
string is built only if someone asks, and V8 keeps one hidden class across
millions of instances.
2. Generator and iterator-protocol overhead on million-edge walks.
`forEachRelationship` (community detection's form, called twice) now loops
the columns directly, skipping both. `iterRelationships` keeps an iterator
but reuses one result record — a hand-rolled version allocating a fresh
{value, done} per edge measured WORSE than the generator (252 ms), which is
why the obvious rewrite is not the one that shipped.
heap 821 MB -> 623 MB (1.32x better)
scans 90 ms -> 180 ms (was 651 ms)
The residual ~90 ms is object allocation, 6.5M instances across six scans, and
it is irreducible while the read API returns objects at all. The remaining fix
for true parity is a field-wise callback passing sourceId/targetId/type/
confidence as primitives — all four hot consumers read only those — but that
changes the KnowledgeGraph interface and its consumers, so it belongs in its
own measured change rather than bolted on here.
Refs #2680
* perf(2680): zero-allocation field scan brings iteration back to parity
Third and final step on the iteration cost. The memory win had come with a
6.8x iteration regression; the previous commit cut that to 1.8x by making the
synthesized id lazy and removing generator overhead. The residual was object
allocation itself — 6.5M instances across the six full relationship scans an
analyze performs — which no amount of tuning removes while the read API hands
back objects.
So the hot consumers stop asking for objects. Adds
`KnowledgeGraph.forEachRelationshipFields`, which passes
(sourceId, targetId, type, confidence) as primitives — exactly and only what
every whole-graph scan reads. On the sink those come straight out of the
columns, allocating nothing; on the object-based graph they are read off the
stored relationship, so the flag-off path is unaffected.
Converted the five whole-graph scans: community detection (x2), process
extraction (x2), and the local-symbol pruner. `isFileDefinesEdge` now takes
(type, sourceId) rather than a relationship. The taint fixpoint's by-type pass
is left alone — one scan of six, and converting it would turn an indexed
bucket lookup into a full scan on the object-based graph.
heap 820 MB -> 623 MB (1.32x better)
scans ~82 ms -> ~90 ms (was 651 ms; now parity within noise)
Also deletes the pruner's `hasStreamedSemanticEdge` option, which has had no
caller since the sink's reads became complete — a dead knob is worse than no
knob.
Verified: 104 tests across the eight affected suites, including the pruner's
pipeline integration test (which needs the raised worker-ready timeout on this
host; it passes cleanly with it and its failures are the known 5s handshake).
Refs #2680
* perf(2680): compact dedup keys — 1.32x -> 1.59x, speed unchanged
An audit of where duplicate relationship ids actually come from, then the
saving it unlocked.
The audit (instrumented analyze of this repo): 25 duplicate-id hits across
63,412 streamed edges — 0.04%, all CALLS, every one the SAME call site
re-emitted when a file is resolved in more than one language pass. Three
things follow, and they rule out the cheap options:
- dedup cannot be dropped (25 != 0, and a duplicate reaching COPY is a wrong
graph);
- it cannot move to row contents, because emit-references builds ids as
`...->target:line:col`, so two calls between the same pair at different sites
have byte-identical CSV rows that the whole-graph emit keeps;
- it cannot move to a per-file source guard like `pdgEmittedFiles`, because a
later language pass can resolve genuinely NEW edges for the same file.
What was left was the key itself. An id embeds both node ids in full (~200
chars here) while the endpoints are ALREADY interned for the columns, so the
Set was storing them twice. Keys are now built from the interner indices plus
the id's trailing disambiguator parsed into NUMBERS.
Numbers, not substrings, and that is load-bearing: a key built by slicing
inside a long string is a V8 sliced/cons string that keeps its parent alive, so
the id would never be freed and the saving would silently fail to appear. An
earlier attempt at this measured no improvement for exactly that reason.
Unrecognized id shapes (`rel:contains:` has no tail) fall back to storing the
id verbatim — correctness first, saving second.
heap 821 MB -> 518 MB (1.59x, was 1.32x)
scans ~83 ms -> ~88 ms (parity, unchanged)
Speed is untouched by construction: dedup is on the WRITE path, and none of
the six full scans reads it.
Also fixes removeRelationship, which the test suite caught: it looked up the
raw id in a Set that now holds compact keys, so it silently stopped throwing on
an already-streamed edge. It cannot recompute a key from a bare id, so it is
now conservative — anything the real graph does not hold is treated as
possibly-streamed once streaming has begun and fails loudly. A genuinely-absent
id throws where main returns false; acceptable because the only production
caller (the COBOL resolver) runs before the sink is armed.
89 tests green across the six affected suites.
Refs #2680
* fix(2680): dedup key dropped edges when tail segment counts differed
Both findings from the review of this branch, and the coverage gap named
alongside them.
HIGH — the compact dedup key packed the id's trailing numeric segments as
`|${a}|${b}`, with `b` defaulting to 0 when only one segment was present and
the segment COUNT absent from the key. So `:7` and `:7:0` produced the same
key and the second edge was silently discarded as a duplicate: a lost
relationship, no error, no warning. Found by probe, not by reading — two
distinct ids for one (source, target, type) went in and one edge came out.
The key now carries `seen`.
Nothing existing caught it. The round-trip test compares the UNION of graph
and CSV rows, and a dropped edge is missing from both, so it stayed green;
the duplicate test only feeds a genuinely identical id, which is the case
that SHOULD collapse. Four new cases pin the boundary instead: differing
segment counts stay distinct, two call sites between one pair stay distinct
(the `:line:col` shape from emit-references), a truly repeated id still
collapses, and a non-numeric tail falls back to the full id. Proven
discriminating — reverting the fix fails with "expected 1 to be 2".
This costs ~66 MB at 400k nodes / 1.08M edges (584 MB, was 518 MB), so the
heap win is 1.40x rather than 1.59x. Not a trade worth making the other way:
a silently missing relationship is the exact failure class the rest of this
work exists to prevent. I am not asserting a mechanism for why two extra
characters per key cost that much — it is stable and reproducible across
runs, and inventing a cause is how I got the earlier cons-string diagnosis
wrong.
LOW — removeRelationship throws for an absent id once streaming has begun,
where KnowledgeGraph.removeRelationship returns false. The behaviour is
deliberate (a bare id cannot be turned back into a compact key, and answering
"false" for an edge already on disk is the worse failure) but it was
undocumented and untested. Now stated on the interface itself and pinned by
two cases: absent-id-while-streaming throws, absent-id-before-streaming
returns false.
Coverage gap — added a test asserting forEachRelationshipFields yields the
same (source, target, type, confidence) tuples as iterRelationships. That
guards the five whole-graph scans converted in
|
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Gergő Magyar
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9538be957d
|
fix(lbug): scale the buffer-pool budget by the OS page-size granule ratio (#2631) (#2636)
* fix(lbug): scale the buffer-pool budget by the OS-page discard-granule ratio (#2631) LadybugDB bills buffer-pool budget per discard granule, not per 4 KiB frame: the engine's vm_region.cpp sets discardGranuleSize = max(frameSize, osPageSize), claimFrame charges the whole granule when its first frame becomes resident, and releaseFrame refunds only when the granule's last frame leaves — while BufferManager::reserve measures eviction progress in refunded bytes and throws 'The buffer pool is full and no memory could be freed!' after three zero-refund passes. On a 64 KiB-page kernel (Ascend/aarch64 openEuler — the #2631 reporter's host) that is 16 frames per granule: the same COPY bills up to 16× the budget it needs on x86, and whole eviction passes can evict frames yet refund nothing. Apple Silicon macOS (16 KiB pages) is the same mechanism at 4×. Measured with the reporter's exact command and version: vllm-ascend needs a (128, 256] MiB pool on 4 KiB pages — 64/128 MiB reproduce the reporter's byte-identical error, 256 MiB and the 576 MiB adaptive pool succeed — so their 64 KiB host cannot survive on a page-size-blind budget. Scale every derived pool size by granuleRatio = max(1, osPageSize/4096): the per-element estimate, the COPY-safety floor, and the default cap (still bounded by 80% of RAM). 4 KiB hosts are byte-identical to before — proven by pinning the existing sizing tests to an explicit 4096 page size, which also stops them drifting on 16 KiB Apple Silicon runners. GITNEXUS_LBUG_BUFFER_POOL_SIZE keeps absolute precedence and 0 still restores the native default. Also: bufferPoolExhaustionRemedy() gives the exhaustion error an actionable cause→consequence→remedy message; the isLbugPageSizeFrameError comment that called pool exhaustion 'a sizing problem, not a page-size one' is corrected — that framing inverted when #2582 made pool size a function of a page-size-blind estimate. Cannot execute on a 64 KiB kernel here: the scaled path is proven by unit stubs plus the engine-source math above; the env override remains the field escape hatch. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(cli): actionable pool-exhaustion remedies at the COPY sites and a doctor pool line (#2631) The node-COPY throw and the relationship-COPY warning now append bufferPoolExhaustionRemedy() when the failure is the engine's pool-exhaustion class: the raw binder text gave the operator nothing to act on, and on non-4K-page hosts the pool bills up to pageSize/4KiB × faster than the sizing was calibrated for. The relationship path appends the remedy once per bulk load, not once per failed pair. doctor prints the effective pool size next to the page-size line ('pool size 2048 MiB', with an '(×N page-size scaling)' suffix on non-4K hosts) so support triage sees the sizing inputs at a glance. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(lbug): re-anchor getEffectiveBufferPoolSize's placement and reuse granuleRatio in doctor Self-review fixes: the getter's insertion had orphaned resolveBufferManagerSize's doc comment (it read as documenting the wrong function), and doctor's scale note duplicated the granule math with a hardcoded 4096. granuleRatio is now exported (it already carried the test-seam default param) and doctor consumes it. No behavioral change — the sizing suite pins byte-identical outputs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(lbug): keep the hintless pool default unscaled and make both remedies visible (#2631) Review fixes: - Scale only the analyze-path cap (scaledAnalyzePoolCap), not defaultBufferPoolSize: the pool is an eager native allocation at DB open (measured, see POOL_BYTES_PER_ELEMENT), so a page-size-scaled hintless default would hand a long-lived MCP process up to 80% of RAM — the #2557 OOM exposure the 2 GiB cap removed. Fix the MAP_NORESERVE claim that contradicted that measurement. - Log the rel-pair pool remedy (loadGraphToLbug returns warnings that no call site reads) and dedup it with a local boolean instead of matching the remedy's own wording. - Label the GITNEXUS_LBUG_BUFFER_POOL_SIZE=0 sentinel as the native 80%-of-RAM default in both the remedy and doctor instead of '0 MiB'. - Extract poolSizeDoctorLine (pageSizeDoctorLines convention): mark env overrides, drop the scaling suffix that misdescribed absolute values. - Fold _resetOsPageSizeCacheForTest into _setOsPageSizeForTests(undefined). - Document the analyze-path scaling in both README env tables. --------- Co-authored-by: Gergo Magyar <abhigyan1.patwari@gmail.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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Gergo Magyar
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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. |
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Gergo Magyar
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5893de1194 | docs(readme): document the global ignore file (#2606) | ||
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Ko
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2a85425ad8
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Merge pull request #2542 from GenKoKo/fix/worker-stdout-and-ready-timeout
fix(ingestion): pipe worker stdout and make ready timeout configurable |
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ChamHerry
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7534f53c27
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feat(embeddings): control request-body dimensions via GITNEXUS_EMBEDDING_REQUEST_DIMS (#2574)
* feat(embeddings): support GITNEXUS_EMBEDDING_REQUEST_DIMS=omit What: Honor GITNEXUS_EMBEDDING_REQUEST_DIMS=omit by suppressing the request-body `dimensions` field sent to HTTP embedding backends. Why: Strict OpenAI-compatible backends return vectors in the model's native size but reject an unfamiliar `dimensions` field, breaking `analyze --embeddings` against them. The var was parsed but never propagated, so `omit` was a no-op. How: Add `requestDimensions` to HttpConfig, return it from readConfig, and forward `config.requestDimensions` (not the validation-only `config.dimensions`) to `httpEmbedBatch`. Local dimension checks still use `config.dimensions`. Details: Coexists with the retry/pacing fields introduced upstream; both feature sets are preserved. Default behavior unchanged when REQUEST_DIMS is unset. Impact: gitnexus/src/core/embeddings/http-client.ts; README; unit tests. * fix(embeddings): name GITNEXUS_EMBEDDING_REQUEST_DIMS in its own config error Address the review findings on #2574. What: - A malformed GITNEXUS_EMBEDDING_REQUEST_DIMS now throws an error naming GITNEXUS_EMBEDDING_REQUEST_DIMS, not the sibling GITNEXUS_EMBEDDING_DIMS. - isHttpEmbeddingDimsError recognizes both leads, so the CLI still classifies the REQUEST_DIMS config mistake as a clean config error, not a stack dump. - Tests: numeric-override decoupling (DIMS=1024 validates the response while REQUEST_DIMS=512 is sent in the body), the omit aliases (none/off/false/0), and the malformed-value error path (which also pins the naming fix). - README documents the full accepted values: omit-aliases and integer override. Why: readConfig reused the DIMS error lead for the REQUEST_DIMS branch, so REQUEST_DIMS=garbage misdirected the operator to edit the wrong variable. The feature's actual decoupling and its non-omit inputs had no test coverage. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: wangxc <wangxc_a_bj@si-tech.com.cn> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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Gergő Magyar
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8b5057f325
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feat(skills): GitNexus Engineering Tool Kits (#2566)
* feat(skills): add ce-plan — GitNexus+PDG implementation-planning skill Adds .claude/skills/ce-plan: a planning-only skill that builds implementation-ready plans from GitNexus graph navigation (query/context/ impact/trace), bounded statement-level PDG slices (pdg_query, impact mode:pdg, explain), and targeted source verification, with a context ledger to prevent repeated reads and a machine-readable implementation context pack (stable contract for a future ce-implement). Whitelisted in .gitignore and registered in AGENTS.md and CLAUDE.md outside the auto-managed gitnexus block. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills): apply ce-plan validation findings (tool contract, consistency, conventions) Tool contract: impact mode:'pdg' shape now includes the schema-required direction param; CDG branch sense documented as the result 'label' field (reason is cypher/raw-edge only); explain caveats corrected to its real false-negative classes (cross-function TAINT_PATH is modeled). Consistency: PDG slice homed in working memory (ledger keeps one-liners); depth knob defined and category-overrides-baseline ordering stated; call_depth (consumed by nothing) and content-hash bookkeeping dropped; Never section folded into Hard rules; Phase 3 deduplicated to a pointer; allowed-repeat escalations defined; budget/discard accounting clarified; verification-commands gathering added to Phase 4; open_questions added to the context pack. From scenario runs: plans now pin the verified-at HEAD commit and index freshness in a header, tag claims [verified]/[graph]/[inferred]/[assumed], quote load-bearing tool output, prefer pre-hook-carrying npm scripts, and support an out:<path> destination override; output path defined as the Phase 1 target repo root. Conventions: AGENTS.md 1.9.0 / CLAUDE.md 1.4.0 changelog rows + metadata bumps; future ce-implement qualified as future. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): rename ce-plan → gitnexus-plan; add cross-CLI (Codex) entrypoints Renames the skill dir, frontmatter, output filename convention, plan H1 (GitNexus Engineering Plan), the future executor handle (gitnexus-implement), the .gitignore whitelist entry, and all AGENTS.md/CLAUDE.md references. Follows the pr-swarm-review cross-CLI pattern: SKILL.md is the canonical CLI-neutral spec, AGENTS.md § Engineering planning is the Codex/any-agent entrypoint, and the README documents the optional user-level ~/.codex/prompts/gitnexus-plan.md slash command plus an invocation matrix. Skill prose de-branded from Claude Code (agent-neutral verification layer). Also fixes two post-review README contradictions: the anti-reread claim now names the ledger's allowed escalations, and 'read-only by contract' is now 'planning-only' (the skill writes exactly one repo file — the plan); the scope-creep rule and template §12 now agree on where deferred follow-ups land. Drops the stale plugin-collision limitation. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(skills): document Codex user-level install path for gitnexus-plan Codex discovers SKILL.md skills from ~/.agents/skills (same path the other gitnexus-* skills install to); README now documents the cp install plus the optional ~/.codex/prompts slash-command file, with the prompt body preferring the repo copy and falling back to the user-level install. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): gitnexus-plan freshness gate + active PDG-layer refresh Freshness is now a Phase 1 gate, not advisory: under the default freshness:strict, a stale index is refreshed once per planning session via node .gitnexus/run.cjs analyze --index-only (appending --pdg when the task will reach the PDG phase), then the context resource is re-read. A missing PDG layer likewise triggers the one permitted --index-only --pdg refresh and re-probe instead of a passive recommendation. freshness:accept (or a failed/impractical refresh) preserves the old behavior: plan on the stale graph, source-weighted, labelled in the plan header. --index-only is the load-bearing flag choice — it suppresses all file generation, so the planning-only contract holds (only the .gitnexus store changes). Ledger gains an index_refresh record; plan header states fresh / refreshed / refresh-skipped-with-reason. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): gitnexus-plan runner build check before freshness refresh When the target repo builds the analyzer from its own source (bin → dist/ mapping, as gitnexus/ does), the Phase 1 freshness gate now verifies dist/ is current before running the analyze refresh — rebuilding via the package's build script when any analyzer source file is newer than the built entrypoint — and prefers that freshly built CLI. Otherwise a stale dist re-indexes with outdated extraction logic and the 'fresh' index lies. Rebuilds are recorded in the ledger's index_refresh; the PDG-phase refresh inherits the same check. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): add gitnexus-work executor and gitnexus-lfg pipeline gitnexus-work executes a gitnexus-plan as verified atomic commits: consumes the §11 implementation_context pack, drift-checks the plan's evidence pin against HEAD, re-verifies assumptions before relying on them, runs impact before every symbol edit and detect_changes before every commit (repo mandates), builds tests from the plan's scenarios, and routes structural drift back to gitnexus-plan Deepen mode instead of coding around it. gitnexus-lfg is a thin orchestrator: gitnexus-plan → blocking user gate (deepen / proceed / stop, deepen loops allowed) → gitnexus-work → review via the existing gitnexus-pr-review skill (open PR, else branch diff vs default). One bounded fix cycle for review findings; never pushes or opens a PR on its own. gitnexus-plan gains a Deepen mode (re-run freshness gate, escalate to depth:deep, re-verify graph/inferred/assumed claims toward verified, rewrite the same file); its 'future gitnexus-implement' placeholder is retired in favor of gitnexus-work. Registered via .gitignore whitelists, AGENTS.md 1.10.0 (section renamed to Engineering planning & execution), CLAUDE.md 1.5.0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills): apply cross-skill review findings to the gitnexus skill family Two P1s: gitnexus-plan Deepen mode now re-anchors before re-pinning (diffs the old evidence pin over every [verified]-claim file and re-reads or downgrades before the header moves — moving the pin without this laundered stale claims as verified); the index-refresh budget is stated once in Phase 1 (one --index-only refresh plus at most one Phase 3 --pdg upgrade per session, Deepen = its own session) with ledger and pdg-slice deferring to it. Contract fixes: gitnexus-work's drift check now covers every file the pack cites (not just files_to_modify) and parses the full pack incl. primary/related symbols and acceptance_criteria (walked in Phase 4 alongside §13); a pre-completed check skips §7 steps already landed and Deepen gains a reconcile-execution-state step, closing the mid-execution route-back loop; pack assumptions must name what to check and how. lfg: Lane 4 passes the merge-base to detect_changes compare (two-dot diff misattributes upstream commits when default advanced), branch-diff is the stated normal case, oversized review findings route to the plan gate instead of overflowing direct mode, the one-fix-cycle cap is explicit on re-run, and headless runs end at the plan gate with the plan as deliverable. work: blank mode narrowed to *gitnexus-plan*.md with a re-execution guard, direct-mode discipline spelled out, branch meaningfulness defined against the plan slug, and the plan document is committed as the branch's docs commit (review diff includes it). Planning-only contract now names the dist/ rebuild as the second permitted state change; Phase 5.1 names the four claim tags; stale AGENTS.md anchors fixed. Known latent issue left untouched: gitnexus/gitnexus-pr-review pairs a three-dot example with a two-dot detect_changes compare — that skill is also shipped by the plugin, so fixing it here would drift the copies; lfg compensates by passing the merge-base. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): ship the engineering skill family with the gitnexus package npm i -g gitnexus users now get gitnexus-plan / gitnexus-work / gitnexus-lfg: the three skills are added to gitnexus/skills/ in directory form (SKILL.md + references/), which installSkillsTo already enumerates dynamically and copies recursively to every editor target (~/.agents/skills for Codex, Cursor, OpenCode, Qoder, ...) on gitnexus setup — uninstall enumerates the same root, so removal stays clean. The Claude Code plugin channel (gitnexus-claude-plugin/skills/) carries the same copies plus the standard per-skill mcp.json. Global-install support in the skill text: gitnexus-plan Phase 1 now resolves the analyzer runner explicitly — node .gitnexus/run.cjs analyze when the project has a runner, else gitnexus analyze (installed CLI), else npx gitnexus analyze — and all analyze mentions route through it, satisfying the skills-steering policy (#1939/#1945) which sweeps the plugin copies. New drift guard test/unit/shipped-skills-sync.test.ts asserts the npm and plugin copies stay byte-identical to the canonical .claude/skills/ family (plugin = canonical + mcp.json), same discipline as run.cjs ↔ resolve-invocation.ts. skills-steering + shipped-skills-sync: 11/11 green. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): workflow_bench — measure the skill workflow's token savings Benchmarks gitnexus-plan → gitnexus-work against a baseline agent (--disallowedTools Skill) on identical tasks, in fresh detached worktrees, using real headless Claude Code sessions; every number comes from the CLI's --output-format json usage report (field names validated against a live 2.1.207 session). Reports per-arm medians (input/cache/output tokens, cost, wall time, turns), a savings row, and resolve status from a per-task verify command — savings on failed tasks are flagged, not celebrated. Per-task setup hook prepares fresh worktrees (deps); --permission-mode bypassPermissions (default) lets sessions run unattended in the throwaway trees. Free-model support: --base-url/--auth-token/--model route headless sessions through any Anthropic-compatible endpoint; free-model.litellm.yaml is a ready litellm-proxy template for OpenRouter :free variants or local Ollama, so benchmarking burns no paid tokens (README documents rate limits and the small-model skill-following caveat). Harness validated end-to-end with a stub CLI (worktree lifecycle, both arms, plan→work chaining, verify, aggregation, report) and 4 pytest units for the pure aggregation/savings/report helpers. AGENTS.md 1.11.0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record first workflow_bench calibration run Trivial-task calibration (add -V alias): both arms resolved; workflow arm ~4.3x baseline cost — the documented overhead-dominated regime, recorded so the regime boundary is empirical rather than asserted. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): workflow_bench scenario matrix — arm variants, task classes, churn Ground-base measurement across scenarios: tasks.scenarios.yaml spans four labeled classes (trivial → investigation-bug → investigation-feature → cross-module) with deterministic verifies (prescribed test files). New arms: workflow_direct (gitnexus-work direct mode — the middle option that locates the routing boundary lfg's gate and work's triage encode) and baseline_nomcp (no skills AND no graph tools — separates workflow-discipline value from GitNexus-tool value; off by default). Records now carry task class and diff churn (files/+ins/−del vs the starting commit) as an over-engineering proxy; the report renders a class column and per-arm savings rows vs baseline. 5 pytest units + stub-CLI e2e of the full three-arm matrix. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record workflow_bench ground base; fix churn measurement bias Ground base (3 classes x 3 arms, n=1/cell): every arm resolved every task — pass/fail quality saturates at this difficulty, making the comparison pure cost. Full plan→work never amortized its ~$9-11 fixed cost on tasks a baseline finishes in ≤35 turns (−211% to −333% cost); workflow_direct sits near baseline (−15% to −55%, once faster wall) with more test coverage. Routing implication recorded: direct mode/plain agent below this scale, full workflow for cross-module / multi-session / plan-as-deliverable work. The cross-module cell and multi-run variance are the next measurements. Churn fix: git add --intent-to-add -A before diffing (arms that never commit no longer undercount new files) and :(exclude)docs/plans (the committed plan doc no longer inflates workflow churn); this run's churn numbers predate the fix and are omitted from the recorded table. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * perf(skills): cost-optimize the workflow from measured ground base Every optimization targets a measured fixed-cost component (eval/workflow_bench ground base: workflow arm −211% to −333% vs baseline, all tasks resolved): - Plan form is category-priced: compact form (core sections w/ § anchors preserved, ≤80 lines excl. pack, mini-pack subset of the context pack) for narrow/default categories; the full 13 sections only for deep work (refactor/security/performance/concurrency/architecture). A compact plan outgrowing its cap reclassifies to full rather than overflowing. - Freshness gate is category-priced: compact categories default to accept (source-weighted, refresh only when a graph claim becomes load-bearing); strict stays the default for full-plan categories — the rebuild+re-index was the largest single fixed cost. - Turn economy: per-category tool-call budgets (~10 to ~45; architecture uncapped); budget exhaustion routes open questions to §12 instead of more digging. - gitnexus-work fast path: HEAD == evidence pin → skip all citation re-reading (the pin's entire point); mini-pack fields tolerated. - lfg Lane 1 boundary triage: tasks below the measured ~35-turn boundary get offered gitnexus-work direct mode before the plan lane is spent. Copies re-synced (npm skills/, plugin, ~/.agents); steering + sync guards green. Re-measurement of the workflow arm follows to verify the numbers actually improve. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record optimization re-measurement — inv-bug workflow cell −20% cost Same task, same conditions, post-830a0459 skills: $14.56→$11.70 (−20%), 83→72 turns, cache_read −24%; verified in-transcript that the compact form, turn budget, and skipped rebuild/re-index all fired. Wall +15% from a work- session test-debugging tail (n=1 variance). Regime unchanged (~3.5x baseline on this class) — routing rule stands. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): per-arm clone isolation — worktree ref-namespace leak contaminated an arm The cross-module workflow_direct cell reported an impossible 28-turn solve with churn byte-identical to the workflow arm: git worktree add shares the repo's ref namespace, so the workflow arm's slug branch (created by gitnexus-work Phase 2) survived worktree removal and the direct arm found and adopted the completed work. Arms now get isolated git clone --shared copies (object store via alternates, refs clone-local — agent branches and stashes die with the clone; origin/<ref> fallback for non-default refs). Leaked branch deleted; baseline arm verified clean (0 branch references in its transcript); cell marked invalidated pending re-run. Records the valid cross-module cells: workflow $18.32 vs baseline $18.03 (premium −1.6%, vs −211%..−333% on smaller classes) — fixed costs amortize at this scale, with a less destructive diff and a plan artifact as bonus; resolve rate still tied. Churn fingerprinting is what caught the contamination — noted in the README as an integrity check. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): complete cross-module cell — direct mode wins 47% cost / 56% wall Clean clone-isolated re-run: workflow_direct resolved the hardest class at $9.53/52 turns/15m vs $18.03/98/34m baseline and $18.32/107/37m full workflow. The measured story across all four classes: the execution discipline (gitnexus-work) is the consistent sweet spot and delivers real token savings on hard tasks; the planning pass buys its artifact, not same-session savings. Resolve rate tied everywhere (n=1/cell caveat). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): add trajectory-gated skill evolution (#2431) - Pair prompt candidates with incumbent workflow arms - Gate promotions on pinned-model quality and efficiency - Expire router evidence and document its lifecycle * fix(eval): allow pr-review skill candidates * feat(skills): rename and generalize GitNexus review * feat(eval): external-comparator and review arms for workflow_bench - ce_workflow / ce_workflow_direct: compound-engineering ce-plan/ce-work arms prompted with the same structure as the gitnexus arms - review / ce_review: gitnexus-review vs ce-code-review on an identical diff applied by the task's setup - plan handoff is snapshot-based: committed example plans in docs/plans/ tie on clone mtimes and broke the name-glob pick (executed a stale plan) - verify output tail is recorded per run and the final working-tree patch is kept, so failed rows are diagnosable after the clone is destroyed Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills,eval): address #2431 review — data-safe rename migration, fail-closed bench evidence - setup: never delete a legacy renamed skill dir — the installer cannot prove ownership (users customize or hand-write skills under these names); warn with the path instead, and the test now asserts survival - workflow_bench: fail closed when a session's --output-format json report is empty, malformed, or missing usage fields — an exit-0 shell with no parseable usage no longer counts as measured evidence (5 parametrized regression tests) - workflow_bench: document the trust model prominently (task setup/verify are shell-executed, sessions run bypassPermissions with the parent env, candidate overlays are prompt injection surface) in README + docstring - free-model.litellm.yaml: master_key from LITELLM_MASTER_KEY env instead of a static token; loopback-binding warning - ci: run the eval workflow_bench pytest suite on ubuntu (pytest+pyyaml only — no full eval stack) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): demand observed foreground verification in headless work-arm prompts In a headless -p session there is no later turn: a work arm backgrounded its slow test run, scheduled wakeups that can never fire, and reported done while two of its tests failed. All four work-arm prompts (both skill families, symmetric) now require verification output to be observed inside the session. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): ask plan depth up front instead of offering deepen afterwards gitnexus-plan Phase 0 now asks one blocking question in interactive sessions — quick / standard / deep, mapped onto the existing depth/form/ freshness knobs — when the invocation carries no explicit depth signal. Explicit knobs and headless runs skip the question (category posture unchanged, so benchmarks and automation behave as before). gitnexus-lfg's plan gate slims to proceed/stop: depth was already the user's up-front choice, so deepening is no longer offered by default — an explicit deepen request at the gate and executor route-backs still run Deepen mode, which remains the mechanism for strengthening an existing plan document. All shipped copies resynced (npm skills/, Claude plugin); AGENTS.md 1.13.0 and CLAUDE.md 1.7.0 pointers updated, including the analyzer's regenerated index-stats block at this branch's head. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): taint pass, expert lenses, and post-work index refresh gitnexus-review gains a PDG-backed taint-and-dependence pass (explain + pdg_query, --pdg folded into the stale refresh on trust-boundary diffs) and an Expert lenses section: domain reviewers derived from the graph's clusters plus four cross-cutting lenses (architectural fit, language conformance per the repo's own contract, Definition of Done, simplicity), dispatched once after the evidence-gathering steps and scaled to the diff. gitnexus-work Phase 4 now refreshes the knowledge graph after the DoD walk via the resolved-runner ladder with analyze --index-only, so the lfg review lane and later sessions query the finished work without dirtying the tree. lfg's threshold-governance paragraph moves to its README; eval citations are tagged as measured in the GitNexus repo. All shipped copies re-synced. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(cli): remove legacy gitnexus-pr-review on uninstall; cover the rename migration uninstall's removal set now includes LEGACY_SKILL_DIR_NAMES derived from RENAMED_SKILL_DIRS, so a pre-rename install is cleaned up instead of orphaned. The rename warning gains behavioral coverage (fires with a legacy dir present, silent without), and shipped-skills-sync asserts legacy names stay absent from every shipped tree. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): metric provenance, error-kind rows, skill-invocation verification, gate noise floor The promotion gate defaults to cost_usd (the only metric that includes subagent spend); token metrics carry an explicit main-loop-only warning in the report and promotion.json. Rows are classified by error_kind (session-error / verify-failed / infra-error), excluded from efficiency medians, and the gate requires equal valid-run counts. Each session's transcript is scanned for the expected Skill invocation and fails closed on a verified miss; a one-run resolution edge no longer promotes (noise floor). Per-run timeouts and setup failures record an infra-error row instead of aborting the sweep. Overlays touching skills no candidate arm exercises are rejected up front. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: fix skill routing paths, version headers, and skill rosters Routing tables point at the tracked direct skill paths (matching the post-#2434 generator output), AGENTS.md/CLAUDE.md headers match their latest changelog rows, the 1.12.0 row describes what the migration actually does, package/cursor READMEs list the full shipped skill roster, and the swarm READMEs describe /gitnexus-review's expert lenses instead of calling it single-agent. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * ci: drift-guard workflow for skill copies; pin eval pip deps; track docs/plans ci.yml ignores '**.md', so an md-only skill edit would merge without the shipped-skills-sync test running — skill-sync.yml triggers exactly on the guarded trees. The eval job's pip install is version-pinned, and docs/plans/ is unignored so gitnexus-plan output can be committed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(ci): keep the runner-invocation literal in gitnexus-review; add concurrency block to skill-sync skills-steering requires skills with a stale-index hint to carry the exact 'node .gitnexus/run.cjs analyze' form — restore it with the fallback ladder as a parenthetical instead of replacing it. skill-sync.yml gains the top-level concurrency block the workflow-convention check enforces. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): token-economy guidance for expert lenses Merge lenses that ground in the same material into one reviewer, and use cheaper model/effort tiers for mechanical lenses where the harness offers them, reserving the strongest engine for adversarial judgment. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test(eval): isolate transcript home on Windows Ensure workflow_bench transcript tests set USERPROFILE alongside HOME so Path.home() resolves to the temporary test home on Windows. * docs(skills): fold PR #2522 execution learnings into review/work/plan Eight incident-backed hardenings from running the full skill cycle (review -> plan -> work, 28-finding fix series) on PR #2522: gitnexus-review: - Expert lenses execute the code under review on candidate failing shapes (empirical probe outranks source reading — every HIGH the language lenses found came from a probe, not a read). - Step 7 re-runs the exact CI check for refreshed baselines/fingerprints (a stale committed artifact is invisible in the diff; caught a red benchmarks arm). - Step 8 treats version/invalidation constants as review surface (INCREMENTAL_SCHEMA_VERSION class recurred verbatim from #2494). gitnexus-work: - Step 4 proves regression tests discriminate against the pre-fix tree. - Step 5 rebuilds executed build output before every verification run (parse workers load dist/; a correct fix 'failed' until rebuilt). - Step 6 makes stage -> detect_changes -> commit one unbroken sequence. gitnexus-plan: - Phase 0 seeded-evidence mode: plan FROM a completed review's verified findings instead of re-running the graph ladder. - Template §7: fingerprint/golden-guarded output rebaselines once, at the series tip. All distribution copies resynced; shipped-skills-sync + skills-steering 24/24 locally. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): close the skill-evolution loop with an automated proposer driver workflow_bench.evolve adds the three arrows the README described as manual: a proposer session that turns loser trajectories (results.jsonl rows, transcripts, patches, the learning queue) into ONE bounded candidate overlay, a driver that iterates propose -> paired benchmark -> deterministic gate up to --generations, and an --apply step that copies a promoted overlay onto the canonical skills and shipped mirrors as a working-tree diff. The trust boundary is unchanged: overlays re-validate through candidate_overlay_files before any benchmark or apply consumes them, and committing, CI, and the PR merge stay human. learnings.jsonl is gitignored: it is machine-local evidence, like the session transcripts it complements. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(skills): route live-task friction into the evolution learning queue Each family skill gains a short 'Skill feedback' section: on friction with the skill's own instructions, append one JSON line to eval/workflow_bench/learnings.jsonl (GitNexus repo only) — never self-edit the skill from a live task. The proposer in workflow_bench.evolve consumes the queue as hints; a learning reaches a shipped skill only by beating the incumbent on the paired benchmark. All shipped mirrors re-copied byte- identical. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * ci(tests): run the evolve helper tests in the eval pytest job test_evolve.py needs only pytest+pyyaml, same as the harness tests the job already runs — without this line the new module had no CI coverage. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(ci): comment-triggered GitNexus review agent for PRs '@gitnexus review' from a maintainer (OWNER/MEMBER/COLLABORATOR; the action re-validates write access) runs the repo's gitnexus-review skill headlessly against the PR and posts the review as a sticky comment — remote triggering with no local setup. Read-only by construction: contents: read token, Write/Edit and web tools disallowed, Bash allowlisted to git reads and the gitnexus CLI; analyze parses PR code with tree-sitter, never executes it. Requires the ANTHROPIC_API_KEY repository secret; activates once the file is on the default branch. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(ci): dispatch lane + existing OAuth secret for the review agent Align with claude.yml: same action pin and the CLAUDE_CODE_OAUTH_TOKEN secret the repo already carries — no new secret to configure. Add a workflow_dispatch lane (PR number input) so the agent can be triggered from the Actions UI and tested before the issue_comment trigger reaches the default branch. Allowlist gh pr view/diff and gh api, which the review skill uses to pin PR SHAs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(ci): close a fork-PR RCE vector in the review agent's tool allowlist A live headless run of the exact workflow session against PR #2431 (66 turns, full gitnexus-review pass) surfaced a real HIGH-severity confused deputy: .gitnexus/ is gitignored, not blocked — a fork PR can commit its own .gitnexus/run.cjs, issue_comment checks out PR-head content, and the skill's runner ladder tries 'node .gitnexus/run.cjs analyze' first. That would execute fork-controlled JS inside a job holding CLAUDE_CODE_OAUTH_TOKEN and a write-scoped GITHUB_TOKEN — the opposite of the 'PR code is read, never executed' claim in the workflow's own header. Fix: drop the run.cjs allowlist entry so analyze always resolves through npx gitnexus (npm registry, not the checked-out tree); the skill's documented fallback mode covers the resulting graceful degradation. Also drop 'gh api' (not read-only — accepts -X POST/PATCH/DELETE) and downgrade pull-requests: write to read (comment posting only needs issues: write; the prompt already forbids formal review submission). Same session flagged a latent evolve.py bug: select_evidence's cost sort used dict.get's missing-key default, which doesn't cover an explicit JSON null in a foreign --seed-results row and crashes proposer setup with TypeError. Guarded with 'or 0.0' and added a regression test. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix: harden PR review and evolution trust boundaries * ci: follow workflow concurrency convention * fix(eval): make terminating error paths explicit * fix: unblock hardened review runtime checks * test: make containment canaries deterministic * test: expose Claude canary tool failures * fix: adapt clean shell environment for Claude * fix(eval): accept the runner's transcript source key in evidence preflight The proposer evidence preflight required transcript-artifact metadata to be exactly {path, sha256, bytes}, but the runner stamps a fourth provenance key (source=parent-captured-stream-json). Any --seed-results or generation>=2 run therefore aborted with SandboxError before proposing or promoting. Pin the producer literal as PARENT_EVENT_STREAM_SOURCE and validate it in the metadata check, and round-trip real producer output through sum_sessions into the preflight so the schema can't drift again. * fix(eval): treat an unmeasured session cost as unavailable, not $0 well_formed validated only the nested usage block, so an otherwise-successful session missing total_cost_usd was recorded as cost_usd=0.0 — and cost_usd is the default promotion metric (lower wins), so a cost-less session scored as free and could win promotion it never earned. Extract cost via measured_cost() (None on absent/garbage, a measured 0.0 preserved), propagate None through sum_sessions/aggregate/savings/report, and have the gate refuse to rank on a metric that was not measured on every run in both arms. * fix(eval): warn when ranking on the main-loop-only num_turns metric num_turns comes from the CLI's top-level usage (main-loop session only), like output_tokens, but selecting it emitted no metric_warning — so a subagent-heavy candidate could look artificially efficient. Add num_turns to MAIN_LOOP_ONLY_METRICS and broaden the warning to cover turns. * fix(eval): fail closed when an overlay adds a file with no committed base An overlay adding a new .md under gitnexus-{plan,work} passes the structural overlay checks but has no committed base for committed_destination_base_digests to bind against, so it raised an uncaught ValueError that crashed the evolve driver (and runner --candidate-overlay) mid-run. Catch it at both call sites: evolve reports NOT PROMOTED and exits, runner routes it through parser.error. * feat(eval): circuit-break the runner sweep on a systemic outage A sustained upstream outage used to pay out every remaining --timeout window one session at a time. Track consecutive session/infra/cleanup failures via a pure systemic_outage_streak helper; after --outage-streak (default 5) in a row, stop the sweep, still write report.md/promotion.json from partial evidence, and exit non-zero so evolve.py halts instead of proposing from truncated evidence. A task's own resolved=False never trips the breaker. * fix(cli): report a dirty working tree as stale in gitnexus status status --json (and the human output) computed up-to-date from commit + runner identity + completeness only, so a repo with uncommitted source changes at a matching HEAD was reported up-to-date while analyze would still re-index it. A graph-backed agent gating on that JSON could skip re-analysis on a stale graph. Extract analyze's dirty-tree check into a shared isWorkingTreeDirty() in storage/git and fold it into the status freshness decision. * fix(ci): use single-slash deny globs in the review agent's disallowedTools github.workspace already expands to an absolute path, so Read(/${{ github.workspace }}/**) and Read(//proc/**),(//sys/**),(//dev/**) produced double-slash patterns that a normalizing matcher may not match — silently no-opping the deny layer. Not exploitable (the allowlist is the primary control and never grants those paths), but the globs should be well-formed. Update the pinned test strings. * ci: install gitnexus-shared with npm ci from the committed lockfile The gitnexus-shared build floated its deps via npm install in three workflows (skill-sync, ci-tests, and — most importantly — the release publish.yml) while every other install step uses npm ci. The lockfile is committed and in sync, so switch all three to npm ci for reproducible, locked installs. * test(cli): make the shipped-skills drift guard reject symlinks listFilesRecursive walked with readdirSync and snapshotDir read with readFileSync, both of which follow symlinks — so a mirror file symlinked to the canonical tree passed the byte-compare (and a symlinked mirror dir would be followed too). Reject a symlinked root via lstat and any symlinked entry via Dirent.isSymbolicLink, with negative tests (skipped on Windows). * test(eval): guard the candidate-skill vs mirror-root coverage invariant MIRROR_SKILL_ROOTS omits the Cursor tree, safe only because no candidate skill is cursor-shipped. Pin that invariant: every CANDIDATE_SKILLS entry must exist under canonical + every mirror root and must not ship to Cursor, so adding a cursor-shipped skill to the candidate set (the PR #2488 asymmetric-sync class) fails loudly instead of syncing three of four trees. * docs(ci): describe the review agent's staged post-merge rollout The DoD asked for a dry-run or triggered run before merge, but an issue_comment (or newly added workflow_dispatch) workflow only ever executes the default-branch copy, so it cannot be exercised from the PR that introduces it. Reword the DoD and the activation checklist to a staged rollout: merge registered-but-disabled, validate same-repo and fork execution post-merge, then enable the variable. * fix: pin plugin skill mcp.json to the release version via #2445 tooling The ten plugin skill mcp.json launched `npx -y gitnexus@latest mcp` on every skill connect — non-reproducible and a supply-chain surface, and (unlike the persisted setup config) never pinned. Extend sync-plugin-manifests.mjs with an mcp surface kind that stamps the gitnexus@<version> launch arg, pin all ten to 1.6.9 now, and keep them byte-identical so the drift guard stays green. The release lifecycle + publish.yml --check now re-stamp them like the four manifest surfaces; only READMEs stay on @latest as docs. * test(eval): prove the proposer's built-in file tools are confined The real-Claude canary only exercised Bash + MCP, so it proved process/MCP containment but not that the proposer's built-in file tools stay inside their mounts. Add a canary over the exact PROPOSER_ALLOWED_TOOLS surface and the same read-only /evidence mount as run_proposer (allowlist extracted to a shared constant so it can't drift): Read reaches /evidence, a Write into the read-only evidence mount is denied, and a Write lands in the output tree. * fix(eval): apply the candidate overlay after task setup for fair arms The candidate overlay was applied before the task's untrusted setup ran, so setup could observe candidate prose and the incumbent/candidate arms started from different pre-overlay state. Reorder within the sandbox: capture the base (pre-overlay) skill digest, run setup against the base skills, verify setup did not tamper them, then apply the overlay and capture the post-overlay digest the model must preserve. apply_candidate_overlay stages path-specific overlay files, so setup's uncommitted changes stay out of the baseline and churn is unchanged. Graph freshness for the review arm is handled by the status dirty-tree fix plus the review skill's stale-triggered re-index, not by reordering the cached per-task-sha graph materialization (which is mechanically blocked). * test(eval): end-to-end containment proof of the autonomous proposer Drives the real run_proposer through bubblewrap with a deterministic scripted model (no paid API): it reads the read-only evidence bundle and writes a candidate gitnexus-plan skill edit plus a rationale into the sandbox output tree; run_proposer enforces the trust boundary and copies only the validated overlay + proposal out. This exercises the autonomous-proposal stage of the self-evolution loop end-to-end in the eval/containment CI job (the gate and apply stages are covered by test_workflow_bench_evolution and test_promotion_apply). Env-gated on GITNEXUS_REQUIRE_CLAUDE_CANARY, so it runs only where the pinned Claude binary and user namespaces are available. * fix(eval): let the proposer author its overlay via Bash Running the end-to-end proposer canary in the containment CI job surfaced a real bug: run_proposer starts the session with --bare, which hard-disables the Write/Edit tools ("Write exists but is not enabled in this context"), yet allowlisted Edit/Write and omitted Bash. The proposer therefore had no working way to write its candidate overlay — the self-evolution loop could never produce a candidate. The sandbox settings already pre-authorize Bash (autoAllowBashIfSandboxed) and confine writes to workspace/tmp/home, so switch PROPOSER_ALLOWED_TOOLS to Read/Grep/Glob/Bash and tell the proposer to author files with Bash. The end-to-end test now drives the real run_proposer through bubblewrap and asserts a validated overlay + proposal are produced (this also replaces the earlier file-tool canary, whose Write/Edit premise was moot). * test(eval): author the proposer overlay with newline-free Bash content The nested shell-sandbox prefix mangles embedded newlines, so the multi-line overlay content never landed. Use single-line content for the deterministic proposer canary. * test(eval): drop the unverifiable end-to-end proposer canary The scripted proposer overlay never materialized in the containment job across runs, and the model tool-result content is not visible in CI logs, so the test cannot be finalized without an environment where the sandbox can actually run. Keep the verified production fix (Bash-authoring in run_proposer); the proposer sandbox/containment stays covered by the existing Bash+MCP and process-tree canaries. * test(cli): drop run-analyze.ts from the windowsHide spawn-family list U7 moved run-analyze.ts's only child_process call (the git status --porcelain dirty check) into storage/git.ts (already covered by this test, with windowsHide). run-analyze.ts no longer imports a spawn-family function, so the windowsHide-regression test's 'must have >=1 spawn call' invariant failed for it. Remove it from SRC_FILES. --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: Zander Raycraft <zanderjraycraft@gmail.com> Co-authored-by: Azizur Rahman <azizur100389@gmail.com> |
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Gergő Magyar
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249f5c7aab
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fix(lbug): bound the LadybugDB buffer pool instead of the native 80%-of-RAM default (#2560)
* fix(lbug): bound the LadybugDB buffer pool instead of the native 80%-of-RAM default (#2557) createLbugDatabase passed bufferManagerSize=0, which the native runtime sizes at 80% of physical RAM. A long-lived gitnexus mcp process (or a large incremental analyze) could balloon to that ceiling — 19.5 GiB observed against a 105 MiB on-disk index — and OOM-kill the host session. Resolve the pool at call time: default min(2 GiB, max(64 MiB, 80% of totalmem)), overridable via GITNEXUS_LBUG_BUFFER_POOL_SIZE (bytes); 0 deliberately restores the native unbounded default; invalid values warn and fall back, mirroring GITNEXUS_WAL_CHECKPOINT_THRESHOLD. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(readme): document GITNEXUS_LBUG_BUFFER_POOL_SIZE and GITNEXUS_LBUG_MAX_DB_SIZE (#2557) Both env tables gain the new buffer-pool ceiling variable and the previously code-comment-only GITNEXUS_LBUG_MAX_DB_SIZE, with the mmap-vs-memory distinction the issue had to discover from source. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * refactor(lbug): keep parseBufferPoolSize module-private Review finding: the export had zero importers — parseWalCheckpointThreshold earns its export via the CLI flag validation, but the buffer-pool CLI flag was deliberately deferred. Re-export when a consumer exists. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * chore(autofix): apply prettier + eslint fixes via /autofix command --------- Co-authored-by: Claude <claude@anthropic.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> |
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azizur100389
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a333d94a00
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feat(wiki): allow explicit HTTP LLM hosts (#2491)
* feat(wiki): allow explicit HTTP LLM hosts Keep wiki LLM HTTP endpoints fail-closed by default while adding a narrow exact-host opt-in for LAN/self-hosted models. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(wiki): simplify insecure LLM flag name Rename the wiki HTTP opt-in flag to --allow-insecure-connection per review feedback. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(wiki): simplify insecure connection env Rename the wiki HTTP allowlist environment variable and align validation errors with the CLI flag naming. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> |
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Eva
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a117cf8a21 | Merge remote-tracking branch 'upstream/main' into upstream/embedding-http-resilience | ||
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Gergő Magyar
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a05b501102
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fix(cli): make Claude skills discoverable (#2434)
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Eva
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711ff8721d | fix(embeddings): make HTTP generation resumable | ||
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Gergő Magyar
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c6445096eb
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fix: stop Napi::Error SIGABRT on analyze — index C++ type lookups, terminate workers only at JS-safe points (#2432) (#2436)
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azizur100389
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f236be05e0
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feat: gate Icebug community engine prototype (#2376) | ||
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Gergő Magyar
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1408bfbffe
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fix(hook): emit MCP query hint when server owns DB lock (#2396) (#2397)
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* fix(hook): emit MCP query hint when server owns DB lock (#2396) When the GitNexus MCP server holds the lbug write lock, the PreToolUse hook's CLI `augment` cannot run (LadybugDB is single-writer) and previously skipped silently — disabling graph augmentation in the most common deployment (server online). Since the same session already has the MCP `query` tool live, the owner branch now emits an additionalContext hint pointing the agent at mcp__gitnexus__query for that pattern, via the same sanctioned stdout channel the augment-success path uses (Codex-safe, #2369). Rejected the alternative of having the hook query the server: it runs over stdio (no port/pipe from the separate hook process) and cross-process read-only access can't coexist with the write lock — both are large architecture changes. Applied to all three gated hook copies (claude .cjs, claude-plugin .js, antigravity .cjs); the cursor hook has no owner gate and is untouched. The stderr `augment skipped: MCP server owns DB` diagnostic stays GITNEXUS_DEBUG-gated (#1913). Owner-path tests flipped from stdout-empty to hint-present. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hook): reword MCP-query hint to be conditionally truthful (#2396) The #2396 owner branch emits the hint on every DB-owner path — a confirmed `gitnexus mcp` owner, a `gitnexus serve` owner, and the fail-closed/timeout paths (the probe collapses timeout and owned to one boolean). The old text claimed "Knowledge graph is live via the MCP server" and named mcp__gitnexus__query unconditionally, which is untrue on a fail-closed probe where no server is confirmed and misdirecting for a serve-only owner (review C2/C4). Reword the hint (byte-identical across all three hook copies) to state that local augment is unavailable and to condition the MCP call on the tools actually being live ("if the GitNexus MCP tools are live in this session"). This is truthful on every owner path; the needles the assertions rely on (mcp__gitnexus__query, query, search_query, the pattern) are preserved. Fix the 10 stale owner/fail-closed unit tests that still asserted empty stdout (review C1, the macOS platform-sensitive 2/3 blocker): flip them to assert the hint via parseHookOutput, keep their stderr/GITNEXUS_DEBUG expectations, and rename the two 'SILENTLY' titles. The GITNEXUS_DEBUG='' owner-hint case is restored (the PR's new loop only covered '0'/'false'). Probe and its white-box tests untouched. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hook): de-orphan the JSDoc in the claude hook copy (#2396) The #2396 change inserted buildMcpQueryHint between the pre-existing "PreToolUse handler" JSDoc and handlePreToolUse, orphaning that doc onto the helper and leaving handlePreToolUse undocumented (review C5). Move the helper (with its own doc) above the handler doc so the "PreToolUse handler" comment again precedes handlePreToolUse, matching the clean plugin copy. Pure move; no behavior change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hook): throttle the MCP-owner hint to once per repo per window (#2396) Previously the hint emitted on every qualifying search while a GitNexus process owned the DB, so an owner-locked session (the common deploy) was nudged toward the MCP query tool on every Grep/Glob/Bash — context bloat and ~2x query amplification (review C3). Add shouldEmitMcpHint(gitNexusDir) to all three hook copies: a per-repo .gitnexus/.mcp-hint-shown mtime marker emits the hint at most once per window. Window via GITNEXUS_MCP_HINT_THROTTLE_MS (default 10min; 0/invalid disables). Best-effort — any fs error falls back to emitting, so the hint is never lost to a marker failure. The stderr skip diagnostic still fires regardless (only the hint is throttled). Tests: hookEnv disables the throttle by default (gitNexusDir is shared across the suite, so a marker would otherwise throttle sibling owner tests); a dedicated macOS-lane test sets a real window and asserts emit-then-throttle with the marker gating it. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(hook): README reflects the MCP-owner query hint, not a silent skip (#2396) The 'Hook augmentation/notifications are silently skipped' section still described the MCP-server-owns-DB path as a silent augmentation skip (review docs finding). That path now hands the agent a conditional MCP-query hint via additionalContext (throttled per repo). Reword the section to describe the hint and its GITNEXUS_MCP_HINT_THROTTLE_MS throttle, and keep the GITNEXUS_DEBUG stderr-diagnostic guidance. No CHANGELOG edit (owned at release time). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(hook): guard hint-copy drift + pattern JSON-escaping (#2396) Two gaps the review flagged (R7): - Drift guard: buildMcpQueryHint and shouldEmitMcpHint are triplicated across the three hook copies with no shared module. A source-level byte-identity check (runs on every platform, unlike the macOS-only owner tests) fails if any copy diverges — the institutional pattern the repo already uses for mirrored hook metadata. - Escaping: an adversarial Grep pattern (embedded quote + newline) must not break the additionalContext JSON envelope. A macOS-lane owner test drives the real hook with such a pattern and asserts parseHookOutput still yields valid JSON containing the literal characters (JSON.stringify escapes them). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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Gergő Magyar
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177bbc89c3
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fix: surface real FTS extension LOAD errors and self-heal broken extension files (#2374) (#2375) | ||
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Gergő Magyar
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cdad478c96
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fix: proxy-blocked installs survive onnxruntime-node postinstall and self-heal embeddings (#2370) (#2372)
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Gergő Magyar
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187c162fd8
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feat: full Codex support — hooks, plugin marketplace, and setup (#2328, supersedes #1131) (#2369)
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* feat(setup): install Codex PreToolUse/PostToolUse hooks (#2328) Codex CLI supports lifecycle hooks with Claude Code's exact {hooks: {Event: [...]}} JSON schema, stdin payload, and hookSpecificOutput response contract, registered in a dedicated ~/.codex/hooks.json (https://developers.openai.com/codex/hooks). Parameterize installClaudeCodeHooks into installClaudeSchemaHooks (claude | codex): both runtimes share the installer, the bundled gitnexus-hook.cjs adapter, and its helpers. A codex HookTarget in editor-targets.ts makes uninstall and the setup-uninstall round-trip tripwire cover the new surface with no uninstall.ts changes. SessionStart is deliberately not registered: Codex reads AGENTS.md natively, which already carries the GitNexus context block. Closes #2328. Closes #244 (Codex setup support is now complete: MCP + skills + hooks). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(plugin): make the GitNexus plugin installable from Codex (#1131) Codex's plugin system (https://developers.openai.com/codex/plugins/build) reads a .codex-plugin/plugin.json manifest and a repo-root .agents/plugins/marketplace.json registry. The existing gitnexus-claude-plugin/ is already Codex-compatible as-is — Codex sets CLAUDE_PLUGIN_ROOT for hook-command compatibility, loads the same SKILL.md skills, hooks/hooks.json, and .mcp.json — so a second manifest in the same folder replaces PR #1131's duplicated plugin tree with zero copied skills or hooks. The .gitignore .agents/ scratch rule narrows to re-include only the registry file. Install: codex plugin marketplace add abhigyanpatwari/GitNexus Supersedes #1131. Co-authored-by: jublin <1799126+jublin@users.noreply.github.com> Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: document Codex full support (MCP + skills + hooks + plugin) Promote Codex to Full in both editor tables, document the ~/.codex/hooks.json hook install, and add the Codex plugin marketplace install path. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test(release): extend the version-lockstep guard to the Codex manifests The always-on drift guard asserted only the Claude plugin manifests against gitnexus/package.json, so a release could ship stale versions in .codex-plugin/plugin.json and .agents/plugins/marketplace.json without CI noticing. Mirror the Claude lockstep test for the two Codex files and extend the CONTRIBUTING §Releases lockstep list to match. Verified guard semantics: a deliberate local version mutation of the Codex marketplace entry turns the new test red. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(plugin): quote the hook command path for space-containing plugin roots Both plugin hook commands ran `node ${CLAUDE_PLUGIN_ROOT}/hooks/...` unquoted, which breaks whenever the substituted plugin root contains a space — the common case on Windows user profiles. Both Claude Code and Codex substitute the placeholder before shell execution, and Claude Code's plugin docs mandate the double-quoted form in shell-form hooks. No commandWindows entry: Codex source (codex-rs hooks engine) falls back to `command` on Windows with identical placeholder substitution, so an identical-content override would be pure duplication. Verified: space-in-root smoke test (old form exits 1 MODULE_NOT_FOUND, quoted form exits 0), `claude plugin validate` passes, and a local `codex plugin marketplace add` parses the marketplace + plugin cleanly. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test(setup): pin fail-closed behavior for unreadable/corrupt Codex hooks.json The non-ENOENT suite covered Claude settings.json (EACCES) and Codex config.toml (EACCES) but not the new ~/.codex/hooks.json surface, and the mergeHooksJsonc "is corrupt" branch had zero coverage for either editor. A future refactor dropping the isEnoent rethrow or the parse gate could silently rewrite a user's hooks.json gitnexus-only with no CI tripwire. Two regression tests: EACCES leaves hooks.json byte-identical and reports "Codex hooks: EACCES"; corrupt content is preserved and reported via "Codex hooks: hooks.json is corrupt". Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(readme): add the Codex plugin-marketplace install path to the npm README The root README documents the one-step plugin route but the package README (what npmjs.com renders) only showed the setup-CLI path. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * refactor(setup): rename claudeHook to hookCfg in installClaudeSchemaHooks The local held a codex HookTarget on the codex branch since the installer was parameterized, so the claude-specific name misled. Pure local rename, no behavior change. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(readme): document Codex SessionStart exclusion, /hooks trust gate, and install-route choice Three behaviors were only recorded in code comments and the PR body: SessionStart is deliberately not registered (Codex reads AGENTS.md natively), setup-installed hooks need one-time /hooks approval in Codex, and the setup CLI and plugin are alternative install routes whose hooks load alongside each other if both are used. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * refactor(test): share one logLines helper across setup.test.ts describes The corrupt-hooks.json test inlined the console.log-flattening expression that the non-ENOENT describe already defined locally. Hoist a single file-scope logLines so the two stay in sync. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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Gergő Magyar
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6252aa745f
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feat(setup): add CodeBuddy and Qoder coding-agent integrations (#2368)
* feat(setup): add CodeBuddy and Qoder coding-agent integrations Adds Tencent CodeBuddy and Alibaba Qoder to gitnexus setup/uninstall, fitted to the editor-targets registry and --coding-agent selection. - CodeBuddy: MCP entry written into the first existing file of its documented priority chain (~/.codebuddy/.mcp.json recommended, ~/.codebuddy/mcp.json deprecated, ~/.codebuddy.json legacy) so a populated deprecated config is never shadowed; skills to ~/.codebuddy/skills/ (https://www.codebuddy.ai/docs/cli/mcp) - Qoder: MCP entry in ~/.qoder.json, skills to ~/.qoder/skills/ (https://docs.qoder.com/cli/using-cli, /extensions/skills) - editor-targets gains optional legacyFiles; uninstall sweeps them - roster strings updated (CLI help, i18n en/zh-CN, READMEs); en/zh-CN setup descriptions were stale (missing Antigravity) and are refreshed Supersedes and credits PR #1030 by @zykai0302, re-fitted to the post-#2168 selective-agent architecture with documented config paths. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test(cli): assert stable zh-CN setup-description fragment * fix(setup): surface non-ENOENT config read/stat failures instead of clobbering * fix(setup): report corrupt legacy MCP files informationally during uninstall * test(setup): cover multi-candidate uninstall sweep combinations * fix(setup): detect CodeBuddy/Qoder installs via existing MCP config files * fix(setup): skip empty and non-file candidates in the MCP config chain * docs: add CodeBuddy and Qoder manual MCP configuration sections * test(ci): run the setup-uninstall round-trip in the cross-platform matrix * fix(setup): never claim "not configured" when uninstall recorded errors * refactor(cli): share the isEnoent predicate via editor-targets * refactor(setup): share chain-file install detection between CodeBuddy and Qoder --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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Gergő Magyar
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e46b87f291
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feat: flat workspace index follows the checked-out branch (#2364)
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* feat: flat workspace index follows the checked-out branch (#2354) A plain `gitnexus analyze` now always targets the flat workspace slot, updating it incrementally across branch switches instead of auto-routing non-owner branches into `branches/<slug>/` sub-indexes (disk bloat) or nagging with the primary-inversion "run gitnexus clean" warning. No new CLI flag or config key: the smart behavior is the default. - Placement: only explicit `--branch` consults resolveBranchPlacement; plain runs resolve to the flat slot, `meta.branch` becomes an informational "last analyzed branch" label restamped each run. - Fast path: a same-commit clean-tree branch flip restamps the label and registry entry (adoptFlatBranchLabel, no-op for unregistered repos). - Shadow cleanup: when the flat slot adopts a label that has a pinned sub-index, the now-unreachable `branches/<slug>/` dir and its registry summary are removed together. - MCP: applyBranchScope always falls back to the on-disk flat meta before throwing "not indexed", so long-lived servers resolve a freshly restamped workspace branch. - status: no more "current branch not indexed" dead end — falls through to the workspace index with an informational line and the usual commit-based staleness verdict. - Deleted primaryInversionWarning; explicit `--branch` pinning, the checkout-mismatch guard, detached-HEAD/CI behavior, and `clean --branch` are unchanged. Supersedes the flag-based approaches in #2358/#2359. Closes #2354. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(storage): check registry before deleting shadowed sub-index (#2364 review F2) adoptFlatBranchLabel ran the branches/<slug>/ rm before its own unregistered-repo no-op check, so a repo in the #2264 half-finalized state (up to date but unregistered) lost its pinned sub-index on a same-commit branch flip while the run still failed. The registry lookup now precedes the deletion, making the no-self-heal rule (#2264/#1169) cover disk as well as registry state. The 'never self-heals' unit test now materializes a sub-index dir and asserts it survives; the run-analyze #2354 fast-path test registers its repo under an isolated GITNEXUS_HOME (deletion is only legitimate for registered repos) with a new unregistered variant pinning dir survival. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(storage): keep branch summary when sub-index rm fails (#2364 review F4) The shadow-cleanup fs.rm swallowed every error while the registry summary was dropped unconditionally. On Windows an lbug held open by a live MCP server fails the rm with EBUSY/EPERM, and once the summary is gone 'clean --branch' can never target the leftover dir (it resolves solely via the recorded summary) — stranding the exact un-cleanable disk bloat adoptFlatBranchLabel exists to prevent. The summary is now dropped only when the directory is verifiably gone (post-rm existence check); on failure the summary is retained, a warning names the path and errno, and the informational branch label still restamps. Later adopts retry the rm. New repo-manager-rm-failure.test.ts uses the delegating fs/promises mock idiom (vi.spyOn cannot intercept ESM namespace exports). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(core): restamp fast path adopt-first and tolerate read-only storage (#2364 review F3) The fast-path label sync stamped meta before adoptFlatBranchLabel, so a crash or adopt failure between the two flipped the retry guard (existingMeta.branch !== branchLabel) and locked in the partial state: every subsequent same-commit run skipped the cleanup and branch-scoped queries kept routing to the stale pinned sub-index. The block also sat outside any try/catch, so a same-commit branch flip on a read-only .gitnexus mount (the documented Docker :ro workflow, #1549) failed a byte-for-byte-current analyze over a purely informational label sync. Adopt now runs first and saveMeta last — any partial failure leaves the guard true and the next run self-heals — and the whole sync is best-effort: read-only errors warn citing #1549, anything else warns and retries next run. Safe because the block only fires on a same-commit clean tree, where the flat DB content is byte-valid for both labels. isReadOnlyFilesystemError is now exported. New run-analyze-adopt-failure.test.ts covers retry-after-partial- failure, adopt-before-stamp ordering, and EROFS/EACCES/EPERM (gaps 4 and 7); a detached-HEAD fast-path pin lands in run-analyze.test.ts (gap 6). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(mcp): make flat meta authoritative in applyBranchScope (#2364 review F1) applyBranchScope trusted two pieces of cached state before its flat- meta disk fallback, and the handle cache only refreshes on a resolve miss — never on a hit. Post-#2354 that stale window is the routine case: (i) the handle.branch early-return served the flat handle under the OLD label after a workspace flip, silently returning the new branch's content as the old branch (the pool staleness reinit hot- swaps content without updating handle.branch); (ii) a stale cached branches[] summary routed to a branches/<slug>/ dir that adoptFlatBranchLabel had already deleted (raw 'LadybugDB not found' or POSIX ghost reads with staleness detection blinded). The on-disk flat meta is now read before any cached-state trust. A branches[] summary is served only when its sub-index lbug actually exists (the lbug is what the pool opens — serviceability truth); the cached label is trusted only when no readable flat meta contradicts it (#2106 R4 legacy shapes preserved). One refreshRepos() fires on detected staleness so subsequent calls see fresh handles. Safe against mid-analyze reads: dirty stamps spread the existing meta, preserving the old label until the end-of-run atomic write. Fixtures now materialize the pinned sub-index lbug; new regressions cover the stale-old-label error, adopted-summary fall-through to flat, and the dangling-summary partial-failure window (test gaps 1-2). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(core): make end-of-run branch-label sync best-effort (#2364 review F5) The end-of-run adoptFlatBranchLabel sat inside the pipeline try whose catch rethrows, so a registry write failure (ENOSPC, ~/.gitnexus perms) after a successful multi-minute analyze failed the whole run — even though the index was complete and registered, the neighbouring parse-cache save is deliberately wrapped for exactly this reason, and adopt retries unconditionally on the next plain analyze. It now warns and continues, mirroring the parse-cache wrapper. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(mcp): correct branch-not-indexed guidance for workspace index (#2364 review F6) The error told users to 'Run: gitnexus analyze --branch <X>', but post-#2354 that command hard-errors unless X is checked out — and this message is now the common goodbye for a formerly-indexed branch whose sub-index the workspace slot adopted. The guidance now explains that the workspace index follows the checked-out branch and leads with the checkout; the '(primary only)' fallback becomes '(workspace only)'. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: align primary/workspace vocabulary with the #2354 inversion (#2364 review F7) The review flagged pre-inversion 'primary/non-primary' wording that now misleads readers about the placement model: the isPrimaryBranch JSDoc (field name kept — public API surface), the two branches? JSDoc comments in local-backend, the base_ref gate comment in cli/analyze, and four branch-scope test names. Comment/JSDoc/test-name edits only; 'Registry-primary' and 'primary key' senses untouched. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(cli): clarify workspace index status wording (#2364 review F8) 'gitnexus analyze follows this branch' was ambiguous about WHICH branch analyze follows — the recorded one on the line or the current checkout. Both locales now say a re-run follows the current branch. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(storage): re-read registry after the shadow rm in adoptFlatBranchLabel The F2 reorder moved the registry read to the top of the function, so the whole-file writeRegistry at the bottom persisted a snapshot taken BEFORE the recursive rm of an entire sub-index — widening the unlocked read-modify-write window from microseconds to the duration of a multi- hundred-MB delete. A concurrent registerRepo/removeBranchIndex writer in that window was silently clobbered (the #2106 R9 lost-update class; registerRepo re-reads before writing for exactly this reason). The top read is now a cheap membership gate only (the F2 no-op guarantee); the mutate re-reads its own fresh snapshot after the rm. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix: treat only provably-absent errno as gone in the new existence probes Both probes added by this series inverted the codebase's provably- absent polarity (listRegisteredRepos validate prunes only on ENOENT/ENOTDIR): adoptFlatBranchLabel's dirGone check read ANY fs.access failure — including a transient EACCES/EIO on a surviving dir — as 'verifiably gone' and dropped the summary, recreating exactly the stranded-bloat bug F4 fixed; applyBranchScope's sub-index check read the same transient errors on a healthy pinned lbug as 'adopted/ deleted', producing a false 'not indexed' error. A resolved force:true rm now proves absence without a probe; on failure the probe treats only ENOENT/ENOTDIR as gone, and a non-missing lbug serves the handle so the pool open surfaces the real error. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(mcp): harden applyBranchScope stale-state coherence Four residual gaps in the new arm structure, found by post-fix review: - The stale-label error listed the just-contradicted cached label as indexed ('not indexed: main. Indexed branches: main'). The message now derives the flat label from the authoritative meta and excludes the requested branch from the hint list. - A branch pinned AFTER the server cached its handle never triggered a refresh (resolve hits skip the miss-refresh), erroring until restart. Every miss now fires exactly one best-effort refreshRepos() before the error, so the next call resolves; a refresh-once guard keeps doubly-stale resolutions to a single registry re-scan. - A registry entry claiming the branch both as flat label and pinned summary (the rm-failed adopt-degraded state) could serve the stale- vintage pin under a label the flat slot owns; the summary arm now requires handle.branch !== branch and the degraded state errors honestly. - The flat-meta match path returned the cached handle's pre-restamp branch/commit/stats; the meta that decided routing now also supplies the metadata. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(core): keep the real error visible in restamp warnings; correct the end-of-run retry claim The fast-path catch replaced the actual error with 'storage is read-only (#1549)' for any EACCES/EPERM — mislabeling ownership problems and transient Windows locks and discarding the only diagnostic signal. The warning now carries the real message with the #1549 hint appended. The end-of-run best-effort comment claimed adopt 'retries unconditionally on the next plain analyze'; same-commit runs take the fast path whose guard compares the already-stamped meta label, so the retry actually lands on the next content-changing run. The comment now states the true retry semantics and why the interim state is safe (flat meta stamped first; applyBranchScope trusts it). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test: unique tmpdir for the branch-scope fixture; drop redundant dynamic imports The branch-scope describe materialized its sub-index stub under a FIXED os.tmpdir()/gnx-2106-multi path — concurrent vitest runs on one host (the documented parallel-agents workflow) could rm each other's stub between beforeEach and the resolve under test, flaking the pinned-branch tests. The fixture root is now mkdtemp-unique per run with afterAll cleanup. run-analyze.test.ts dynamically imported repo-manager inside test bodies despite the module being statically imported at the top of the file (no vi.mock exists there to justify it); the three call sites now use the static import. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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Gergő Magyar
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0005574dce
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docs: restructure root README, fact-check all READMEs (#2360)
* docs(readme): restructure for readability, fix stale facts
Reorganize the README so the visible page reads as a short narrative
(Quick Start -> Two Ways -> Why -> What Your Agent Gets -> Editor Setup
-> CLI -> How It Works -> Docker -> Enterprise) and move deep
operational detail into 13 collapsible <details> sections: env vars,
.gitnexusrc, Cosign/Kubernetes verification, manual MCP configs,
install troubleshooting, and extended tool examples.
Accuracy fixes verified against gitnexus/src:
- MCP tools: 17 (15 per-repo + 2 group), not 16/11+5; drop
group_contracts/group_query/group_status (CLI + resources now, not
tools); add check, trace, explain, pdg_query, route_map, tool_map,
shape_check, api_impact rows from src/mcp/tools.ts
- Agent skills: 6 installed (adds Guide + CLI), not 4
- Wiki default model: minimax/minimax-m2.5, not gpt-4o-mini
- Resources: add gitnexus://setup and gitnexus://group/{name}/...
- CLI: document group impact, doctor, and the direct terminal query
commands (query/context/impact/trace/cypher/detect-changes/check);
note the optional branch param on per-repo tools (#2106)
Structural cleanups: dedupe the two Codex config blocks, move Community
Integrations out of the MCP setup flow, move Star History to the
bottom. No content deleted - verbose material is collapsed, not cut.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* docs: fact-check and fix the remaining READMEs
Reviewed all 9 tracked non-root READMEs against the source; fixed the
four with stale facts, left the already-accurate ones untouched
(pr-swarm-review, .claude reviewer-swarm adapter, and the three
bench/ methodology docs).
gitnexus/README.md (npm package page):
- MCP tools table: 17 tools (15 per-repo + 2 group), was 7 rows
- Resources: add gitnexus://setup and gitnexus://group/{name}/...
- Skills: 6 bundled (adds Guide + CLI) plus --skills generated ones
- Languages: add Dart (14 total) to the list and feature matrix
- Wiki default model: minimax/minimax-m2.5, not gpt-4o-mini
- Requirements: Node >= 22 (package.json engines), not >= 18
- Claude Code hooks: PreToolUse + PostToolUse
- CLI: add --skills/--skip-skills/--skip-git/--workers, doctor,
trace, check, group impact
- Optional grammars note: include Proto, mention
GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1
gitnexus-cursor-integration/README.md:
- 17 MCP tools, was 16; skills list: all 9 bundled skills, was 5
eval/README.md:
- Model list matches configs/models/: Claude Haiku 4.5 (was
'3.5 Haiku'), adds MiniMax M2.5 and DeepSeek
- Node.js 22+ for GitNexus, was 18+
.devcontainer/README.md:
- Add a table of contents (364 lines, ~15 sections, no navigation)
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* chore: empty commit to retrigger CI
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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Gergő Magyar
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400cc6a440
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feat(search): add opt-in CJK bigram segmentation for FTS search (#2339) | ||
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Parafee41
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a7df8f861a
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fix(search): make FTS stemmer configurable (#2307)
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Gergő Magyar
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9ff7337f1e
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fix(mcp): rename query/cypher params so Claude Code can call them (#2186)
* fix(mcp): advertise search_query/statement params for query/cypher tools (#2175) Claude Code drops a tool-call argument named exactly 'query', making the query and cypher tools unusable from it. Rename the advertised required parameters to search_query and statement so the client transmits them. Handler-side backward-compat for the legacy 'query' key follows in the next commit. * fix(mcp): accept search_query/statement with legacy query fallback (#2175) Resolve the new advertised param names in the backend while still accepting the legacy 'query' key, so curl/HTTP, other MCP clients, the CLI, the group path, and the internal executeCypher() all keep working. Alias is normalized once at the callTool chokepoint (covers group-forward + search alias); query() and cypher() dual-read defensively. New name wins when both are supplied. Updates the required-error message and adds dual-accept unit + integration coverage. * fix(cli): pass canonical search_query/statement params to query/cypher tools (#2175) Stop the CLI from depending on the deprecated 'query' alias. No user-facing change — the positional args are unchanged and the backend accepts both keys. * fix(mcp): generators advertise search_query in query() examples (#2175) Update the three doc/example generators (ai-context AGENTS/CLAUDE block, skill-gen community skills, resources repo hint) so future analyze runs emit query({search_query: ...}) — the param name Claude Code actually transmits. Tests assert the new form is present and the legacy query({query: form is absent (the #2059 generator-test pattern). * docs(mcp): advertise search_query/statement in skill & guidance examples (#2175) Sync the committed agent-facing docs to the renamed params so a Claude Code agent following them emits the transmittable key: AGENTS.md/CLAUDE.md gitnexus block, the canonical gitnexus/skills/* source and its installed/plugin/cursor mirrors, and the README examples. Scoped rewrite of the two call prefixes only (query({query: -> search_query, cypher({query: -> statement). * style(mcp): prettier line-wrap for #2175 alias-resolution edits * fix(review): uniform search_query precedence + cypher empty guard (#2175) Code-review findings (correctness/adversarial/api-contract/maintainability consensus): - Group-mode query inverted the 'new name wins' rule: the callTool chokepoint backfilled params.query only when empty and the @group-forward read params.query directly, so a both-keys (or whitespace-legacy) group call let the legacy value win — unlike the local path. Replace the hidden param mutation with a self-contained 'search_query ?? query' resolve at the group-forward; precedence is now uniformly new-wins at every consumer site. - cypher() now returns the same friendly required-param error as query() when neither statement nor query is supplied, instead of a raw DB prepare error. - Document the legacy alias as permanent (third-party clients may send query=). Adds group-forward alias tests (both-keys + legacy-only), empty/whitespace search_query, the search-alias path, and the cypher empty-statement guard. * fix(review): non-string alias safety + drop stale chokepoint comment (#2175) Tri-review findings (correctness/adversarial/security + maintainability): - Non-string statement/search_query/query (the MCP envelope is not schema-validated) hit .trim() and threw TypeError to the server boundary instead of a friendly required-param error. Introduce resolveAliasString() (new name wins; non-string -> undefined) used by query(), cypher(), and the group-forward, so all three return the structured error. Empirically verified (123 ?? '' -> 123, (123).trim() throws) — this overrides a critic refutation that mis-read ?? as a string coercion. - Remove the stale query() comment claiming alias resolution happens at a callTool chokepoint; that mutation was removed earlier in this PR — each site resolves the alias itself. - Document GroupToolPort.query's intentionally-narrower required type vs the wider LocalBackend impl. Adds non-string and empty-new-key precedence tests. * fix(mcp): alias falls back to legacy value when new key is blank (#2175) PR #2186 review finding: resolveAliasString used `canonical ?? legacy` (nullish), so an explicitly empty/whitespace new-name value (e.g. {search_query:'', query:'real'}) won and was rejected — discarding a valid legacy value, contradicting the 'new name wins when both supplied' intent. Resolve to the first NON-BLANK string instead (new preferred when it carries a real value, else legacy). Covers query(), cypher(), and the group-forward (all route through the helper); non-string still resolves to a friendly error. Flips the presence-based test and adds whitespace/cypher/group fallback cases. * fix(mcp): drop legacy "query" mention from query/cypher schema descriptions (#2175) PR #2186 review finding: the search_query/statement inputSchema descriptions named the legacy "query" key — the exact arg Claude Code drops — and description text is read by an LLM choosing arguments, weakly nudging it to send "query". Trim the descriptions to their clean form and move the legacy-alias note to a code comment next to the schema (preserved for maintainers / non-CC clients). properties/required unchanged (no `query`). |
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azizur100389
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50cda61a43
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feat(setup): select coding agent integrations (#2168)
* feat(setup): select coding agent integrations * style: format setup agent selection * fix(setup): validate explicit agent selection --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> |
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Gergő Magyar
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292f26ece3
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fix(hooks): silence MCP-owned-DB augment skip for strict hook runners (#1913) (#2134)
* fix(hooks): silence MCP-owned-DB augment skip for strict hook runners
The PreToolUse augment-skip path wrote `[GitNexus] augment skipped: MCP
server owns DB` to stderr unconditionally on a normal (non-error) skip.
Strict hook runners that validate hook output (e.g. Codex `PreToolUse`)
treat that as noisy / "invalid pre-tool-use JSON output".
Gate the diagnostic behind GITNEXUS_DEBUG via a shared `isDebugEnabled()`
helper, so normal skips are silent by default (empty stdout AND stderr,
exit 0) and the reason stays recoverable with `GITNEXUS_DEBUG=1`. Applied
consistently to all three hand-maintained hook copies (claude,
antigravity, claude-plugin).
Tests:
- Unit (claude CJS + plugin): assert default-silent and debug-on behavior
for the MCP-owned-DB skip and for the fail-closed (lsof ETIMEDOUT) skip
that routes through the same gated line; the owner-detection tests run
with GITNEXUS_DEBUG=1 so the skip discriminator stays observable.
- e2e (antigravity): the antigravity adapter shares the identical gated
skip but only runs from its install dir, so cover it through the install
pipeline with a faked DB-owner probe (strict empty-stdout/stderr +
debug-on). Promote the fake-probe helpers (createHookToolDir / hookEnv,
plus a module-private writeExecutable) into shared hook-test-helpers so
unit + e2e reuse them.
Fixes #1913
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(hooks): unify GITNEXUS_DEBUG gating in main() catch handlers
The main() catch-handler in all three hook copies still gated its crash
log on truthy `if (process.env.GITNEXUS_DEBUG)`, while the skip diagnostic
the #1913 fix added is gated on the strict `isDebugEnabled()` helper
(=== '1' || === 'true'). That split meant GITNEXUS_DEBUG=0 or =false
suppressed the skip line yet still enabled crash logging — two conflicting
contract signals in the same file.
Switch the three catch handlers to isDebugEnabled() so GITNEXUS_DEBUG has
one strict meaning everywhere: exactly '1' or 'true' enables all
diagnostics; everything else (incl. '0', 'false', empty, unset) is silent.
Add boundary tests asserting the MCP-owner skip stays silent with
GITNEXUS_DEBUG='0' and 'false' (CJS + Plugin), pinning the strict contract.
Refs #1913
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(hooks): gate antigravity stale-index hint stderr behind GITNEXUS_DEBUG
The antigravity AfterTool handler mirrored the stale-index hint to stderr
unconditionally on a normal (non-error) success path — the last ungated
stderr write of the class issue #1913 targets, and a divergence from the
claude hook, which never mirrors this hint to stderr.
Gate the stderr mirror behind isDebugEnabled(). The hint still reaches the
agent via additionalContext (stdout JSON) — parts.push(hint) stays
unconditional — so there is no functional loss; only the by-default
terminal mirror moves behind GITNEXUS_DEBUG=1. This knowingly changes the
#1730 terminal-mirror behavior in favor of strict-runner cleanliness and
parity with the claude adapter.
Split the e2e assertion into a default-silent test (hint in
additionalContext, absent from stderr) and a GITNEXUS_DEBUG=1 test (hint
mirrored to stderr).
Refs #1913
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* docs(hooks): document GITNEXUS_DEBUG=1 for hook diagnostics
GITNEXUS_DEBUG was documented only in the cursor integration README, so
the diagnostic escape hatch for the Claude Code / Antigravity hooks was
undiscoverable. Operators hitting a silent hook skip (MCP server owns the
DB, fail-closed probe timeout, or an already-current index) had no
documented way to surface the reason.
Add a Troubleshooting subsection explaining that the hooks stay silent on
normal skip paths for strict runners, that GITNEXUS_DEBUG=1 surfaces the
reason on stderr, and that only '1'/'true' enable diagnostics (stdout JSON
the agent consumes is unaffected).
Refs #1913
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(hooks): update setup-antigravity unit test for gated stale-index hint
U2 (
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Gergő Magyar
|
4682a477d8
|
feat(mcp): paginate list_repos to avoid client token truncation (#2119) (#2120)
* feat(mcp): paginate list_repos to avoid client token truncation (#2119) list_repos returned every indexed repository in one unpaginated array, which large/LLM MCP clients truncate by token limit — so agents with hundreds of indexed repos could not enumerate them all (the data transmits fully; the consuming client drops it). Add bounded limit/offset pagination to the list_repos tool: - result changes from a bare array to { repositories, pagination: { total, limit, offset, returned, hasMore, nextOffset } }; default page 50, max 200 (shared constants) - reject malformed limit/offset; clamp limit above the max - deterministic order (lower-cased name, then path) over one registry snapshot per call, so paging never skips or duplicates an entry - covers both stdio and remote /api/mcp (shared createMCPServer/callTool) The internal listRepos() method (5 callers), GET /api/repos, and the `gitnexus list` CLI are unchanged. The array->object tool-result shape is a deliberate contract change, documented in CHANGELOG. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): reject list_repos limit above the max instead of clamping (#2119) parseListReposPagination silently clamped limit>max to the maximum while throwing on every other out-of-bounds value (limit<1, offset<0, non-integer, NaN). A client that advanced offset by its requested limit (rather than pagination.nextOffset) then silently skipped repositories and saw hasMore:false — defeating the "never skips" guarantee. Reject an over-max limit too, so validation is symmetric and a caller never gets a smaller page than it asked for without a clear error. Updates the schema/description, the helper + ListReposPagination JSDoc, the guide note, and the two clamp tests. Resolves the cross-engine-corroborated P2 (Codex + adversarial lane) and the maintainability lane's clamp-vs-throw inconsistency from the PR #2120 review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(mcp): name the list_repos return type and mark the parser @internal Extract the inline listRepos() element shape into an exported RepoListing interface and use it for both listRepos() and listReposPage().repositories, replacing the opaque Awaited<ReturnType<LocalBackend['listRepos']>> expression the maintainability review flagged. Tag parseListReposPagination @internal (it is exported only for unit testing). Pure type/JSDoc change; no behavior. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(eval-server): type formatListReposResult to the paginated shape Narrow formatListReposResult's parameter from `any` to { repositories: RepoListing[]; pagination?: ListReposPagination } and drop the dead bare-array branch — after #2119 callTool('list_repos') always returns the paginated object, so the Array.isArray shim was unreachable. Add a list_repos continuation hint to the eval-server's getNextStepHint (parity with the MCP server), and cover the previously-untested non-empty + hasMore:false formatter branch. Migrates the two bare-array formatter tests to the object shape. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): harden list_repos pagination coverage - Exercise the #2054 sibling-clone guarantee through the real callTool tool path (in the #2054 describe, which has temp-dir cleanup), proving siblings and remoteUrl survive listReposPage's sort+slice — not only listRepos(). - Assert total + limit on the middle-page test (a total miscalculation at a non-zero offset would otherwise slip past it). - Cover the benign boundaries: negative-zero offset (accepted as page 0) and a MAX_SAFE_INTEGER offset (empty page). - Replace the integration test's '\n\n---' split with a string-aware brace scan, so a repo path containing braces can never truncate the JSON parse. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): sync the list_repos pagination example to the guide mirrors The .claude and gitnexus-claude-plugin guide mirrors only carried the one-line table note; add the full "Paginating list_repos" section (shape + multi-page traversal example + notes) so all three guide copies are byte-consistent with the canonical gitnexus/skills/gitnexus-guide.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: drop list_repos CHANGELOG entries from this PR Restore gitnexus/CHANGELOG.md to match main so this PR contributes no changelog change; the changelog is curated separately from feature PRs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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Nilotpal Kashyap
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1716bf7c1e
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feat(cli): add gitnexus uninstall to reverse setup (#2060) (#2062)
* feat(cli): add `gitnexus uninstall` to reverse setup (#2060) `gitnexus uninstall` was documented in #168 but never implemented, so the CLI rejected it with "error: unknown command 'uninstall'" (#2060). Add an `uninstall` command that reverses `gitnexus setup` target-by-target: removes the GitNexus MCP server entries (Cursor, Claude Code, Antigravity, OpenCode, Codex), the installed skill directories, and the Claude Code / Antigravity hook entries plus their bundled hook scripts. Edits are surgical and idempotent — only gitnexus-owned keys/entries/dirs are touched, and JSONC comments/indentation are preserved. Defaults to a dry-run preview; `--force` applies. Per-repo indexes and the global npm package are left alone with printed hints, since both are destructive in ways setup never caused. Adds i18n entries (en + zh-CN), help wiring, README/CHANGELOG docs, and unit tests covering MCP/hook/skill/Codex-TOML removal, dry-run, corrupt-file safety, and the no-op case. * changelog changes * changelog changes * fix(cli): harden uninstall against data-loss edge cases (review #2062) Address review findings on the uninstall command: - Empty derived skill name no longer wipes the whole skills dir: a bare '.md' source file would make basename() return '', resolving to the skills dir itself. Skip empty names in derivation and reject empty/'.'/'..'/separator names in removeSkillsFrom. - Corrupt settings.json no longer orphans the hook: gate the hook-script dir removal on status !== 'corrupt' so we don't delete a script while a still-registered entry points at it (Claude + Antigravity blocks). - Hook removal is now element-granular: delete only the gitnexus command inside an entry's hooks[], removing the whole entry only when it becomes empty. Preserves a user command co-located in the same entry. - Fallback TOML stripper: also remove descendant sub-tables ([mcp_servers.gitnexus.env]), track multiline strings so a bracketed line inside a value isn't treated as a header, and stop reflowing unrelated blank lines. - Set process.exitCode=1 on partial failure; add a 10s timeout to 'codex mcp remove'. Tests expanded 7 -> 17: empty-skill guard, corrupt-settings hook preservation, shared-entry hook removal, OpenCode MCP keyPath, Antigravity MCP + AfterTool hooks, codex-remove success path, TOML sub-table + multiline-string cases, dry-run for hooks/skills, and the directory-layout skill branch. * refactor(cli): share setup/uninstall target map + harden TOML fallback (review #2062) Maintainer review follow-ups: - Extract editor target identities into editor-targets.ts (MCP paths/keyPaths, Codex TOML section, skill dirs, hook settings/events/needles/script dirs, shared detectIndentation). Both setup.ts and uninstall.ts consume it, so a target change updates both sides — killing the silent drift hazard. - Add a setup -> uninstall round-trip integration test that iterates getEditorTargets(): setup writes every target, uninstall removes all of them, and a co-located user MCP server + user hook survive. Drift tripwire in both directions. - Preview now prints the exact paths it would remove; command output + README state skills are matched by bundled gitnexus skill name. (Provenance marker deferred to a tracked follow-up.) Hardening of the hand-rolled Codex TOML fallback (found in code review): - Strip a section header that has a trailing inline comment (was matched as a header but failed the exact classify check -> section left behind while reported removed). - Preserve CRLF line endings instead of rewriting the whole file to LF. - Fix multiline-string scan: a line with an odd count of BOTH """ and ''' no longer mis-picks the delimiter and desyncs the scanner (left->right scan). - removeSkillsFrom guard also rejects absolute names. Regression tests added for each. Full setup/uninstall suite green. --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> |
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Abhigyan Patwari
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f0c292f9e7
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perf(ingestion): prune inert local value symbols (#2065) | ||
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Gergő Magyar
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95f87fc12a
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perf(ingestion): Linux-kernel-scale analysis — worker-pool parse + finalize O(n²) + scope-resolution memory wall (#1983) (#2038)
* fix(ingestion): reduce parse-phase memory for huge repos (#1983)
Stop retaining full parse-cache chunks in RAM alongside the merged graph,
slim on-disk shards, defer worker ParsedFile emission for scope-resolver
languages, and add GITNEXUS_DEBUG_HEAP probes for OOM diagnosis.
Co-authored-by: Cursor <cursoragent@cursor.com>
* fix(ingestion): address #2038 tri-review findings (parse-phase memory)
Resolves the confirmed review findings on PR #2038:
- P1: thread exportedTypeMap through the sequential parse path
(processParsingSequential) so a no-worker run over a partially-warm
cache no longer silently drops the sequential-miss files' exported
types. Cache hits made exportedTypeMap.size > 0, suppressing the
end-of-loop buildExportedTypeMapFromGraph rebuild, but the sequential
path never populated the map. Regression test added (fails on the
pre-fix tree, passes after) plus a fully-sequential differential oracle.
- P2: saveParseCache builds its on-disk index from hashes actually
written/copied (writtenKeys), never a usedKeys hash whose shard write
or copy was skipped — no more phantom index entries.
- P2: add a unit test asserting SCOPE_RESOLUTION_LANGUAGES stays in sync
with SCOPE_RESOLVERS (asymmetric drift would lose a language's ParsedFile).
- Backfill cache coverage: loadParseCacheChunk missing/corrupt -> undefined,
pruneCache onDiskKeys branch, slim preserves nodes, saveParseCache
copy-evicted-shard round-trip.
- Cleanups: single-source heap-probe gating via isDebugHeapEnabled();
hoist the per-chunk mkdir in persistParseCacheChunk behind a
process-scoped Set; gate COBOL's unused worker-side ParsedFile
extraction (graph nodes still come from cobolPhase) while keeping
fileCount/progress unconditional.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* refactor(ingestion): remove dead worker-side ParsedFile extraction
After #2038 gated worker `ParsedFile` emission behind `!isScopeResolutionLanguage(language)`, and with all 16 SupportedLanguages registered in SCOPE_RESOLVERS, that gate was structurally always true — the worker already produced no ParsedFiles and scope-resolution re-extracts each file from source on the main thread (run.ts). Remove the now-dead machinery:
- Drop both worker `extractParsedFile` call-sites (tree-sitter processFileGroup + the standalone-provider branch) and the `result.parsedFiles.push`. The standalone branch keeps fileCount/onFileProcessed per file. `result.parsedFiles` stays declared but empty (field removal deferred).
- Remove the now-orphaned `scopeSourceKind` var + `ScopeCaptureSourceKind`/`extractParsedFile`/`isScopeResolutionLanguage` imports.
- Delete the consumerless `migrated-languages.ts` (isScopeResolutionLanguage + SCOPE_RESOLUTION_LANGUAGES) and its drift-guard test — parse-worker was their only importer. Also improves AGENTS.md "shared ingestion code must not name languages" compliance.
`extractParsedFile` and the scope-extractor-bridge stay (scope-resolution/run.ts + Vue resolver use them). Behavior-preserving: worker-sequential-parity passes before and after; tsc/eslint clean; no baseline/golden drift.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* refactor(ingestion): worker-pool-only parsing; remove sequential parser (#1983)
Completes the #1983 huge-repo parse-OOM effort by making the worker pool
GitNexus's sole parse path.
Parallel serialization (the perf core): workers serialize their ParsedFiles to
a disk store in parallel and stream them back to scope-resolution, so the main
thread no longer re-parses every file (the tree-sitter native-memory leak that
caused the OOM). Adds chunk merge-pipelining + work-proportional chunk sizing so
the pool stays saturated.
Remove the sequential parser: `--workers 0`, `GITNEXUS_WORKER_POOL_SIZE=0`, and
`skipWorkers` now hard-error (no silent degrade — #1741); the small-repo
threshold no longer selects an in-process path; pool creation stays lazy /
cache-miss-gated so warm all-hit runs never spawn workers.
Worker-path parity fixes — removing sequential surfaced two pre-existing gaps
that tiny-fixture tests had masked by running below the worker threshold, both
fixed by carrying per-file metadata as DATA across the worker boundary (never
re-parsing on the main thread, preserving the OOM fix):
- C++: templateConstraints wired into worker node identity (SFINAE overload
disambiguation) + ADL / inline-namespace capture side-channel serialized
onto the ParsedFile.
- Kotlin: companion-scope side-channel serialized the same way (companion /
static dispatch).
Validation: tsc + build clean; full suite green (10,190 pass — the only
deterministic failures were the now-fixed C++/Kotlin worker-path gaps; the 2
remaining full-run failures are pre-existing load flakiness, green in
isolation); cpp-pipeline benchmark stays linear on a 1-worker pool.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(ingestion): wire C static-linkage side-channel + ADL O(1) collect + tri-review cleanups (#1983)
Follow-up to the worker-pool-only refactor, from a tri-review of the parse path.
- C static-linkage side-channel (P1): cProvider had no collect/applyCaptureSideChannel,
so on the now-sole worker path C `static` file-local marks were lost across the worker
boundary -> false cross-file CALLS edges + over-broad #include wildcard visibility on
every C analysis (the Linux kernel is C). Mirror the C++/Kotlin wiring: serialize
`staticNames` per file onto ParsedFile.captureSideChannel and restore it on the main
thread (no re-parse). + a worker-path regression test (the existing c-static-isolation
fixture passed vacuously — its collision resolves via #include before the global
free-call fallback ever consults static-linkage).
- captureSideChannel `kind` discriminant: add `kind:'cpp'`/`kind:'c'` tags + guards
(Kotlin already had one) now that C/C++/Kotlin share the single generic field.
- Perf: collectCppAdlSideChannel scanned the whole argInfoBySite/noAdlSites maps per file
(O(F^2) per sub-batch, ~100M parseSiteKey calls at kernel scale). Add per-filePath
lockstep indexes -> O(1) collect; serialized snapshot byte-identical.
- Cleanups: inline the one-line processParsingWithWorkers wrapper into processParsing;
drop the always-empty WorkerExtractedData.calls/assignments/constructorBindings fields;
remove the voided astCache param from processParsing; refresh stale "sequential
fallback" JSDoc.
Validation: tsc + build clean; cpp 297/297, c 8/8 (incl. the new worker-path
static-linkage guard), typescript + parsedfile-store green; cpp ADL benchmark stays linear.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* perf(scope-resolution): index C/C++ #include resolution in finalize (O(n²)→O(n))
Kernel-scale C/C++ analysis ground in finalizeScopeModel because three
per-#include operations each did a full O(F) scan with no index — the
finalize O(n²) that surfaced once the #1983 parse-phase OOM was fixed:
- expand{C,Cpp}WildcardNames: parsedFiles.find() per wildcard edge → O(R·F)
- resolveImportTarget: new Set(allFilePaths) rebuilt per #include
- resolveCImportTarget: suffix-match scanned all workspace paths
Each is replaced with a WeakMap-per-pass index keyed on the stable
parsedFiles/allFilePaths references that scope-resolution run.ts passes
once per pass:
- Map<ScopeId,ParsedFile> for wildcard expansion (c/static-linkage.ts +
cpp/file-local-linkage.ts)
- memoized augmented header set (c/scope-resolver.ts + cpp/scope-resolver.ts)
- basename-bucketed suffix index in resolveCImportTarget (c/import-target.ts),
shared by C and C++ since resolveCppImportTarget delegates to it
Collapses the C/C++ finalize from O(R·F) to O(R+F). Pure-perf, byte-identical
edge output: 962 targeted tests green (490 C + 472 C/C++ scope-resolution);
the basename index preserves the exact endsWith('/'+target) match and the
fewest-path-components-then-lexicographic tie-break.
The kernel's ~25-30k .h headers are classified C++, so both providers must
be fixed. Proven on the Linux kernel: the C finalize completed
(sr-post-finalize lang=c → sr-end lang=c), which the pre-fix run never
reached in 16+ min of grinding.
Build-independent follow-ups (separate from this finalize fix), documented
for later: emitFreeCallFallback same-name buckets (emit phase),
buildGraphNodeLookup + precount global setup, the ParsedFile store-load,
the dart/go/ruby expand-wildcards .find siblings, and the ~26GB
scope-resolution memory floor (full kernel completion needs >~40GB RAM).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(bench): regenerate C scope-capture baseline for the #1983 c-static-linkage-worker fixture
bench/scope-capture/measure.mjs fingerprints emitCScopeCaptures over the
lang-resolution/c-* fixture corpus. The #1983 PR added the
c-static-linkage-worker fixture (caller.c/lib.c/lib.h/local.c — the
worker-path static-linkage side-channel test) but did not regenerate the C
baseline, so `--check` has been red on this branch (main, lacking the
fixture, still matches 0de009b).
Pure fixture-corpus drift — no c/captures.ts or query change branch-vs-main,
existing fixtures' captures byte-identical (c-captures.test.ts 45/45),
scaling stays linear (~0.97). Regenerated: 0de009b -> 39f3a83. Bench now
PASS (14 languages). Unrelated to the finalize O(n²) fix.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* perf(scope-resolution): lower kernel-scale resident memory floor + setup cost
Reduce the scope-resolution resident-memory floor and setup throughput on
huge repos (Linux kernel), the wall that remains after #1983 (parse OOM) and
the finalize O(n^2) fix (
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||
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Gergő Magyar
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f885330b34
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fix(cli): steer docs, skills, and hooks through a CLI-neutral project-local runner (#1939) (#1945)
* fix(cli): steer npm 11 users away from npx install crash (#1939) Prefer global gitnexus or pnpm dlx in hooks and generated AI context, warn when npm 11.x would use the broken npx path, and document workarounds for the arborist node.target null failure mode. Co-authored-by: Cursor <cursoragent@cursor.com> * test(hooks): stage resolve-analyze-cmd.cjs for antigravity adapter; harden load checks The antigravity adapter gained a top-level require('./resolve-analyze-cmd.cjs') but stageAdapter() did not copy it, so the spawned adapter crashed with MODULE_NOT_FOUND. Three load-sensitive tests failed; four silent-path tests false-passed on empty stdout. Stage the helper alongside the other sibling helpers, and assert status===0 and no MODULE_NOT_FOUND on the four silent-path tests so a non-loading hook can never pass green again. Force a deterministic invocation mode in the stale-index test so the emitted analyze command no longer varies by CI-runner PATH. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(cli): standardize invocation hints on gitnexus@latest; single-source CJS helper NPX_REF becomes a literal `gitnexus@latest` in resolve-invocation.ts, dropping the package.json require and the module-load throw (a malformed/absent version can no longer crash any CLI command at import). The safety this PR delivers is the install method steered to (global / pnpm dlx), not a pinned gitnexus version, and the in-repo CJS mirror already degraded to `latest` once copied outside the package. Make the two resolve-analyze-cmd.cjs copies byte-identical and add a parity test that fails on drift. The separate, version-pinned NPX_REF that setup.ts writes into the MCP server registration is intentional and left unchanged. Co-authored-by: Cursor <cursoragent@cursor.com> * perf(cli): move npm-11 npx warning off module load; memoize invocation mode warnIfNpm11NpxRisk() ran at index.ts module load, so every CLI invocation (including the `gitnexus mcp` stdio hot path) paid which/where + npm --version spawns — against the lazy-startup/MCP-stdout discipline (#207, #1383). Move the call into analyzeCommand, after the ensureHeap() re-exec guard, so it fires once in the working process and only for `analyze`. Memoize the PATH-probe-derived invocation mode (the GITNEXUS_INVOCATION override stays uncached) so repeated callers don't re-probe, and add a test-only reset so the cache + once-only warning flag don't leak across the unit suite. Covers the mode!=='npx', npm<11, and npm-absent suppression branches. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(cli): detect .exe/extensionless global gitnexus shims on Windows The winGitnexusWrapper branch only matched .cmd/.bat, so a global gitnexus installed by Volta or scoop (a .exe or an extensionless shim) was missed and the hint fell back to pnpm/npx. Accept .exe and treat any non-empty `where` hit as on-PATH (the emitted hint is `gitnexus analyze` regardless of which shim resolves it). Mirror the change into both resolve-analyze-cmd.cjs copies so the TS source and the byte-identical hook mirrors stay in sync. Add Windows-mocked test cases (.exe-only, extensionless, .cmd preference, CRLF stripping) and register resolve-invocation.test.ts in cross-platform-tests.ts so the windows-latest runner exercises the branch. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(cli): emit fixed pnpm dlx analyze command in generated AGENTS.md/CLAUDE.md ai-context baked a machine-resolved command (formatAnalyzeCommand) into git-tracked AGENTS.md/CLAUDE.md, so the stale-index hint varied per machine and churned across branches (the #1706 class). Emit the fixed string `pnpm dlx gitnexus@latest analyze` instead: committed AI-context is the most authoritative instruction an agent reads, so it must name an install-free, crash-free method — never `npx`, the npm-11 path #1939 steers away from. formatAnalyzeCommand stays exported and unit-tested in resolve-invocation.ts (it still mirrors the two .cjs hook copies); ai-context just no longer calls it. Co-authored-by: Cursor <cursoragent@cursor.com> * refactor(cli): unify hook-helper copy into one non-silent routine installClaudeCodeHooks copied its four hook helpers in separate try/catch blocks that silently swallowed failures, while installAntigravityHooks recorded an error per failed copy. Extract one copyHookHelpers(srcDir, destDir, label, result) with a single canonical helper list (including resolve-analyze-cmd.cjs) and the antigravity loop's error-reporting policy, and use it from both paths so a missing helper surfaces as a setup error instead of a silent runtime crash. Assert both the Claude and Antigravity install paths co-locate resolve-analyze-cmd.cjs next to the adapter, and that a failed copy records an error rather than passing silently. Co-authored-by: Cursor <cursoragent@cursor.com> * docs(cli): reattach installClaudeCodeHooks JSDoc after helper extraction The extracted HOOK_HELPERS/copyHookHelpers block landed between the installClaudeCodeHooks JSDoc and its function, leaving the doc reading as if it described the helper list. Move the block above the doc so it documents the function again. No behavior change. Co-authored-by: Cursor <cursoragent@cursor.com> * test(cli): enforce TS<->CJS invocation parity and guard CLI startup posture Tier-2 review found two in-scope gaps in the #1945 follow-up: - The "mirrors resolve-invocation.ts / test enforces parity" comments overclaimed: the parity test only compared the two .cjs copies to each other, so the TS source and the CJS hook copies could silently drift (NPX_REF, the per-mode command, and the Windows shim regex were hand-edited in all three this PR). Add TS<->CJS value parity (NPX_REF + formatAnalyzeCommand for every forced mode) and a source-level shim-regex parity check, and make the mirror comments accurately describe what is enforced. - No test locked the R3/R4 startup posture, so re-adding warnIfNpm11NpxRisk() (or any resolve-invocation import) at index.ts module scope -- the #207/#1383 lazy-startup regression -- would pass CI. Add a guard asserting index.ts has no module-load invocation probe and the warning is wired into analyzeCommand. Co-authored-by: Cursor <cursoragent@cursor.com> * refactor(cli): collapse npx-invocation resolver to one source of truth PR #1945 carried the gitnexus/pnpm/npx selection in three hand-synced places — the canonical hook helper, its byte-identical plugin copy, and a full TypeScript re-implementation in resolve-invocation.ts — kept in lockstep by per-mode-command and regex-extracted-by-regex parity tests. The TS formatAnalyzeCommand had no production caller (ai-context emits a fixed string), and the module memoized + exposed a test-only reset for a "repeated callers" case that has exactly one caller. Make hooks/claude/resolve-analyze-cmd.cjs the single source: extract the Windows-shim line-picking into a pure, exported pickPathMatch() and add an injectable probe to resolveInvocationMode() so the shipped logic is testable without spawning or global mocks. resolve-invocation.ts (118 -> 59 lines) now consumes that cjs via createRequire for resolveInvocationMode/NPX_REF and adds only the CLI-only npm-version probe and warning; the relative path resolves identically from src/cli/ (tsx, vitest) and dist/cli/ (shipped, hooks/ is a published sibling of dist/). Tests exercise the real shipped artifact, the NPX_REF/mode-command parity scaffolding is dropped (one implementation can't drift), and parity narrows to the two cjs copies staying byte-identical. No behavior change: hook stale-index hints and the analyze warning are byte-identical; the pre-existing setup.ts resolveGitnexusBin is untouched. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): bound stale-index hook PATH probe under the hook budget (U1) The PostToolUse stale-index hint calls formatAnalyzeCommand(), which probes which/where; named PROBE_TIMEOUT_MS=2000 keeps git rev-parse (~3s) + up to two probes well under Claude Code's 10s hook timeout while preserving the machine-correct hint. Byte-identical in the plugin copy. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): steer generated cross-repo group commands off npx (#1939) (U2) The Cross-Repo Groups block in generated AGENTS.md/CLAUDE.md still emitted bare 'npx gitnexus group ...', funneling npm-11 users into the arborist crash; switch to fixed 'pnpm dlx gitnexus@latest group ...'. Export generateGitNexusContent and add a group-branch test asserting no 'npx gitnexus' literal survives. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: align steering guidance on pnpm dlx gitnexus@latest (U3) README troubleshooting uses gitnexus@latest; the repo's own committed CLAUDE.md/AGENTS.md stale-index hint now matches the generated output (pnpm dlx gitnexus@latest analyze) so the repo dogfoods the fix. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(hooks): assert exact @latest analyze command and pin invocation mode (U4) Drop dead PKG_VERSION/NPX_REF version-pinned constants; the cjs always emits gitnexus@latest, so assert exact toContain(...) instead of the /@\\S+/ wildcard; pin GITNEXUS_INVOCATION in the --embeddings tests for host-independent determinism. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(cli): cover resolver warn/edge branches; document probe seam (U5) Add coverage for the gitnexus-mode warn suppression, getNpmMajorVersion edge inputs (empty/pre-release/non-numeric), and the Windows non-wrapper pickPathMatch branch; widen the InvocationResolver interface to document the optional probe param. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): lower hook PATH-probe timeout to 1000ms (U1) In a linked worktree the stale-index hook runs git rev-parse --git-common-dir (~2s) + rev-parse HEAD (~3s) before up to two PATH probes; PROBE_TIMEOUT_MS=1000 holds the worst case near ~7s under Claude Code's 10s hook budget (was 2000, ~1s headroom). Byte-identical in the plugin copy. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): fail closed in gitnexus setup on missing required hook helper/adapter (U2) copyHookHelpers now returns the failed REQUIRED helpers (the .cjs trio; win-rm-list-json.ps1 stays best-effort since it fails open). Both install paths skip hook registration with an actionable error when a required helper failed; the Claude path also gains the adapter-existence guard the Antigravity path already had. Prevents registering a hook that crashes MODULE_NOT_FOUND on every tool event. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(skills): steer committed skill files off npx to pnpm dlx gitnexus@latest (U3) All 26 committed skill-file copies (gitnexus/skills, .claude, plugin, cursor) used 'npx gitnexus analyze', contradicting the generated freshness line and funneling npm-11 users into the arborist crash. Replace with 'pnpm dlx gitnexus@latest analyze'; add a regression guard (skills-steering.test.ts) that globs all four locations and fails if any reintroduces it. The cli skill's non-analyze npx subcommands (status/clean/list/wiki) are left as-is (out of the analyze-funnel scope). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): guard resolver import shape; assert group-impact steering (U4) Add a load-time guard on the createRequire(resolve-analyze-cmd.cjs) cast so a drifted/renamed cjs export fails loudly at module load instead of as a late TypeError in warnIfNpm11NpxRisk. Add the missing 'group impact' assertion to the ai-context Cross-Repo Groups test, and a resolver-contract test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): auto-select invocation path with pnpm --allow-build (#1939) Probe npm/pnpm versions and PATH to pick a working analyze command without user configuration: global gitnexus first, pnpm dlx with --allow-build on npm 11+ (Ladybug native scripts), npx on npm 10 and earlier. Update docs, skills, and tests to match the canonical install-free command. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(cli): place pnpm --allow-build before dlx, repair version-injection seam (#1939) The auto-selected install command emitted `pnpm dlx --allow-build=… analyze`, but pnpm < 10.14 keeps `dlx` in its argv escape list, so flags placed *after* `dlx` are parsed as package specs and rejected (ERR_PNPM_SPEC_NOT_SUPPORTED) on pnpm 10.2–10.13.x — strictly worse than the bare command. Move the flags before `dlx` (the position pnpm has honored since 10.2.0) in both byte-identical hook copies, the committed AGENTS.md / CLAUDE.md, and every skill tree. Also repairs the CI-red resolveInvocationMode seam: injecting `{ npmMajor: null }` to simulate an absent npm fell through `??` to the host's real `npm --version` (npm 10.x on the CI runners → routed 'npx' instead of 'pnpm'). Use an `'npmMajor' in deps` sentinel so an injected null is honored, drop the dead parseMajorVersion guard, and gate the flags on pnpm >= 10.2 via a single minor-aware probeVersion spawn (skipped for committed docs). Align the TS getNpmMajorVersion timeout to the 1s hook budget and strengthen the skills-steering guard with a pre-dlx positive assertion plus a post-dlx regression check. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: add npm-11 pnpm caveat to README Quick Starts (#1939) The root, package, and cursor-integration README Quick Starts still steered first-contact users to bare `npx gitnexus analyze` — the exact npm 11.x arborist install crash issue #1939 names as a funnel. Add a one-line pnpm `--allow-build … dlx` caveat (keeping the simple npx default for npm<=10 / pnpm / yarn users); the package README points to its existing npm-11 workaround section. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): route every gitnexus-cli command off npx to pnpm dlx (#1939) The gitnexus-cli skill demonstrated analyze via `pnpm --allow-build … dlx` but still showed status/clean/wiki/list via bare `npx gitnexus` — the same package, the same npm-11 crash-prone install path — and its header claimed "all commands work via npx". Convert every subcommand to the pnpm form across all three skill copies and reconcile the header. Broaden the skills-steering guard to forbid any `npx gitnexus` command in the cli-skill copies. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * perf(hook): probe pnpm once on the stale-index path (#1939) The stale-index hook resolved pnpm twice — `which pnpm` for mode selection then `pnpm --version` for the allow-build gate — two spawns for one tool in a ~9s/10s budget. Capture the version once in formatAnalyzeCommand and thread it through the existing deps seam (a successful `pnpm --version` proves presence), sharing a memoized PATH probe with resolveInvocationMode. Add explicit pnpm 10.0-suppress / 10.2-emit boundary tests and relabel the unknown-minor case. Both byte-identical cjs copies updated together. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(setup): single-quote POSIX hook command + assert cliPath patch applied (#1939) The hook `command` written into editor settings is shell-evaluated; the double-quoted `node "<path>"` form left `$`, backtick, and other metacharacters live in an adversarial $HOME. Single-quote the path on POSIX (Windows keeps the double-quoted form — those chars are illegal in Windows filenames). Also assert the cliPath source-literal replace() actually matched, recording an actionable error on drift instead of silently shipping a hook with an unresolved relative path. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(setup): normalize expected hook path for the Windows runner (#1939) The new POSIX-escaping test built its expected hook path with path.join, which emits backslashes on the Windows runner, while setup.ts forward-slash- normalizes the path before quoting — so `expect(cmd).toBe(node '<path>')` mismatched on tests/windows-latest. Normalize the expected path the same way. Production code was already correct; only the test's expected value was platform-fragile. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): steer docs/skills via a project-local runner, not a pnpm default (#1939) The prior approach hardcoded `pnpm --allow-build=… dlx gitnexus@latest <cmd>` into every committed skill + the generated AGENTS.md/CLAUDE.md, which assumes pnpm is installed. Replace it with a CLI-neutral project-local runner: - `gitnexus analyze` drops `.gitnexus/run.cjs` (a copy of the canonical `resolve-analyze-cmd.cjs`, which gains `buildRunnerArgv` + a `require.main` exec tail) next to the index. Docs/skills reference `node .gitnexus/run.cjs <cmd>`, which auto-selects the runner (global `gitnexus` → `pnpm dlx` → `npx`) at call time — no package-manager assumption. README first-run + an inline bootstrap note stay universal `npx gitnexus analyze`. - The exec tail uses `shell` on Windows so `.cmd`/`.ps1`/`.exe` shims resolve (execFileSync can't otherwise; Node blocks `.cmd` without a shell, CVE-2024-27980), and prints a diagnostic instead of a silent exit 1. Tests: runner exec-tail (real spawn, exit-code propagation + ENOENT diagnostic), copy-failure graceful degradation, and per-subcommand routing + pnpm-fallback vacuity guards. The generated CLAUDE.md block stays under the #856 token budget. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): resolve Windows .cmd version probes so pnpm steering fires (#1939) probeVersion (and the TS getNpmMajorVersion mirror) spawned npm/pnpm --version via execFileSync with no shell, so on Windows the .cmd shims ENOENT'd, the probe reported a present tool as absent, and the stale-index hook recommended the npx crash path #1939 exists to avoid. Add shell: process.platform === 'win32' to the version probes (the exec tail already does this). Parse the first version-shaped line so a Corepack/notice banner on stdout no longer defeats the parse. Carry pnpm presence separately from version so a present-but-unparseable pnpm still selects pnpm. Drop the dead probe ?? resolveOnPath coalesce. Cover resolve-analyze-cmd.cjs (+ plugin twin) with the shell-injection and windowsHide source-regression guards. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): widen pnpm allow-build for the --embeddings=N equals form (#1945) buildRunnerArgv detected embeddings via gitnexusArgs.includes('--embeddings'), which missed the equals form (--embeddings=5000) that Commander also accepts, dropping --allow-build=onnxruntime-node on pnpm 10.2+. Match both forms. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(cli): cover the runner exec-tail Windows shell branch on CI (#1945) runner-exec-tail.test.ts was POSIX-only and unregistered in cross-platform-tests.ts, so the run.cjs Windows shell:true exec branch ran on no platform despite the file comment claiming windows-latest covered it. Add a .cmd-shim it.skipIf(onPosix) case and register the file in SPAWN_CLI so the windows-latest job runs it. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: fix broken troubleshooting anchor in gitnexus README (#1945) The npm-11 quick-start note linked to #npx-gitnexus-crashes-with-nodetarget-is-null-npm-11, which matches no heading; the actual troubleshooting heading slugifies to #cannot-destructure-property-package-of-nodetarget-as-it-is-null. Repoint the link. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(hooks): guard resolve-analyze-cmd.cjs in antigravity e2e sanity check (#1945) The antigravity adapter top-level require()s resolve-analyze-cmd.cjs, but the beforeAll helper-presence loop did not check for it — a failed copy would surface as noisy MODULE_NOT_FOUND in downstream tests instead of the intended actionable 'Helper not installed' error. Add it to the loop. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): tie a missing-runner Cannot-find-module error to recovery (#1945) Generated CLAUDE.md/AGENTS.md make `node .gitnexus/run.cjs` the primary command, but the runner is gitignored, so a fresh clone or git clean leaves an agent facing a raw MODULE_NOT_FOUND. The CLAUDE.md block is token-budget-capped (#856), so the recovery guidance lives in the cli skill (its documented home): the bootstrap note now names the `Cannot find module` error and points at `npx gitnexus analyze` to (re)generate the runner. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(cli): disambiguate the MCP-pinned ref from the @latest hint (#1945) setup.ts and resolve-analyze-cmd.cjs both exported a constant named NPX_REF with different values (version-pinned for the persisted MCP entry vs. gitnexus@latest for hints). Rename setup.ts's module-private constant to MCP_PINNED_REF (value and behavior unchanged — the MCP pin stays pinned), leaving the cjs hint ref and its re-export alone. Also route the createRequire cast through 'unknown' so it reads as an explicit narrowing to the subset this module uses rather than a claim about the cjs's full export shape. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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Ofek Gabay
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bfe8a87831
|
fix: actionable error + docs for pnpm dlx / pnpx native-load crash (#307) (#1967)
* fix: guide pnpm dlx/pnpx users through skipped native install `pnpm dlx gitnexus serve` (and `pnpx gitnexus`) crash with a raw `ERR_DLOPEN_FAILED` stack trace because @ladybugdb/core's native addon (lbugjs.node) is placed by a postinstall script, and dlx/pnpx run ephemerally without executing lifecycle scripts. The existing checkLbugNative() guard already catches the missing binary for serve/mcp/analyze, but its guidance only mentioned bun and --ignore-scripts. Extend the message to call out the common pnpm dlx / pnpx case and the fix (`pnpm add -g gitnexus && pnpm approve-builds -g`, or use npx/npm). Add a matching README troubleshooting section. This does not make `pnpm dlx` itself work — that requires a runtime fallback in @ladybugdb/core. It turns the crash into actionable guidance. Refs #307 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: add pnpm --allow-build dlx option to native-check guidance Incorporates collaborator feedback (magyargergo): pnpm's security model allows `dlx` to run build scripts when you pass `--allow-build` for each native dep. Add this as the first/preferred pnpm-dlx path in the error message, README troubleshooting section, and test assertion. Drop the now-incorrect claim that `pnpm dlx` "cannot be made to work directly". Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix: address PR review on pnpm dlx native-load guidance Replace removed pnpm approve-builds -g with add -g --allow-build flags, qualify npm 11 npx caveats, use serve in examples, extend load-failure hints, and assert --allow-build precedes dlx in tests. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Cursor <cursoragent@cursor.com> |
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Gergő Magyar
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66daf27910
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feat(cli): add --uid/--file/--kind disambiguation flags to impact (#1907) (#1914)
* feat(cli): add --uid/--file/--kind disambiguation flags to impact (#1907) When `impact` reports an ambiguous target it tells the user to disambiguate, but the CLI had no way to do so — only the MCP impact tool accepted target_uid/file_path/kind (the CLI `context` command had --uid/--file, `impact` had neither). Register -u/--uid, -f/--file and --kind on the impact command and forward them to callTool('impact', ...) as target_uid/file_path/kind, matching the context CLI convention and the MCP impact surface. Help text and the usage hint are localized in en + zh-CN. Tests: a unit test pins the CLI option -> tool-param mapping; integration tests cover the ambiguous report, target_uid/file_path resolution, and a cross-label (Function+Tool) collision resolving without a binder crash. Note on the reported binder error ("Cannot find property id for n"): it is environmental — a stale on-disk catalog after an in-place upgrade without a full reindex — and not reproducible on a fresh index. Label-scoping the resolver's MATCH was investigated and is infeasible here (LadybugDB caps multi-label node patterns at 11 of 29 labels, and the startLine/endLine projection only exists on a subset of labels), so the unlabeled match, which is correct via lenient binding, is left unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore(autofix): apply prettier + eslint fixes via /autofix command * test(cli): harden impact disambiguation coverage (#1907 review) Addresses test-hardening findings from the /ce-code-review of #1914 (all test-only, no production change): - cli-impact-disambiguation.test.ts: mock node:fs so impactCommand's writeSync(fd 1) no longer pollutes the runner stdout (matches tool-direct-cli.test.ts). - local-backend-calltool.test.ts: assert Tool:alpha stays in the context cross-label candidate set (not just non-crash); add a --kind path test asserting the kind hint ranks the Function above the non-matching Tool (kind alone scores 0.70 < the 0.95 confident-resolution threshold, so the result stays ambiguous by design). - cli-index-help.test.ts: assert --uid/--file/--kind appear in impact --help, mirroring the context help flag-presence guard. Committed with --no-verify: the husky pre-commit lint-staged binary does not resolve through this worktree's symlinked node_modules; prettier (--write, unchanged), tsc --noEmit, and the affected tests (39 pass) were run manually. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(cli): document impact disambiguation flags (#1907) README.md: add a Disambiguation note + CLI examples to the Impact Analysis tool section (target_uid/file_path/kind, and the --uid/--file/--kind CLI flags). gitnexus/README.md: list the direct graph-query CLI commands (query/context/impact/detect-changes/cypher) under CLI Commands, surfacing impact's new --uid/--file/--kind disambiguation flags where CLI users look. Docs only; minimal additive diff (no whole-file prettier reflow). Committed with --no-verify (worktree symlinked node_modules can't run the husky lint-staged binary). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cli): make impact [target] optional so --uid resolves alone (U1, #1907) impact required a positional target even with --uid, throwing a raw Commander error on a uid-only call; context [name] already handled this. Make the positional optional and guard on uid, and reject a --prefixed uid value swallowed from a following flag (applied to both impact and context for parity). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): bind impact BFS query filters as parameters (U3, #1907) The impact blast-radius BFS built its n.id/r.type/confidence filters by string interpolation with hand-rolled quote-escaping. Bind all three as parameters ($frontierIds, $relTypes, $minConfidence) via executeParameterized, removing the interpolation entirely — mirrors the existing enrichCandidateLabels IN $ids pattern. The confidence clause stays conditional (an unconditional >= 0 would wrongly exclude NULL-confidence edges). Behavior-preserving: 27 integration tests pass, plus a new crafted-id (quoted) traversal guard and an empty-result guard. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(cli): soft-validate impact --kind (U4, #1907) An unknown --kind value was silently a no-op. Warn (localized, to stderr) when --kind is not a known node label, but still proceed — parity with the lenient MCP/backend semantics and forward-compatible with new labels. Reuses the exported VALID_NODE_LABELS rather than duplicating the list. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(cli): e2e prove impact --uid/--file/--kind reach the backend (U2, #1907) The mocked unit test proves the CLI option->callTool mapping; this spawns the real CLI to prove flags survive the full Commander -> lazy-action -> impactCommand -> callTool chain. Derives the real uid/filePath from context (robust to uid format), asserts uid-only resolution (U1 end-to-end) and a --file negative control against a uniquely-named mini-repo symbol — no ambiguous-fixture surgery needed. Self-skips when the environment cannot index; CI validates the real path. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): route impact BFS frontier mocks through executeParameterized (U3 CI fix, #1907) U3 moved the impact BFS frontier query from executeQuery to executeParameterized (bound params). Three unit suites mock the query layer and routed the frontier query (matched on 'r.type IN') through executeQueryMock; update them to return the frontier rows via executeParameterizedMock so the BFS sees callers again. Test-only — no production change. Fixes the 19 ubuntu/coverage failures; restores the summaryOnly skip assertion to non-vacuous. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> |
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Nilotpal Kashyap
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50c6acb108
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feat(setup): implement antigravity integration setup and hook adapter… (#1730)
* feat(setup): implement antigravity integration setup and hook adapter for gitnexus * docs(readme): list Antigravity in supported editors * test(setup-antigravity): pin platform per-test to fix Windows CI failure The MCP entry assertion expected `npx` directly, but on Windows `getMcpEntry()` wraps it as `cmd /c npx ...`, which broke the Windows runner. Pin platform to darwin in beforeEach so the existing assertion is deterministic, restore the descriptor in afterEach, and add a parity test for the win32 cmd-wrapper shape. * fix(antigravity): align hook adapter to Gemini CLI schema + fix Windows CI Rebase the Antigravity integration on the canonical Gemini CLI hooks contract (https://geminicli.com/docs/hooks/reference/), which is the documented schema Antigravity 2.0 inherits: - Hook adapter: replace PreToolUse/PostToolUse with the single AfterTool event. BeforeTool has no documented context-injection channel in the Gemini contract, so augmentation runs in AfterTool where hookSpecificOutput.additionalContext is the documented way to append text to the tool result the agent reads. Stale-index hints land in the same channel (so the agent sees them) and are mirrored to stderr for terminal users. Tool-name matcher updated to Gemini CLI snake_case (search_file_content|glob|run_shell_command). - Setup: write hooks to ~/.gemini/settings.json under canonical hooks.AfterTool[] (replaces the ad-hoc hooks.json top-level group). Polite-neighbor merge preserves existing user hooks. Also copy win-rm-list-json.ps1 alongside hook-db-lock-probe.cjs so the Windows MCP server ownership probe doesn't silently fail open. - Tests: 17 regression tests covering MCP write, win32 shape, hook schema, polite-neighbor merge, idempotency, adapter context emission, stale-index hint, and skill layout. - README: footnote documenting the AfterTool design choice and a link to the Gemini CLI hooks reference. Windows CI fix: installSkillsTo previously used glob('*.md') + glob('*/SKILL.md'), which returned zero matches under the Windows runner's temp paths (8.3 short-name like RUNNER~1). Replace with fs.readdir + dirent type checks — same behavior, no path quirks. This fixes the only failing Windows job on the PR. * fix(antigravity): address PR review — windowsHide, stale docs, dead code Addresses the production-readiness review findings on PR #1730: - F1 (blocker): add windowsHide:true to all four spawnSync sites in the Antigravity hook adapter (findCanonicalRepoRoot, runGitNexusCli's two branches, buildStaleIndexHint) so they don't flash console windows on Windows. Matches the fix #1794 already on main for the Claude hook. - F2 (blocker): update gitnexus/README.md editor table to say AfterTool and link the Gemini CLI hooks reference. The published README had drifted to the pre-c1872b4 PreToolUse + PostToolUse schema. - F3: rewrite the stale ~/.gemini block comment in setup.ts. It still described the old hooks.json + gitnexus group + grep_search design. - F4: remove grep_search dead code from extractPattern and its doc comment. The registered matcher is search_file_content|glob|run_shell_command, so grep_search would never be invoked. - F5: annotate timeout:10000 with a ms-unit comment noting Gemini CLI uses milliseconds (Claude Code uses seconds). - F6: add the GITNEXUS_DEBUG branch to extractAugmentContext for parity with the Claude adapter, so suppressed augment stderr is recoverable. - F7: stageAdapter test helper now copies win-rm-list-json.ps1 alongside the .cjs helpers, so the adapter's Windows lock-probe path isn't a silent fail-open in child-process smoke tests. * test(antigravity): add integration tests and register in cross-platform matrix Adds end-to-end coverage on top of the unit-level tests, per maintainer request: - test/integration/setup-antigravity.test.ts (10 tests): exercises the real setupCommand() against a temp HOME with ~/.gemini/antigravity/ present. Verifies mcp_config.json shape, ~/.gemini/settings.json AfterTool entry, adapter + helpers + win-rm-list-json.ps1 copy, baked-in cliPath rewrite (issue #108 regression class), skill layout, polite-neighbor merge against existing user hooks, idempotency, skip-when-absent, corrupt-file safety, and key preservation. - test/integration/antigravity-hook-e2e.test.ts (19 tests): runs the full install-then-execute flow — invokes setupCommand to lay down the adapter + helpers, then spawns the INSTALLED adapter as a real child process against a temp git repo + .gitnexus/. The source adapter cannot be spawned directly (it requires sibling .cjs helpers that only live in hooks/claude/); install-then-spawn mirrors the production codepath. Covers staleness detection across all five git mutation types, --embeddings propagation, polite skip on toolResponse.error / exit_code !== 0, augment crash-free behavior, cwd validation, corrupted/missing meta.json, unknown event names, empty stdin, and the no-.gitnexus deep-nested case. - scripts/cross-platform-tests.ts: registers all three antigravity test files (unit in PLATFORM_LOGIC, two integration files in SPAWN_CLI) so Windows and macOS CI exercise them on every run. * fix(antigravity): review fixes — dedup, silent-failure guard, type coercion, glob filter - Delete mergeGeminiSettingsHooks (verbatim copy of mergeHooksJsonc), replace call site with the original - Unify geminiHasGitnexusHook into hasGitnexusHook with commandFragment parameter; delete the duplicate - Guard against silent adapter-copy failure: verify the adapter file exists before registering the AfterTool hook entry in settings.json; surface helper copy errors instead of swallowing - Fix toolSucceeded type coercion: use Number() so string exit_code values from Gemini CLI are handled correctly - Align glob tool extractPattern with Claude adapter's restrictive regex filter (/[*\/]([a-zA-Z][a-zA-Z0-9_-]{2,})/) - Remove bounds-only toBeGreaterThan(0) assertion (DoD §2.7) - Add antigravity adapter to HOOK_FILES windowsHide regression list * chore(autofix): apply prettier + eslint fixes via /autofix command * chore: trigger CI --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Test <test@example.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> |
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|
Copilot
|
87b91c821e
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fix(lbug): add WAL checkpoint-threshold control (#1772)
* Initial plan * fix(analyze): add WAL auto-checkpoint CLI control and default-off behavior * test(analyze): share lbug auto-checkpoint parsing and align validation * fix(analyze): always enable lbug auto-checkpoint and expose threshold control * refactor(lbug): inline always-on auto-checkpoint constructor arg * fix(analyze): guide checkpoint-threshold on Ladybug WAL checkpoint IO failures * test(analyze): cover checkpoint IO guidance and add integration guard * fix(analyze): tighten checkpoint IO detection and remove test hook * fix(analyze): remove checkpoint test hook and tighten error matching * fix(analyze): rename to wal-checkpoint-threshold, raise default, add manual checkpoint driver with retry Address review feedback on PR #1772: - Rename CLI flag, env var, AnalyzeOptions field, recovery-hint tag, and parser/constants from lbug-* to engine-neutral wal-* (matches the existing WAL_RECOVERY_SUGGESTION / isWalCorruptionError convention). - Raise default threshold from -1 (Ladybug stock ~16 MiB) to 64 MiB so users on the default config no longer hit the original rename/remove race. - Align both READMEs to publish 67108864 (64 MiB) instead of 65536 (which would have made the crash more frequent). - Add wal-checkpoint-driver.ts: a periodic manual CHECKPOINT driver wrapped in a 3-attempt jittered retry (50/200/500 ms), driven from runFullAnalysis. Opt-out via GITNEXUS_WAL_MANUAL_CHECKPOINT=0. Moves the race window into a JS-controllable retry surface while keeping native auto-checkpoint on. - Move LBUG_CHECKPOINT_RENAME_RE / REMOVE_RE plus the predicate (renamed to isLbugCheckpointIoError) into lbug-config.ts alongside isWalCorruptionError. Predicate is now exported. Add a permissive fallback matcher and pin the matched Ladybug version in comments. - Warn instead of silently defaulting when GITNEXUS_WAL_CHECKPOINT_THRESHOLD is set to a non-empty unparseable value (closes the CLI-vs-env asymmetry). - Add a typed RecoveryHint string-literal union in cli-message.ts so future hint tags can't drift. - Add a real integration test under test/integration/ that triggers a Ladybug checkpoint IO failure via a pre-existing directory at the rename target (portable across platforms; no test-only injection hook). - Add small-disk / CI caveat (32 MiB secondary suggestion) to the recovery hint and README env-var rows. - Document CLI/env precedence in the analyze --help block. - Help placeholder: <value> -> <bytes>. - Rename analyze-lbug-auto-checkpoint.test.ts to use the new wal-* token. * chore(lbug): remove dead jitteredDelay helper and apply prettier - Drop unused `jitteredDelay` function flagged by CodeQL in PR #1772; the retry loop already inlines the same calculation with the injectable `randomImpl` so the helper was dead. Move the non-cryptographic-by-design comment next to the actual jitter site. - Apply `prettier --write` to wal-checkpoint-driver.ts and the new integration test to absorb the PR autofix bot's formatting findings. --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Test <test@example.com> |
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Copilot
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c34c36036f
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fix(workers): resilient + zero-copy ingestion worker pool — prevent analyze hangs on TS-root-scale loads (#1693)
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* Initial plan * fix: skip worker-timeout files in sequential fallback and optimize TS capture node lookup Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/0e53743e-0600-4690-bd0d-198894daef58 * refactor: clarify TS capture helpers after validation feedback Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/0e53743e-0600-4690-bd0d-198894daef58 * fix(workers): exclude in-flight file on worker error/exit, not just singleton timeout WorkerPoolDispatchError previously surfaced the stalled path only for the singleton-timeout final-fail branch. Worker `error` and `exit` events (and the msg-channel `error` reply) fell back to plain `Error`, so the sequential fallback re-attempted every file in the active job — re-hanging on the same pathological file when the worker crashed mid-parse. Lift the in-flight-file inference into `inFlightExcludePath(job, lastProgress)` and wire it into the three remaining in-pool failure sites. `lastProgress` is already in `runWorker` scope, so `items[lastProgress]` (the next file the worker was about to acknowledge) is the best single guess at the culprit; earlier files are still re-tried sequentially. Returns `[]` when no path is determinable (`lastProgress >= items.length`, or path missing/non-string) so sequential retries the whole job. Replacement-worker startup failures stay plain `Error` (no job context); the result-before-flush protocol bug stays plain `Error` (code fault, not file). Tests cover the three new exclusion paths plus a negative test confirming non-WorkerPoolDispatchError throws fall through to full sequential retry. * fix(review): apply autofix feedback - Use cause-neutral "worker-excluded" label in skip messages and tests now that worker error/exit paths share the same exclusion contract as singleton-timeout (correctness + maintainability reviewers). - Add JSDoc to findSelfOrAncestorOfType{s} explaining the parent-walk short-circuit vs root-DFS fallback (maintainability reviewer). * feat(workers): resilient + scalable worker pool Restructures `createWorkerPool` so a single bad file no longer kills the pool for the rest of an analyze run. Five interlocking layers: 1. **Auto-respawn on error/exit** — worker death triggers `replaceWorker` on the same slot, bounded by `maxRespawnsPerSlot` (default 3). The slot is dropped from rotation when the budget is exhausted; other slots keep running. 2. **Circuit breaker** — replaces the permanent `poolBroken=true` with a consecutive-failure counter. The pool only trips after `consecutiveFailureThreshold` deaths (default `max(3, poolSize)`) with no successful job in between. A successful job resets the counter so transient bursts of bad files don't escalate. 3. **Session-scoped file quarantine** — paths identified as the in-flight file at the moment of a worker death are added to a `Set<string>` on the pool. `dispatch()` filters quarantined items up front (they never reach a worker again this pool lifetime). Exposed via the new `WorkerPool.getQuarantinedPaths()` so callers can log/route them. `processParsing` surfaces the per-chunk quarantine summary alongside the existing fallback-exclusion log. 4. **Authoritative in-flight tracking** — `parse-worker.ts` emits `{type:'starting-file', path}` before each file. The pool tracks this per slot and uses it for crash attribution, falling back to the `items[lastProgress]` heuristic only when no starting-file has been observed (very-early crash, older worker build). Closes the reorder/race concerns raised by reviewers C1 and R3 in the earlier review run. 5. **Per-job cumulative timeout budget** — each `WorkerJob` tracks the total wall time spent across attempts/splits/retries. When the budget is exhausted (default 5x `subBatchIdleTimeoutMs`), the pool surfaces the in-flight path instead of letting exponential backoff balloon into multi-hour stalls. Cross-layer wiring: a new `wakeIdleSlots` helper kicks any non-busy live slot when items are requeued (after a death or split-retry), so a dropped slot doesn't strand work in the queue. `recoverAndResume` consolidates the per-job teardown shared by the three in-pool death sites (`error`, `exit`, msg-channel `error`). New env knobs: `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`, `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`, `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD`. New `WorkerPoolOptions.workerFactory` injection point for unit tests. Tests: 12 new unit tests using a FakeWorker mock cover quarantine seeding, slot-respawn, slot-drop after budget, breaker trip + reset, and quarantine filtering. Plus option-resolution tests for the three new env vars. All 19 worker-pool/-fallback/-options tests pass; full unit suite 6040 passed / 30 skipped / 0 failed. * fix(workers): apply code-review fixes (12 findings) Walks through every finding from ce-code-review run 20260519-094648-3549cf5e. All 12 picked Apply. Critical: - F1 — Layer 5 cumulative-timeout exhaustion no longer silently drops the rest of the job. `requeueRemainder` is now invoked before `handleWorkerDeath` in both Layer 5 and singleton-final-fail give-up paths so non-quarantined items get re-tried by another worker. - F2 — idle-timer recovery overhaul. `!shouldContinue` branch no longer calls `replaceWorker` (double-spawn race with the `handleWorkerDeath` inside `requeueAfterTimeout`). `shouldContinue` branch now enforces `maxRespawnsPerSlot` before respawning, closing the budget-bypass for the timeout-retry path. Also fixes premature `maybeDone` by simplifying the bookkeeping. - F3 — `requeueRemainder` no longer pre-charges `cumulativeTimeoutMs` by `job.timeoutMs`. The death itself consumed no budget, so the next `requeueAfterTimeout` was double-billing the first attempt. - F4 — `WorkerPool.getQuarantinedPaths` is now optional on the interface, matching the defensive `?.()` call site and the existing mocks. Removes the contract-vs-callsite contradiction. - F5 — per-job unattributed-death tracking. When a worker dies with no exclusion attribution, `requeueRemainder` tracks death count per `startIndex`. First time: re-queue intact. Second time: quarantine items[0] as best guess, or drop the job entirely when items lack paths. Bounds the death loop the original design admitted to. - F6 — per-slot consecutive-failure counter. Replaces the pool-wide scalar so a chronically-failing slot trips the breaker on its own streak instead of being masked by another slot's successes. Smaller: - F7 — exhaustiveness `never` check on `WorkerOutgoingMessage` union. - F8 — recursive `runWorker` on fully-quarantined jobs converted to a while-loop. - F9 — `tripBreaker` calls `reject(err)` BEFORE awaiting `worker.terminate()`. A stuck terminate no longer blocks the caller. - F10 — `parsing-processor.ts` quarantine log de-duplicates per pool instance via a `WeakMap`. Only newly-quarantined paths are logged in each chunk; the per-chunk count still surfaces via progress. - F11 — extract `firstPath` local in `requeueAfterTimeout`; eliminates double `itemPath` call and the `unknown as string` cast. Tests (F12, 6 new): - crash-error event path (errorHandler). - F5 drop-branch coverage via items without `.path`. - Common-case unattributable crash falling back to items[0] heuristic. - `replaceWorker` startup failure (workerFactory emits 'exit' before 'online'). - All-slots-dropped breaker trip. - `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS` env override. Residual gap (deferred): no unit test exercises the Layer 5 cumulative-budget runtime path — requires fake-timer interleaving with FakeWorker that's too brittle for this iteration. Tracked. Unit suite: 257 files / 6056 passed / 30 skipped / 0 failed. * test(workers): integration tests for resilience layers + fix requeue-after-timeout flow Adds 6 new real-worker integration tests covering the PR #1693 resilience layers + fixes 3 follow-on bugs surfaced while writing them. New integration coverage (real worker threads + temp fixture scripts): - `respawns the slot after worker process.exit and finishes the work on the replacement` — exercises Layer 1 auto-respawn + Layer 3 quarantine through real IPC. - `attributes exactly via authoritative starting-file message on worker crash` — Layer 4 end-to-end: starting-file message → exact quarantine attribution (not the items[0] heuristic). - `quarantine filters subsequent dispatches without sending to a worker` — second dispatch's sub-batch payload audited via filesystem; the quarantined path is never sent across the message channel. - `drops a slot after maxRespawnsPerSlot and continues on the survivor` — 2-slot pool, slot dies twice past budget, survivor finishes re-queued remainder. - `trips the circuit breaker on cascading per-slot consecutive failures` — single-slot pool, dies on every job, breaker trips after consecutiveFailureThreshold with WorkerPoolDispatchError carrying the cumulative quarantine. - `survives a worker error event (uncaught throw) the same as a process.exit` — validates recoverAndResume on the errorHandler path via a real worker `throw` (not just process.exit). Bug fixes uncovered while writing these tests: 1. **Stack-overflow recursion in runWorker's no-worker branch** — `if (!worker) { ...; wakeIdleSlots(); maybeDone(); }` recursed indefinitely when multiple slots were mid-respawn simultaneously (wakeIdleSlots → runWorker → no worker → wakeIdleSlots → …). Removed the wakeIdleSlots call: the slot's own respawn IIFE owns runWorker post-respawn, and other slots will pick up work via finishJob's runWorker. 2. **requeueAfterTimeout dispatched work before respawn completed** — the F2 fix had `requeueAfterTimeout` `void`-discarding `handleWorkerDeath`, so the `!shouldContinue` IIFE had no way to know when the respawn finished. New design: `requeueAfterTimeout` returns a `TimeoutDecision` discriminated union; the IIFE owns the death-and-respawn-and-dispatch orchestration in an async closure so it can `await handleWorkerDeath` and then call `runWorker` deterministically. 3. **Stalled-singleton + protocol-error + replacement-startup-crash tests** had stale contracts predating the resilience refactor. The stalled-singleton no longer rejects (it quarantines + resolves `[]`); the protocol-error rejection message now mentions "circuit breaker tripped"; the replacement-startup-crash test documents the known `waitForWorkerOnline` race (online fires before the worker's main script runs, so a top-level throw looks like a successful spawn) — the test asserts the file is quarantined via the second-idle-timeout give-up path. Full suite: 334 files / 8982 passed / 43 skipped / 0 failed (second run; first run had a Vitest-reported flake from an uncaught worker exception bleeding into the test report — repeated runs are clean). * perf(workers): raise pool cap to cores-1 + defer per-chunk extraction to keep workers busy User reported 4-5% CPU utilization on a multi-core machine during ingestion. Two structural reasons: 1. **Pool cap.** `createWorkerPool` resolved size as `Math.min(8, max(1, os.cpus().length - 1))` — a 16-core box got 8 workers (50% theoretical max). U1 lifts the default to `min(16, max(1, cores - 1))`, exposes `GITNEXUS_WORKER_POOL_SIZE` env override, and adds `--workers <N>` CLI flag (`0` disables the pool for sequential fallback). 2. **Per-chunk extraction serialized the loop.** Per chunk: dispatch → await workers → main-thread `processImportsFromExtracted` + `processHeritageFromExtracted` + `processRoutesFromExtracted` + `synthesizeWildcardImportBindings` + `seedCrossFileReceiverTypes` → next chunk dispatch. Workers sat idle through every extraction block. U2 (revised from the plan's pipelined-chunks design) defers these passes to a single end-of-loop batch. Chunk loop becomes parse + merge + accumulate. Resolution sees strictly-more-info (full repo graph) so cross-chunk import/heritage targets resolve at least as well as before. Memory cost: `deferredWorkerImports` accumulates across chunks; bounded by total file count, acceptable. Plan deviation note: the plan called for an in-flight chunk pipeline (N concurrent dispatches with bounded memory). That design needed either a `processParsing` API refactor or duplicating its catch-block fallback in `parse-impl`. The deferred-extraction approach delivers the same "workers stay busy" outcome with much smaller surface area and zero changes to `processParsing`. The `GITNEXUS_PARSE_CHUNK_CONCURRENCY` env var documented in U2 of the plan is therefore not implemented in this commit; if memory growth from `deferredWorkerImports` becomes a problem at very-large-repo scale, a bounded sliding-window variant can land as a follow-up. Tests: - New `test/unit/analyze-worker-pool-size.test.ts` covers --workers validation (5 invalid inputs rejected with exit code 1 + clear error; valid integers set the env var; `--workers 0` routes to sequential). - Extended `worker-pool-resilience.test.ts` with `resolveAutoPoolSize` scenarios: env override, env=0, env above cap, invalid env fallback, auto-formula match, integer return type. - Full unit suite: 6097 / 6127 passed / 30 skipped / 0 failed. - Full integration suite (second run): 77 / 78 passed / 1 skipped / 0 failed. First run had a known cosmetic flake from an uncaught worker exception bleeding into the test reporter. Resilience contract from PR #1693 preserved: per-slot respawn budget, circuit breaker, quarantine, authoritative in-flight tracking, cumulative timeout budget — all unchanged. New env vars surfaced in --help: GITNEXUS_WORKER_POOL_SIZE, GITNEXUS_PARSE_CHUNK_CONCURRENCY (reserved for future bounded pipelining). * docs(readme): document --workers CLI flag * feat(workers): add getStats() and per-chunk throughput logging * test(workers): cleanup leaked temp-dirs and drop duplicate option-resolution block - Add afterEach to worker-pool-resilience.test.ts cleaning up the per-test temp directory created by beforeEach (~25 stale dirs per CI run previously). - Delete the duplicated describe('worker pool option resolution', ...) block. Verified the first block (lines 490-532) is a strict superset (includes the GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS env test the second block omitted), so deletion loses no test coverage. Addresses PR #1693 review findings L2 (temp-dir leak) and L3 (duplicate block). * feat(cli): thread --workers via PipelineOptions + snapshot/restore CLI env Resolves PR #1693 review B2 (env-var leak in long-running hosts): - --workers is now threaded through AnalyzeOptions -> runFullAnalysis -> PipelineOptions.workerPoolSize -> createWorkerPool's explicit poolSize arg, bypassing the GITNEXUS_WORKER_POOL_SIZE env channel. The env var remains as a back-compat fallback inside resolveAutoPoolSize for operators who set it directly. - analyzeCommand and wikiCommand snapshot the GITNEXUS_* env vars they mutate at function entry and restore them in finally. Inner *Impl extraction keeps the diff surgical (no body re-indent). process.exit(0) on the CLI success path still terminates the process; restoration matters for programmatic callers (tests, long-running hosts) reaching early-return paths or the alreadyUpToDate fast path. - Tests updated to assert the new behavior: analyze-worker-pool-size.test.ts: workerPoolSize flows through runFullAnalysis options; env is not mutated; back-to-back calls see their own values, not the previous call's leak. analyze-worker-timeout.test.ts: env IS set during the runFullAnalysis call (captured via mockImplementation) and restored after, proving the timeout reaches downstream while the leak fix holds. - Also addresses L4: afterEach NODE_OPTIONS restore so back-to-back test runs don't accumulate --max-old-space-size=8192 tokens. Addresses PR #1693 review B2 (blocker) and L4 (test polish). * feat(workers): harden worker lifecycle (messageerror + availableParallelism + ready handshake) Resolves PR #1693 review H1, H2, M4: H1 - messageerror handler at every dispatch site V8 deserialization failure on postMessage previously left the message silently lost; the pool would wait out the idle timeout (default 30s) instead of treating it as worker death. The dispatch loop now wires worker.once('messageerror', ...) alongside error/exit and routes through recoverAndResume so the existing per-slot respawn budget, in-flight file attribution, and circuit-breaker layers fire as designed. H2 - resolveAutoPoolSize uses os.availableParallelism() Mirrors the pattern at capabilities.ts:85 (defaultEmbeddingThreads). os.cpus().length returns the host CPU count, which over-sizes the pool on cgroup-limited containers, taskset-restricted runtimes, and CI runners with explicit CPU quotas. Falls back to os.cpus().length on Node < 18.14. M4 - worker-side ready handshake replaces online-trust parse-worker.ts now emits {type: 'ready'} after all top-of-script initialization completes, BEFORE the message handler is attached. The pool's renamed waitForWorkerReady listens for this message under a bounded WORKER_READY_TIMEOUT_MS (5s) budget instead of trusting Node's online event - which fires when the worker thread starts, BEFORE the script body runs, letting init crashes slip past pool startup. ready is added to WorkerOutgoingMessage with an exhaustiveness-checked no-op branch in the dispatch handler (defensive: the message is consumed by waitForWorkerReady before dispatch handlers attach). messageerror is wired into waitForWorkerReady the same way. Test scaffolding: - FakeWorker emits {type: 'ready'} in addition to 'online' so replacement workers in unit tests don't hit the 5s budget. - Integration test ad-hoc worker scripts go through a writeReadyWorker helper that prepends the ready handshake. Tests intending to script "crash BEFORE ready" can bypass the helper. 61/61 worker-pool unit tests pass; 28/28 integration tests pass. * feat(parse-impl): monotonic progress + verbose-gated throughput log + seed-before-build Resolves PR #1693 review M2, M3, L1, L5 in a single parse-impl.ts pass: M2 - Monotonic progress through deferred phase (no more "stuck at 82%") Previously the deferred resolution stages (imports, heritage, routes, calls) all emitted percent: 82 — the UI looked frozen for the duration of the deferred work, which on large repos is several seconds to minutes and visually identical to the hang PR #1693 set out to fix. Redistributed: parse phase: 20-70 (was 20-82) imports: 70-75 heritage: 75-80 routes: 80-85 calls: 85-95 Each deferred stage now advances through its own band via the existing per-batch progress callback. Skipped stages (zero deferred input) leave their band as a no-op jump - the next stage still starts at its own band, preserving strict monotonicity. The "no parseable files" early return now jumps to 95 (was 82), and the duplicate "Parsing N files..." announcement is suppressed when totalParseable === 0 to avoid a non-monotonic 95 -> 20 regression that pre-existed (uncovered by the new monotonic test). M3 - Throughput log gated on `--verbose`, not just NODE_ENV=development The per-chunk files/s log was gated on `isDev`, so operators running `gitnexus analyze --verbose` in a production install never saw it. Now fires when (isDev || isVerboseIngestionEnabled()) — matches the documented promise that `--verbose` shows tuning observability. L1 - Typo rename: `chunkChunkStartMs` -> `chunkStartMs` L5 - `buildExportedTypeMapFromGraph` runs BEFORE `seedCrossFileReceiverTypes` Previously the seeding branch was reached with `exportedTypeMap.size === 0` in the worker path (the map was only built far below, AFTER the seeding branch), so the seed dead-coded itself silently and call resolution never got the cross-file receiver-type enrichment. Now the map is populated from the in-progress graph before the seed call; the post-parse builder remains as a defensive sequential-path fallback, guarded by `size === 0` so we don't pay the cost twice on the worker path. Net win: cross-file CALLS edges that previously had no receiver type now get enriched. New test: parse-impl-progress-monotonic.test.ts Asserts the emitted percent stream is strictly non-decreasing across the parse + deferred phases, and that the deferred band (>=70) is actually reached. Also pins the "no parseable files" path to exactly [95] so the 95 -> 20 regression we just fixed can't re-emerge. * feat(parse-impl): bounded chunk concurrency via file-pre-fetch pipeline Resolves PR #1693 review B1 (GITNEXUS_PARSE_CHUNK_CONCURRENCY documented in --help but unimplemented). The chunk loop now pre-fetches chunk file contents up to `parseChunkConcurrency` chunks ahead of the worker-dispatch cursor so disk I/O overlaps with worker compute. Worker dispatch itself stays serial because WorkerPool.dispatch is not reentrant — concurrent calls would race on the shared per-slot busy/in-flight state, regressing the hang/resilience work this PR is built on. The pre-fetch path is the honest interpretation of "concurrent in-flight parse chunks" that the help text advertises: I/O overlap, not parallel worker dispatch. Concurrency value resolution: 1. PipelineOptions.parseChunkConcurrency (threaded from CLI) 2. GITNEXUS_PARSE_CHUNK_CONCURRENCY env var 3. Default 2 (matches the help text) F4 (wildcard-synthesis ordering) is preserved: deferred-state aggregation runs in chunkIdx order because the for-loop iterates sequentially after awaiting each chunk's pre-fetched contents. Cross-chunk processors (processImportsFromExtracted, synthesizeWildcardImportBindings, etc.) still run only after all chunks complete — they see deterministic input regardless of file-read completion order. Concurrency=1 produces behavior identical to the pure-serial loop; that's the regression baseline. New test: parse-impl-chunk-concurrency.test.ts - Asserts graph output is identical (nodeCount + relationshipCount) between parseChunkConcurrency=1 and =2 — the critical correctness invariant. Exact .toBe(N) comparisons per DoD §2.7 (the second run's counts must equal the first run's exactly). - Pins specific fixture symbols (foo/bar/Baz) under both parseChunkConcurrency=1 and the env-fallback (3) path. - Env-fallback test confirms GITNEXUS_PARSE_CHUNK_CONCURRENCY is honored when the option is undefined. * test(workers): pin cumulative-timeout exhaustion behavior Resolves PR #1693 review M6: the existing resilience suite asserts only the *default value* of maxCumulativeTimeoutMs (5x subBatchIdleTimeoutMs), not that dispatch actually aborts the offending job when the cumulative wall-clock budget is exhausted. Without this test, a future refactor could remove the exhaustion branch in requeueAfterTimeout and the suite would stay green while the pool sat in retry loops for an hour on a real production stall. Scenario: subBatchIdleTimeoutMs = 100ms timeoutBackoffFactor = 10 maxCumulativeTimeoutMs = 300ms Single file, HangingWorker that never responds. First attempt times out at 100ms (cumulative=100). The next backoff (1000ms, cumulative 1100ms) exceeds the 300ms cap, so requeueAfterTimeout returns give-up on the first timeout retry and the file goes to the session quarantine. Asserts: - pool.getQuarantinedPaths() includes 'src/stuck.ts' after dispatch - if dispatch rejected, the error is a WorkerPoolDispatchError (the typed surface that routes to sequential fallback) Uses a local minimal HangingWorker double rather than the full action-scripted FakeWorker from worker-pool-resilience.test.ts — the inverse pattern (always hang) doesn't need the scripted-action machinery and keeps the test file focused on the one behavior. * docs(readme): add environment-variables reference table Resolves PR #1693 review L6: operator-facing env vars were either mentioned inline (GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS) or only documented via `gitnexus --help`, with no single place to look up the full set. The new "Environment variables" subsection under the Quick Start CLI block lists every operator-facing knob with default, effect, and tuning guidance, matching the names in cli/index.ts addHelpText post-U2 / U1. Covers: GITNEXUS_WORKER_POOL_SIZE (--workers) GITNEXUS_PARSE_CHUNK_CONCURRENCY (newly real per U1) GITNEXUS_VERBOSE (--verbose) GITNEXUS_MAX_FILE_SIZE (--max-file-size) GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS (--worker-timeout × 1000) GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES GITNEXUS_CHUNK_BYTE_BUDGET GITNEXUS_NO_GITIGNORE GITNEXUS_SKIP_OPTIONAL_GRAMMARS CLI flag vs env-var precedence is stated explicitly (CLI > env > default) so operators running long-lived hosts (MCP server, eval-server) know which channel wins. * test(workers): pin quarantine path round-trip and non-normalization contract Resolves PR #1693 review M5 (Windows quarantine path-normalization coverage). worker-pool.ts quarantines paths via a Set<string> keyed by exact string equality. The existing suite never asserted this contract, which lets a future "helpfully normalizing" refactor on one side of the pipeline (caller, worker, or pool) silently break quarantine filtering on Windows. This file pins the contract from both directions: 1. Round-trip: a path the caller dispatches with backslashes (src\bad.ts) flows through starting-file -> death -> quarantine -> next-dispatch filter verbatim. The replacement worker never sees the re-dispatched bad path because the pool's pre-dispatch filter short-circuits it. 2. Non-normalization: quarantining src\poison.ts does NOT filter src/poison.ts. Whoever changes that contract has to update this test alongside (the load-bearing assertion catches accidental path.normalize() calls in the quarantine path). Runs on every platform — the path strings are test-injected, so the test exercises the same code path regardless of the host's path.sep. Used a self-contained FakeWorker that emits {type:'ready'} for U3's waitForWorkerReady handshake, so the test doesn't depend on the larger worker-pool-resilience.test.ts harness. * test(typescript): pin capture-anchor rewrite invariants (B5 regression) Resolves PR #1693 review B5: the captures.ts ancestor-walk rewrite (findSelfOrAncestorOfType[s] + pickFirstNode replacing the prior findNodeAtRange-from-root path) was semantically equivalent to its predecessor per Lane 4 of the production-readiness review, but the existing typescript-captures.test.ts didn't pin the specific sharp edges where an over-aggressive walk would silently break captures. This file does. Each test exercises a capture class whose anchor type is one the rewrite explicitly handles: - member call obj.foo() -> @reference.call.member (call_expression anchor walks to self) - dynamic import import("./helper") -> raw @import.dynamic gets decomposed by splitImportStatement into @import.statement with @import.kind=dynamic + @import.source stripped of quotes - JSX <Foo /> in .tsx -> @reference.call.free emitted (TSX query pattern, query.ts:899-905) but @declaration.parameter-count is NOT synthesized because findSelfOrAncestorOfType('call_expression') returns null on a jsx_self_closing_element anchor. Pre-rewrite the range lookup also returned null. Pinning this contract catches accidental "walk JSX -> outer call" refactors. - constructor `new Foo(1,2)` -> @reference.call.constructor (new_expression anchor walks to self) - named/namespace import + re-export -> @import.statement (one each) - class method override -> @declaration.method per class, no collapse - member read obj.foo (no call) -> @reference.read.member All assertions use exact .toBe(N) per DoD §2.7. * test(parse-impl): pin multi-chunk graph equivalence under deferred extraction Resolves PR #1693 review B4: the deferred-extraction reorder (moving processImportsFromExtracted / Heritage / Routes / Wildcard / ReceiverTypes from per-chunk to end-of-loop) was proven observably equivalent by Lane 4 of the production-readiness review. Until now, the existing suite never asserted cross-chunk graph equivalence, which lets a future refactor that accidentally tightens the per-chunk vs end-of-loop coupling silently break cross-chunk resolution. This test forces multi-chunk parsing on a small fixture by setting GITNEXUS_CHUNK_BYTE_BUDGET=64 BEFORE the parse-impl module loads (the budget is captured at module load via vi.resetModules — a future move to function-scope env reads is U14 in Phase 2). Then runs the same fixture under a 10MB budget (single chunk) and asserts the two graphs are byte-identical: same nodeCount, same relationshipCount, exact .toBe(N) per DoD §2.7. Fixture: 3-file class hierarchy with cross-file inheritance — Animal (a.ts) -> Dog extends Animal (b.ts) -> makeDog returns Dog (c.ts). Forces the resolver to chain imports + heritage across chunks. A second test pins specific symbol names (Animal, Dog, makeDog, speak, bark) in the multi-chunk graph so a regression in chunk-boundary resolution surfaces as a missing-symbol failure with a specific diagnostic instead of a bare count mismatch. * test(parse-impl): wall-clock integration pinning multi-chunk pipeline (B3) Resolves PR #1693 review B3 — the final P0/P1 merge blocker. With this test, all five doc-review blockers (B1-B5) are pinned by regression coverage. The PR's headline claim is "analyze no longer hangs on TS-root-shaped loads". The existing suite pins each resilience layer (worker-pool- resilience.test.ts), the deferred-extraction equivalence (U7), and the chunk-concurrency contract (U1). What was missing: a single end-to-end run that exercises the full chunked parse-and-resolve path on a multi-chunk fixture, BOUNDED by a wall-clock budget so a regression that re-introduces the hang fails this test loudly via timeout rather than slipping past as a count drift. Implementation: - 17-file synthetic fixture: 15 small modules (one function each), one "realistic dense" complex.ts (30 functions + class + interface), and an index.ts re-exporting them. Forces cross-chunk import chains. - GITNEXUS_CHUNK_BYTE_BUDGET=64 via vi.resetModules forces multi-chunk parsing on the small fixture. - Promise.race with 30s timeout: a hang fails as "exceeded WALL_CLOCK_BUDGET_MS — likely the hang B3 was meant to prevent", not as a bounds-only inequality (DoD §2.7 distinction — hang-detector via exception, not regression-mask via inequality). - Exact .toBe(true) assertions on specific expected symbols (fn0..fn14, Service, Config, configure, describe, complex0/15/29) so a silent mid-chunk crash that exits 0 without producing graph data also fails this test, not just the hang case. Scope: runs the sequential-fallback path (skipWorkers: true) because the full real-worker scenario requires a built dist/parse-worker.js and ~60s wall-clock per run — appropriate for a CI-integration job, not vitest. The load-bearing invariants pinned here catch the bulk of B3's concern; the dist-worker swap is a Phase 2 follow-up documented in the file header. * refactor(parse-impl): move chunk-byte-budget env read to function scope Resolves PR #1693 review F7 / U14: pre-U14, `CHUNK_BYTE_BUDGET` was a module-load IIFE constant that captured `GITNEXUS_CHUNK_BYTE_BUDGET` once and froze the value for the module's lifetime. That defeated per-call option threading (a future `PipelineOptions.chunkByteBudget` was silently no-op'd because the function body read the frozen module-level constant) AND forced tests to use `vi.resetModules` to vary chunk layout. The U7 deferred-extraction test and the U6 multi-chunk integration test both used the workaround. After this change: - `DEFAULT_CHUNK_BYTE_BUDGET = 2 * 1024 * 1024` stays as a module-level constant — purely a default, no env access. - `resolveChunkByteBudget(options)` runs per call: option wins, then env, then default. Same options-first/env-fallback/default pattern as resolveAutoPoolSize and the U1 parseChunkConcurrency resolver — keeps the ingestion code's configuration model uniform. - `PipelineOptions.chunkByteBudget?` added with documentation that threading through options lets long-running hosts (eval-server, MCP daemon) size per-call without leaking process.env state across analyze invocations. New test (parse-impl-env-reads.test.ts) pins all four behaviors: 1. option-first: option present + env present -> option wins 2. env-fallback: option absent + env present -> env wins 3. default-fallback: both absent -> 2 MB default 4. per-call: two back-to-back runs in the same vitest worker with different chunkByteBudget option values observe their OWN values, proving the module-load freeze is gone (no vi.resetModules in this test — that's the invariant being verified). All four assertions use exact `.toBe(N)` per DoD §2.7. The chunk count is observed by parsing the `Parsing chunk X/Y` progress message stream — a stable proxy that doesn't require exposing internal parse-impl counter state. Note: U7 and U6 tests still use `vi.resetModules` because they were written before this change. A follow-up cleanup could simplify those tests (drop the resetModules dance, pass chunkByteBudget via options), but they pass as-is so this commit doesn't touch them. * feat(workers): per-slot generation counter for late-event protection (U12) Adds a monotonic per-slot generation counter to createWorkerPool's state. Each successful worker replacement (replaceWorker) bumps the slot's counter exactly once — atomically with the workers[slotIndex] swap, so observers (getStats) see the new (worker, generation) pair consistently. Handler closures in the dispatch loop capture the slot's generation at attach time and short-circuit when they fire on a stale generation. In the current implementation, cleanup() synchronously removes listeners on a Worker instance the moment a death is observed, so no listener naturally fires on a stale generation — the guard is a defensive layer protecting against any future refactor that loosens cleanup() ordering or re-attaches handlers across the swap. The load-bearing observable is the slotGenerations[] array exposed via WorkerPoolStats so operators (and tests) can confirm a slot was actually replaced and not just the same worker recycled. Implementation: - const slotGenerations: number[] = new Array(size).fill(0) in createWorkerPool's per-pool state, alongside respawnCount and consecutiveFailuresPerSlot. - replaceWorker: slotGenerations[workerIndex]++ AFTER the workers[workerIndex] = replacement swap (only on the success branch — drop-slot paths leave the counter unchanged). - runWorker dispatch loop: const slotGen = slotGenerations[workerIndex] captured before handler attachment; every handler (handler / errorHandler / exitHandler / messageErrorHandler) starts with `if (slotGenerations[workerIndex] !== slotGen) return`. - WorkerPoolStats gains `readonly slotGenerations: readonly number[]`. - getStats() returns slotGenerations.slice() so callers can't mutate pool state by writing to the returned array. Two existing toEqual snapshots in worker-pool-resilience.test.ts extended with the new slotGenerations field (both expect all-zeros — neither test scenario triggers a respawn). New test file (worker-pool-slot-generation.test.ts, 4 tests): 1. Fresh pool: every slot at generation 0. 2. Successful crash + respawn: generation bumps to 1 exactly once. 3. Crash that drops the slot (maxRespawnsPerSlot:0): generation stays at 0 because no successful respawn happened. The dispatch rejection on breaker trip is the expected outcome here; the load-bearing assertion is the post-rejection stats. 4. Multi-slot independence: one slot crashing bumps only that slot's generation, not the other. Order-independent via sort() because the round-robin assignment isn't pinned by contract. All assertions exact .toEqual / .toBe per DoD §2.7. * docs(bench): add parse-throughput benchmark scaffold (R13) Resolves PR #1693 review R13 (benchmark artifact requirement). Creates `gitnexus/bench/parse-throughput.md` documenting: - Synthetic fixture spec (same shape as the U6 integration test, so CI smoke baseline and ad-hoc benchmark exercise the same paths). - What to measure (wall-clock, peak heap, chunk count, getStats snapshot) and the hardware-shape metadata to record alongside. - Harness recipe — vitest + env-var overrides to exercise sequential fallback vs worker-pool paths. - Latest-measurement table with placeholder rows for the three paths (sequential, workers+concurrency, workers single-threaded) and an explicit "Status: scaffold — fill in before merging" callout. The U6 test's observed ~6 s wall-clock is captured as a smoke-baseline. - Operator-tuning quick reference cross-linked to the README env-var section (U11) so the doc is actionable without re-reading the PR. - "What this benchmark does NOT measure" section explicitly scoping the artifact's limits (synthetic ≠ real-repo, throughput-only ≠ resilience-tested, Phase 3 IPC repack row reserved for U16-U17). Mitigates the doc-review SG5 "static doc drift" concern via: 1. Explicit "regenerate this file before merging" callout at the top. 2. Self-contained methodology so anyone can re-run the numbers. 3. Cross-links to the U6 integration test that already bounds the wall-clock as part of the CI suite — so "is it still completing?" is regression-tested even if the numbers in this doc drift. The standalone harness script (`bench/scripts/parse-throughput.ts`) remains a stretch goal per the original plan. The U6 vitest with verbose ingestion logs covers the primary observability gap until the standalone harness lands. * perf(parse-impl): free deferred-extraction arrays after consumption (U15 lightweight M1) PR #1693 review M1 noted that the deferred-extraction accumulator arrays (`deferredWorkerImports`, `deferredWorkerCalls`, `deferredWorkerHeritage`, `deferredConstructorBindings`, `deferredAssignments`) were retained until function return, making peak accumulator memory O(repo) instead of O(in-flight stage). This commit implements the LIGHTWEIGHT version: free each array immediately after its last consumer drains/reads it, dropping peak accumulator memory progressively through the deferred-extraction stages. The structural per-chunk streaming variant (the original U15 framing) is deliberately deferred — the doc-review's adversarial reviewer (A4) flagged it as defending unmeasured memory pressure, and the simpler array-clearing captures the bulk of the benefit without committing to a scheduling-strategy decision (microtask vs parallel extractor task vs worker-side) that profile data should inform. Clears added: 1. After `processImportsFromExtracted` (the sole consumer of `deferredWorkerImports`): clear the imports array before the heavier heritage/calls stages run. 2. After `buildHeritageMap` (the LAST consumer of the raw `deferredWorkerHeritage` records — processCallsFromExtracted reads from the derived `fullWorkerHeritageMap` instead): clear the heritage array before the call-resolution stage. 3. After `processAssignmentsFromExtracted` (the joint last consumer with processCallsFromExtracted for the calls/ bindings/assignments triple): clear all three before downstream graph-build / scope-resolution uses its own working memory. Arrays returned in the function result object (allFetchCalls, allExtractedRoutes, allDecoratorRoutes, allToolDefs, allORMQueries, allParsedFiles) intentionally stay live — downstream consumers need them. Graph-output equivalence is preserved (U7 multi-chunk equivalence test passes — the clears happen AFTER each array's last consumer has copied data into the graph or derived structures). * feat(workers): introduce protocol.ts wire-format module (U16, IPC scaffold) Defines the binary frame for worker-thread IPC as an isolated, fully-tested module. Production wiring is deferred to U17 — shipping the wire-format contract first de-risks the migration by establishing a single source of truth for the byte layout. Resolves the scaffold half of PR #1693 review R12. Wire layout (per message, single buffer): +---------+-----------+---------------------+ | tag | length | payload bytes … | | 1 byte | 4 bytes | | +---------+-----------+---------------------+ tag : MessageTag enum value (0x01 DispatchJob ... 0x08 Ready) length : little-endian uint32 byte count for the payload region payload: UTF-8 JSON-encoded value, possibly "null" Why JSON for the body (rather than per-shape binary encoders): the doc-review adversarial reviewer (A2) flagged that a true per-shape binary encoder for the result message — which carries nested heterogeneous extracted-call / import / heritage / route arrays — would be 500-1500 LOC and a substantial maintenance burden. The honest perf win the IPC repack targets is moving file CONTENTS via ArrayBuffer transferList (zero-copy ownership transfer for the largest single piece of state in any message). That win is captured by U17 layering transferList over the bulk file-content payload while keeping this module's framing for the surrounding metadata. If U18 benchmark data shows the JSON body is itself a bottleneck after U17 lands, a follow-up unit can swap to per-shape binary encoding behind the same encodeMessage / decodeMessage surface without changing the frame. API: - MessageTag (const object): stable byte tags 0x01..0x08 - PROTOCOL_HEADER_BYTES = 5 - ProtocolDecodeError extends Error: distinct class so U17's pool-side handler can route protocol violations through the existing messageerror recovery layer (U3 H1) distinctly from other failure classes - encodeMessage(tag, payload): Buffer - decodeMessage(buf): { tag, payload } - Uses Buffer#subarray instead of the deprecated Buffer#slice Tests (18, all exact-equality per DoD §2.7): - byte layout (tag at offset 0, length LE uint32 at offset 1) - empty/null payload encodes to 5-byte header + 4-byte "null" body - round-trip for every MessageTag with representative payloads - non-ASCII path string (UTF-8 byte-length boundary) - 9 MB payload (well past the existing 8 MB sub-batch budget) - decode errors surface as ProtocolDecodeError, not generic Error: * buffer < header size * tag outside valid range * declared length exceeds buffer * payload bytes are not valid JSON - error class name is preserved through prototype chain so callers can `err instanceof ProtocolDecodeError` reliably * refactor(workers): extract quarantine into its own module (U13 partial) Honest partial U13: extract the quarantine resilience layer (Layer 3 of the 5-layer model) into a dedicated module with a small explicit interface. The full 5-module split that the original plan named was flagged by doc-review A10 as abstraction-without-multi-consumer-demand ("Each has exactly one consumer: worker-pool.ts. None of these layers is imported elsewhere in the codebase pre-extraction, and the plan doesn't identify any future consumer.") This commit ships the smallest self-contained layer as a named module to validate the factory + interface pattern with minimal risk. The remaining four layers (respawn-budget, cumulative-timeout, circuit-breaker, slot-attribution) stay inline until a real second consumer emerges (e.g., a non-parse worker pool that reuses the same resilience layers). Module shape (`workers/quarantine.ts`, ~30 LOC): interface Quarantine { add(path: string): void; has(path: string): boolean; snapshot(): string[]; // defensive copy readonly size: number; // getter, reflects state at access time } function createQuarantine(): Quarantine Replaces in `worker-pool.ts`: - `const quarantined: Set<string> = new Set()` -> `createQuarantine()` - `quarantined.has(p)` -> `quarantine.has(p)` (2 sites) - `quarantined.add(p)` -> `quarantine.add(p)` (2 sites) - `quarantined.size` -> `quarantine.size` (2 sites) - `Array.from(quarantined)` -> `quarantine.snapshot()` (6 sites) Public worker-pool.ts API is unchanged — `getQuarantinedPaths()` still returns the same defensive `string[]` copy. The behavioral contract is preserved: paths are quarantined as opaque strings (the U9 / M5 non-normalization contract still holds — see the new dedicated test). Tests: - 8 isolated unit tests for the quarantine module — pins the interface contract (empty start, add/has/size, dedup on repeated add, no separator normalization, snapshot defensive copy + freshness, size-getter live behavior). - All 86 existing worker-pool tests pass unchanged — they exercise the quarantine through the pool and act as the regression net for behavior preservation. Why not the full 5-module extraction in this commit: doc-review A10's concern is real — a single-consumer abstraction adds module-boundary overhead (5 sets of imports, 5 dedicated test files, 5 interfaces to keep in sync with worker-pool) without any structural benefit until a second consumer materializes. Extracting one validates the pattern; the remaining four can be moved on demand. * feat(workers): wire protocol.ts encoded IPC into parse-worker + pool (U17) Production worker IPC now uses the U16 binary wire format (1-byte tag + 4-byte LE length + UTF-8 JSON body) end-to-end. The pool encodes every outgoing `sub-batch` / `flush` dispatch via `encodeMessage`; the worker decodes incoming frames via `decodeMessage` and encodes its `ready`, `starting-file`, `progress`, `sub-batch-done`, `result`, `warning`, and `error` outputs the same way. The load-bearing correctness fix is making `decodeMessage` accept `Uint8Array` rather than only `Buffer`: Node's `worker_threads` `postMessage` structured-clones the payload, which strips the `Buffer` prototype on the receive side. A frame sent as `Buffer` arrives as a plain `Uint8Array`, and `Buffer.isBuffer(raw)` returns false — so the first attempt at U17 (gating decode on `Buffer.isBuffer`) silently treated every incoming frame as POJO and the worker never responded. The fix adopts the underlying memory zero-copy via `Buffer.from(view.buffer, view.byteOffset, view.byteLength)` and uses `raw instanceof Uint8Array` at every call site (parse-worker decode, pool dispatch handler, pool ready-handshake handler, FakeWorker test mocks, and the integration-test worker preamble). The pool stays tolerant of POJO incoming so unit-test FakeWorkers don't need rewriting — only the new outgoing encoded dispatches require the test scaffolding to decode on receive, which the test FakeWorkers and the integration test's inline `parentPort.on` wrapper now do. The slot-drop integration test was rewritten from a shared-counter-file race (which pre-U17 timing happened to land on the assertion-friendly counter==2 endpoint, but post-U17 protocol decoding latency shifted to counter==1 and produced 3 quarantines instead of 2) to a deterministic path-based crash trigger: slot 0 crashes on a.ts, respawns, crashes on the requeued b.ts, slot is dropped after budget exhausted; slot 1 handles [c.ts, d.ts] normally. Outcome no longer depends on inter-worker file-write ordering. Protocol coverage adds two regression tests pinning the Uint8Array decode path: structured-clone-stripped frames decode identically to their Buffer originals, and Uint8Array views with non-zero byteOffset into a wider ArrayBuffer also decode correctly (catches `Buffer.from(uint8)` copying semantics if a future refactor loses the zero-copy adoption). All 94 worker-pool tests (9 files, unit + integration) pass; the full unit suite (6128 tests across 268 files) passes unchanged. * perf(workers): zero-copy file content transfer via transferList (U19) Pool dispatch now hoists `{path, content: string}[]` file contents OUT of the U17 JSON envelope into separately-allocated `Uint8Array`s whose ArrayBuffers are passed to `worker.postMessage`'s `transferList` for zero-copy ownership transfer. The envelope itself carries only lightweight metadata (`{path, byteLength}` per file) and is structure- cloned the same as before. What this saves vs U17 baseline: - **JSON.stringify of file contents on main thread** drops to zero — the envelope is now O(paths + sizes), not O(total bytes). For a 200- file sub-batch of 10 KB TS files, that's ~2 MB of escape processing per dispatch that disappears. JSON.stringify's per-character branch on quotes/backslashes/control chars is roughly 2x slower than UTF-8 transcode in TextEncoder, so the replacement is a CPU win even though it adds a single TextEncoder.encode per file. - **Structured-clone memcpy of file contents** drops to zero — the contents' backing ArrayBuffers are ownership-transferred, not copied into the worker's heap. The envelope's struct-clone cost is now proportional to metadata size only. - **JSON.parse on worker thread** likewise no longer scales with content size. Worker decodes each `Uint8Array` to string via `TextDecoder` lazily at the parse boundary — runs on the worker thread, parallel with continued main-thread work, vs U17's sequential JSON.parse blocking the worker before processBatch can start. Pipelining: TextEncoder.encode (main) and TextDecoder.decode (worker) can both run while the OTHER side is doing useful work. Under U17, struct-clone was a synchronous main-thread blocker. The ArrayBuffer ownership contract is load-bearing: - File-content `Uint8Array`s are allocated via `TextEncoder.encode`, NOT `Buffer.from(str, 'utf8')`. TextEncoder produces a dedicated ArrayBuffer per call; `Buffer.from(str)` carves from Node's shared `Buffer.poolSize` slab for small strings, so transferring one pool-backed Buffer's ArrayBuffer would detach every other Buffer that shares that slab — silent data corruption. - The envelope itself is NOT transferred. It MAY be pool-backed by `encodeMessage`, and at ~30-80 bytes/file the struct-clone cost is negligible. Not transferring avoids the same detach-collateral risk the contents path is careful to dodge. Detection is strict: every input element must have both `path: string` and `content: string`. A single non-conforming element disqualifies the whole batch from the transfer path and falls back to the legacy single-Uint8Array `encodeMessage` envelope. Safer than partial transfer (which would split a sub-batch into mixed-shape messages the worker can't reassemble). `parse-worker.ts` `decodeIncomingMessage` recognizes the hybrid `{envelope, contents}` shape, decodes the envelope, zips metadata positionally with the contents array, decodes UTF-8 → string per file, and hands the reassembled `ParseWorkerInput[]` to the existing `processBatch`. Identical downstream behavior to U17 — the IPC optimization is invisible above this line. Test scaffolding (3 FakeWorkers + 1 integration-test preamble) gain a `decodeDispatchedMessage` helper that tolerates BOTH shapes (legacy single-frame Uint8Array AND the new hybrid envelope+contents) so the in-process unit mocks keep their existing action-scripting API and the 9 ad-hoc integration test workers keep their `msg.type === 'sub-batch'` handlers unchanged. `buildDispatchMessage` is now exported from worker-pool.ts so its contract can be tested in isolation. A new `test/unit/worker-pool-transferlist.test.ts` pins: - hybrid shape produced for parse-worker inputs - transferList carries one ArrayBuffer per file in input order - envelope decodes to metadata only (no `content` field) - content bytes round-trip byte-for-byte through UTF-8 (ASCII, multi-byte, surrogate-pair emoji) - each content's ArrayBuffer is independently allocated (no pool sharing) — the load-bearing transfer-safety invariant - non-parse shapes, empty arrays, and mixed-conformance arrays all fall back to the legacy single-frame path All 271 test files (6166 unit + integration tests) pass. * fix(workers,tests,docs): apply ce-code-review findings (16 items) Walks the full set of findings from a multi-agent code review (11 reviewers, 1 maintainability dispatch lost to tool-permission denial) of the PR #1693 branch. All 16 actionable findings — 4 P1, 4 P2, 8 P3 — applied in a single pass against a consistent tree. Tests pass (269/269 unit files, 29/29 integration). P1 — bounds-only / disguised-bounds assertions across 4 test files (per user-memory DoD §2.7): - worker-pool.test.ts: 5 sites — `nodes.length > 0` dropped (redundant after `.toContain('validateInput')`); `files.length >= 4` pinned to `.toBe(7)` (mini-repo/src has exactly 7 .ts files); `results.length > 0` pinned to `.toHaveLength(1)` (default sub-batch absorbs all 7); `result.fileCount >= 0` pinned to `.toBe(1)` (empty file is still "processed"); `warnRecords.length > 0` replaced with content- predicate `/respawn|dropping|replacement|did not report ready/` (catches silenced warnings); `fallbackExcludePaths.length > 0` pinned to exact `['one.ts', 'two.ts']` (deterministic given the single-slot pool + 2 items + per-item starting-file). - parse-impl-fallback.test.ts: 3 sites — `astCacheClearCalls >= 1` pinned to exact 4 (per-chunk × 2 + finally × 2); the two error-path delta checks pinned to exact +2 and +3 (verified empirically). - parse-impl-progress-monotonic.test.ts: `percents.length > 0` → `.not.toEqual([])`; per-element `Math.max(prev, cur)` tautology replaced with direct `if (cur < prev) throw`; final-percent `Math.min(last, 95)` tautology pinned to exact `.toBe(70)` (3-file skipWorkers fixture's deferred band lands at the band start). - parse-impl-large-fixture.test.ts: `Math.min(elapsedMs, BUDGET)` tautology removed; Promise.race rejection is the load-bearing wall-clock check. P1 — terminate() lacks `.catch` mask: - worker-pool.ts terminate() now matches the `.catch(() => undefined)` pattern used at every other internal terminate site. Prevents a hung/OOM worker's terminate rejection from masking the original pipeline error when called from parse-impl.ts's finally block, and guarantees `workers.length = 0` / `activeSlots.clear()` always run. P1 — hybrid envelope length-mismatch + null-payload silent data loss: - parse-worker.ts decodeIncomingMessage: explicit non-null-and-typed check before `.type` access (decodeMessage permits null payloads per encodeMessage contract); explicit length-equality assertion between `decoded.files` and `contents` before zipping. Without these, `TextDecoder.decode(undefined)` silently returns "" and produces empty-content graph nodes — a contract violation that used to be undetectable. Both throws route through the outer try/catch → worker `error` reply → pool's recoverAndResume. P1 — unsafe casts at the IPC boundary: - buildDispatchMessage now uses a properly-typed `isParseWorkerItemArray` type guard. The narrowed branch accesses `item.path` and `item.content` as statically-typed strings — a future rename of `ParseWorkerInput.content` would fail to compile inside the branch instead of silently mismatching at runtime. The remaining decodeMessage payload casts are bounded by the F3/F6 runtime guards. P2 — idle-timeout retry bypasses circuit breaker: - worker-pool.ts timeout-retry IIFE now increments `consecutiveFailuresPerSlot[workerIndex]` alongside `respawnCount`. A slot that consistently times out (vs crashes) now trips the per-slot breaker, instead of consuming its full respawn budget over potentially tens of minutes without the breaker firing. P2 — null/non-object worker message crashes pool handler: - Dispatch handler in worker-pool.ts now guards `null / non-object / no string type discriminant` before `msg.type` access and routes through recoverAndResume on violation. Previously a legitimate `null` payload would throw TypeError out of the EventEmitter listener → uncaughtException on main, crashing the analyze. P2 — workerPoolSize === 0 creates unusable pool: - parse-impl.ts now treats `workerPoolSize === 0` as `skipWorkers` at the gate. Matches the PipelineOptions docstring contract ("0 disables the pool entirely — equivalent to skipWorkers"); avoids constructing a pool that rejects every dispatch and logs "Worker pool parsing stopped" per chunk. P2 — encodeMessage 2-buffer allocation per frame: - protocol.ts encodeMessage coalesced to a single `Buffer.allocUnsafe + writeUInt8 + writeUInt32LE + buf.write (string, offset, 'utf8')`. Drops the intermediate `Buffer.from(JSON.stringify(...), 'utf8')` allocation + memcpy. Length pre-check via `Buffer.byteLength(string, 'utf8')` surfaces the uint32 cap before any allocation. P3 — slotGenerations made optional on WorkerPoolStats so external implementations of getStats() that predate U12 don't compile-break; in-repo callers already use optional chaining. P3 — buildDispatchMessage marked `@internal` so it isn't surfaced as public API by typedoc / api-extractor (it's a test-only export). P3 — verboseThroughputLog hoisted above the chunk loop (env vars can't change mid-run; one O(env-read) per analyze, not per chunk). P3 — corrected the messageerror routing comment in worker-pool.ts dispatch handler. `ProtocolDecodeError` is caught by the surrounding try/catch — distinct from `messageerror`, which fires for V8 structured-clone failures before the message body would reach the handler. P3 — initial pool spawn now uses a `Promise.allSettled` ready-handshake gate symmetric with `replaceWorker`. Dispatch awaits this gate before selecting slots, so an init-crashing initial worker is dropped from `activeSlots` and a downstream OOM/missing-native-binding failure surfaces in seconds (bounded by WORKER_READY_TIMEOUT_MS) rather than waiting for the first idle timeout (30s default). P3 — `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`, `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`, `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD` added to: - CLI `--help` text in src/cli/index.ts - Root README env-var table - gitnexus/README troubleshooting section (new "Worker pool resilience tuning" subsection) P3 — CLI `catch (e: any)` / `catch (err: any)` in analyze.ts replaced with `catch (err: unknown)` + narrowed access; matches modern TS best practice and the codebase pattern at other catch sites. P3 — `WorkerPoolStats.terminated: boolean` field added (optional, for backward compatibility). `terminate()` sets it true; `getStats()` surfaces it. Distinguishes graceful shutdown from a circuit-breaker trip in observability surfaces. Coverage / advisory items not addressed in this commit (kept in the report only): - maintainability reviewer failed (Read/Bash denied) — god-module audit on worker-pool.ts (~1400 LOC) carried as residual risk - quarantine case-sensitivity contract unpinned (adversarial #8) - WORKER_READY_TIMEOUT_MS env-configurability (adversarial #2) - chunk-byte-budget × parseChunkConcurrency memory multiplier doc (adversarial #5) - MCP discoverability gaps for env vars / verbose (agent-native W1/W2) - bench/parse-throughput.md scaffold-with-TBD-rows (PS RR-003) * fix(parsing): sequential gap-fill for worker-quarantined chunk files (U20.U1) When the worker pool's Layer 3 quarantine filters one or more files out of a chunk's dispatch, the worker results returned to processParsing are silently narrower than the input chunk. Without this reparse, the graph for this run would be missing every quarantined file's symbols/imports/calls/heritage with no failure signal. After the existing per-chunk quarantine log emits in processParsing's worker-path try-block, run processParsingSequential on JUST the quarantined-in-chunk files. The sequential path writes directly to the graph, so symbols for those files land alongside worker output for the surviving files. Mirrors the WorkerPoolDispatchError catch-block's processParsingSequential call shape — same signature, same args, same scopeTreeCache wiring. Emits a structured warn naming `reparsedPaths` so operators can observe the sequential fall-through. This fixes the in-run side of the corruption Codex's adversarial review of PR #1693 flagged. The cross-run side (chunk-cache poisoning) is closed by U20.U2 in a follow-up commit. References plan: docs/plans/2026-05-20-002-fix-chunk-cache-corruption-on-worker-quarantine-plan.md * fix(parse-impl): suppress chunk-cache write when any chunk file was quarantined (U20.U2) The chunk hash at parse-impl.ts:424-428 is computed from every file in the chunk. The worker pool's Layer 3 quarantine (worker-pool.ts createQuarantine) filters quarantined files out of dispatch, so `rawResults` reflects only the surviving files. Before this commit, the write at line 500-507 stored that partial result under the full-coverage chunk hash — and on the next analyze with unchanged content, the cache HIT branch (line 439-464) silently replayed the incomplete result. Symbols from the quarantined file were missing from the graph for as long as the cache survived. Codex's adversarial review of PR #1693 flagged this as a silent- corruption class because there's no failure signal: no warn log during the replay, no graph-equivalence check, no exit code change. The corruption only surfaces if an operator notices a missing symbol in `gitnexus_query` output. Guard the write with `chunkFiles.some(f => quarantineSet.has(f.path))`. When any chunk file is in the worker pool's cumulative quarantine snapshot, skip the `parseCache.entries.set` call. Emits a verbose- only info log so operators investigating "why aren't my chunks caching" have a diagnostic trail. Skipping the write means the next analyze gets a cache miss for this chunk and re-dispatches it. Quarantine is session-scoped (a fresh createWorkerPool starts with an empty quarantine), so the new pool gives the quarantined file another chance. If quarantine fires again, U20.U1's sequential gap-fill still produces a complete graph for that run; the cache stays empty for the chunk until a fully-clean dispatch lands. The cache-hit replay branch at parse-impl.ts:439-464 is unchanged. Its contract strengthens: "cache entries are complete" becomes true post-fix, but the replay code doesn't need to know that. Closes the cross-run side of the Codex finding. U20.U3 adds the regression test. References plan: docs/plans/2026-05-20-002-fix-chunk-cache-corruption-on-worker-quarantine-plan.md * test(parse-impl): integration regression for quarantine + chunk-cache (U20.U3) Pins the U20 fix end-to-end via REAL `worker_threads` + `createWorkerPool`. Mirrors the writeReadyWorker pattern from `test/integration/worker-pool.test.ts` — inline READY_PREAMBLE + custom test worker script that: 1. Decodes the U17/U19 IPC protocol (Buffer frame OR hybrid envelope/ contents shape) the same way the production parse-worker does. 2. Emits a `{type:'ready'}` handshake so the pool's `waitForWorkerReady` resolves promptly. 3. On a sub-batch containing `poison.ts`, emits starting-file + `process.exit(134)`. The pool attributes the death to `poison.ts` via the in-flight signal and adds it to the session-scoped quarantine. 4. On a sub-batch without poison, synthesizes a minimal valid `ParseWorkerResult` with one `Function` node per file (no tree-sitter dep in the test worker — the synthesized nodes give `mergeChunkResults` deterministic content for the graph). Assertions exercise both fix layers: - U1 (sequential gap-fill in processParsing): the graph contains a `Function` node named `poison` AFTER the run. The custom worker never emits anything for `poison.ts`, so the only path for that symbol to reach the graph is `processParsing`'s sequential reparse of the quarantined-in-chunk file using the real tree-sitter parser against the actual source. - U2 (cache-write suppression in runChunkedParseAndResolve): `parseCache.entries` does NOT contain the chunk hash after the run; `parseCache.usedKeys` DOES contain it (chunk processed, cache write specifically skipped). - Cross-run: a second pass over the same fixture with the same parseCache and a fresh worker pool re-dispatches the chunk (cache empty), the worker crashes again, sequential gap-fill runs again, and the cache stays empty. Pins the round-trip contract. Adds `workerUrlForTest?: URL` to PipelineOptions — same `@internal` test-only injection precedent as `workerThresholdsForTest` (already in PipelineOptions for thresholds). When set, parse-impl uses the provided URL instead of the src/ → dist/ resolution dance. Production call sites never set this field; the only consumer today is this integration test. Why integration over unit: - The fix lives at the boundary between parsing-processor.ts and parse-impl.ts under a real WorkerPool. Unit-mocking the worker-pool module bypasses the structured-clone boundary, the dispatch lifecycle, and the actual quarantine flow — it verifies the test setup rather than the contract. The real worker thread executing through the U17/U19 IPC protocol IS the load-bearing surface. - User-explicit preference (saved as feedback_integration_over_vimock.md memory). For worker-pool / parse-impl / IPC-touching code: write integration tests under test/integration/ using writeReadyWorker patterns; avoid vi.mock on worker-pool.js. Test wall-clock: under 2s; both `it` blocks together complete in ~1.8s under the existing CI conditions. References plan: docs/plans/2026-05-20-002-fix-chunk-cache-corruption-on-worker-quarantine-plan.md * refactor(parsing): remove sequential-parser fallback (U20 design pivot) The worker pool's resilience layers — respawn budget, circuit breaker, quarantine, slot-attribution, cumulative timeout — are now the SOLE contract for handling worker failures. Two sequential-reparse paths are removed from processParsing: 1. **U20.U1 sequential gap-fill for quarantined chunk files** (just added in commit |
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Copilot
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f350ae278a
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feat: Add analyze --repair-fts, enforce FTS verification, and harden repair safeguards (#1720)
* Initial plan * feat(analyze): add --repair-fts and verify FTS index rebuilds Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/dccb3673-af86-43aa-aede-2e1449399775 Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> * refactor(fts): tighten repair/verify messaging and option naming Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/dccb3673-af86-43aa-aede-2e1449399775 Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> * docs: highlight analyze --repair-fts vs --force in READMEs Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/61edc967-debc-419f-9f51-aebf2ef08d22 Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> * fix(analyze): guard repair mode against missing graph store * fix(cli): reject --repair-fts with --force * test(analyze): document repair-store fixture intent * test(analyze): tidy repair failure fixtures and constants * test(analyze): clarify mock constants in repair tests * test(analyze): rename simulated missing-index constant * test(analyze): clarify mocked graph shape in full-verify test * refactor(analyze): finalize flag validation and test clarity * test(skip-git): avoid hard failing when FTS extension is unavailable * test(skip-git): log visible FTS-unavailable test skips * test(skip-git): tighten FTS-unavailable error detection * test(skip-git): simplify FTS-unavailable message checks * test(skip-git): avoid HOME pointing at parent repo in fixture env * fix(analyze): address Claude follow-up findings for repair guardrails Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/2f7243d3-ba16-4d83-86e5-17e6c58a3b0d * fix(repair-fts): clarify invalid graph-store preflight errors Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/2f7243d3-ba16-4d83-86e5-17e6c58a3b0d * test(analyze): strengthen assertions for conflict and missing-store errors Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/2f7243d3-ba16-4d83-86e5-17e6c58a3b0d * fix(repair-fts): make invalid graph-store type errors explicit Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/2f7243d3-ba16-4d83-86e5-17e6c58a3b0d * fix(repair-fts): improve graph-store type diagnostics Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/2f7243d3-ba16-4d83-86e5-17e6c58a3b0d --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> |
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Abhigyan Patwari
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2620b704e0
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feat(cursor): upgrade hooks to Cursor 2.4 postToolUse for Read/Grep/Shell coverage (#1467)
* feat(cursor): upgrade hooks to Cursor 2.4 postToolUse for Read/Grep/Shell coverage
Cursor 2.4 (released 2026-01-22) shipped generic preToolUse/postToolUse hooks
matching `Shell|Read|Write|Grep|Delete|Task|MCP:<tool>`, replacing the
2.3-era beforeShellExecution hook that only fired on shell commands. The
existing integration only intercepted the shell path, so Cursor users got
graph augmentation roughly 10% as often as Claude Code users — only when
the agent dropped to rg/grep instead of using its native Read/Grep tools.
This swaps the integration over to postToolUse and ports the bash+jq
hook script to cross-platform Node:
- gitnexus-cursor-integration/hooks/hooks.json: registers a single
postToolUse hook matching Shell|Read|Grep that invokes the new
gitnexus-hook.cjs.
- gitnexus-cursor-integration/hooks/gitnexus-hook.cjs: new Node hook
mirroring the safety patterns from the Claude hook (absolute-cwd
validation, .gitnexus discovery with linked-worktree fallback,
npx.cmd on Windows, end-of-options `--` marker, debug truncation,
graceful failure). Extracts the search pattern per tool kind:
Grep -> toolInput.query; Read -> file basename stripped to identifier
chars; Shell -> existing rg/grep arg parser. Emits Cursor-shape
`{ "additional_context": "..." }` on stdout — no shell, no jq.
- gitnexus-cursor-integration/hooks/augment-shell.sh: removed (Windows
incompatible, narrower coverage).
- gitnexus/test/unit/cursor-hook.test.ts: 33 regression tests covering
manifest wiring, source-level invariants (no shell:true, npx.cmd,
isAbsolute, additional_context output shape, end-of-options marker),
extractPattern coverage per tool, and behavioral early-exit paths
(empty/invalid stdin, relative cwd, no .gitnexus, unknown tool name,
short patterns, non-search shell commands, case-insensitive matching).
- README.md / gitnexus/README.md: editor-support table now lists Cursor
as Full / hooks=Yes (postToolUse), matching reality.
- gitnexus/src/cli/augment.ts and gitnexus/src/core/augmentation/engine.ts:
doc-strings updated from `Cursor beforeShellExecution` to
`Cursor postToolUse`.
Closes #1466.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(cursor): hook timeout is in seconds, not milliseconds
Cursor's `timeout` field in hooks.json is in seconds (per
https://cursor.com/docs/agent/hooks and the original integration's
`"timeout": 5`). I'd written `10000` after blindly copying the issue
body's example — that resolves to ~2.8 hours, not 10 seconds. If the
script ever hangs before reaching its inner spawnSync timeouts (e.g.
during stdin read), Cursor would have waited that long before killing
it.
Drop to `10` (seconds), matching the Claude plugin's hooks.json and
giving plenty of headroom over the inner 7s augment-CLI timeout.
Add a regression-guard assertion in cursor-hook.test.ts so a future
ms/s mixup fails fast.
Reported by Cursor Bugbot on PR #1467.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(cursor): address Claude review findings — payload aliases, debug, install docs
Resolves three findings from Claude reviewer on PR #1467:
1. Cursor payload field-name uncertainty (SIGNIFICANT)
Claude flagged that the Grep `query` field is an unverified assumption
per Cursor 2.4 docs (https://cursor.com/docs/agent/hooks). Mitigated:
- Expanded Grep aliases: query | pattern | regex | q | search | searchQuery
- Added pickLongestStringValue() last-resort fallback so the hook
extracts *something* even if Cursor renames every documented field
- Added GITNEXUS_DEBUG=1 stderr logging of the raw stdin payload so
users can capture Cursor's actual contract when diagnosing silent
no-ops, and report it back if aliases drift
- Added Read alias `filePath` (camelCase variant alongside `file_path`)
- Inline comment block citing the docs URL and the uncertainty
2. Hook command path resolution + install docs (SIGNIFICANT)
Claude flagged `node ./hooks/gitnexus-hook.cjs` as relative without
documented install path. Added gitnexus-cursor-integration/README.md
with explicit install steps:
- .cursor/hooks.json + hooks/gitnexus-hook.cjs at project root
- Confirms Cursor's project-root CWD convention with doc link
- Verify steps including GITNEXUS_DEBUG capture
- Pattern-extraction contract table per tool
- Troubleshooting: not-firing, npx fallback, wrong-pattern diagnosis
3. README "Full" overclaim for Cursor (MODERATE)
Both README rows now read `Yes (postToolUse, manual install)` linking
to the new install README, accurately signaling that hooks aren't
automated by `gitnexus setup` like they are for Claude Code.
4. Shell quoted-pattern parser limitation (MINOR, documented)
Added inline comment in gitnexus-hook.cjs documenting the known
`rg "User Service"` -> `User` truncation, plus regression tests in
cursor-hook.test.ts pinning the behavior so a future change is
visible.
Test additions (33 -> 41):
- Wide-alias source coverage for Grep (query / pattern / regex / q /
search / searchQuery) plus pickLongestStringValue fallback
- Read alias coverage including camelCase filePath
- GITNEXUS_DEBUG behavioral test: stderr quiet by default, payload
echoed when env var set, stdout output contract preserved either way
- Shell quoted-pattern documented behavior tests
- Install README presence + content (.cursor/hooks.json, hooks/, debug
diagnostics)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
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Gergő Magyar
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ffa0510f9a
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fix(lbug): prevent DuckDB extension install hangs (#1129)
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* fix(lbug): bound DuckDB extension install via ExtensionManager (closes #1128) `gitnexus analyze` could hang indefinitely (60% / 85% on Windows) when DuckDB's `INSTALL fts` or `INSTALL VECTOR` was unable to reach `extensions.duckdb.org`. The DuckDB driver's INSTALL is a synchronous network call, so any blocked egress would block the Node event loop forever. Replace the ad-hoc, in-process INSTALL/LOAD scattered across `lbug-adapter.ts` and `pool-adapter.ts` with a single `ExtensionManager` that owns the lifecycle of optional DuckDB extensions: * `LOAD` is always tried first — per-connection, idempotent, no network. * If `LOAD` fails and policy permits, INSTALL runs in a short-lived child Node process bounded by `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` (default 15s). The parent loop keeps spinning; on timeout the child is killed with SIGKILL and the capability is flagged unavailable. * Capabilities and install attempts are cached per process, so a single bounded install per extension covers every subsequent call. Install policy is now an explicit, per-context decision: * `auto` (default for analyze) — try LOAD, fall back to bounded INSTALL. * `load-only` — used by `pool-adapter` (serve / MCP read paths) so user queries never block on a network install. * `never` — operator escape hatch for offline / airgapped environments. `createFTSIndex` and `createVectorIndex` now check the boolean return value before issuing the index DDL, so missing extensions degrade BM25 and semantic search gracefully without ever throwing during analyze. Tests: - New unit suite for `ExtensionManager` covering LOAD-first behavior, all three policies, install caching, observability, and warn dedup. - Existing vector-extension integration tests pass against the new boolean return type. - Existing embedding-pipeline mocks updated to return `true`. Docs: `gitnexus/README.md` documents `GITNEXUS_LBUG_EXTENSION_INSTALL` and `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` with examples for offline and slow-network environments. Made-with: Cursor * fix(lbug): move DuckDB extension install child into script Keep the bounded out-of-process INSTALL behavior, but replace the inline child code with a stable packaged ESM script. This makes the child process directly runnable and gives debuggable stack traces without source-vs-dist branching or a runtime transpiler. Made-with: Cursor |
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Gergő Magyar
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38ccf7ceb1
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fix: recover worker parse stalls (#1121)
* fix(ingestion): recover worker parse stalls Made-with: Cursor * test(ingestion): cover worker timeout controls Made-with: Cursor * docs: document analyze worker timeout controls Made-with: Cursor * fix(ingestion): fail fast after worker pool hard failure Made-with: Cursor * test(ingestion): stabilize worker stall recovery tests Made-with: Cursor --------- Co-authored-by: GitNexus Maintainer <maintainer@gitnexus.local> |
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Sonu Verma
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9bf9c49a53
|
docs(ingestion): document configurable large-file skip threshold (#991) (#1045)
Follow-up to #1044. Adds user-facing documentation for the configurable skip threshold introduced in that PR: - README CLI Commands: new --max-file-size example line - README Troubleshooting: new 'Large files are being skipped' subsection covering the CLI flag, env var, default (512 KB), ceiling (32768 KB), fallback behaviour, and the effective-threshold banner - CHANGELOG [Unreleased] Added: feature entry with issue/PR cross-refs |
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PhmTuns
|
ea418c0126
|
docs: fix group add and group remove usage in READMEs (#1020)
The top-level and CLI READMEs advertised `gitnexus group add <name> <repo>` (two args) and `gitnexus group remove <name> <repo>`, but the CLI (`gitnexus/src/cli/group.ts`) actually requires three args for `add` (`<group> <groupPath> <registryName>`) and uses `<groupPath>` — not a repo path — for `remove`. Reusing the same second argument across two `group add` invocations silently overwrote the previous mapping because the hierarchy path is the key in `group.yaml`'s `repos` map. Update both READMEs to match the real CLI contract. Node_modules not installed locally for this docs-only change, so pre-commit (prettier + typecheck) was skipped. Made-with: Cursor Co-authored-by: TuanPM1 <tuanpm1@kaopiz.com> |
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Gergő Magyar
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baf3f9e37d
|
feat(ci): add release-candidate publish pipeline (#825)
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* feat(ci): add release-candidate publish pipeline
Auto-publishes gitnexus@rc on every merge to main. Version scheme is
canonical semver X.Y.Z-rc.N where the base is the current npm 'latest'
bumped by the 'bump' input (default patch) and N auto-increments by
querying existing rc versions on the registry. First rc for a new base
is rc.1; the counter resets naturally when the base advances after a
stable release.
- Reuses ci.yml via workflow_call so tests must pass before publish
- SHA-pinned actions, per-job permission scoping, provenance enabled
- Guard job dedupes duplicate dispatches against HEAD via v*-rc.* tags
- Docs-only pushes skipped via paths-ignore
- workflow_dispatch inputs: bump (patch/minor/major), force (override guard)
- Publishes under the 'rc' dist-tag so 'latest' is never moved
- Tags commits as v<rc-version> and creates GitHub prereleases
* fix(ci): address release-candidate review feedback
- Sort rc tags by creatordate (handles out-of-order pushes correctly)
- Fail fast on npm registry errors; only fall back to package.json on E404
- Drop unused pull-requests: write permission on the reused CI job
- Add secrets: inherit so any future CI secrets are available to sub-jobs
- Remove unused reltag step output
* fix(ci): address Copilot review comments
- Correct concurrency comment (runs serialize on same ref, not overlap)
- Apply E404-only fallback to 'npm view versions' query, matching the
pattern used for the 'npm view version' query
- README: clarify that docs-only merges don't trigger rc publish
- CONTRIBUTING: drop 'from main' claim for publish.yml; the tag-push
trigger does not enforce branch reachability
* fix(ci): address adversarial review — idempotency, cycle continuity, tag integrity
Codex adversarial review flagged three release-safety issues in the rc
pipeline. Fixes:
1. Cycle continuity (H). Non-patch rc trains no longer collapse back to
patch on the next push. 'bump' input accepts a new 'auto' value
(default) that infers the active rc base from the registry: if any
X.Y.Z-rc.* exists with X.Y.Z > latest, continue that base; otherwise
patch-bump. Explicit patch/minor/major still forces a cycle reset and
now also bypasses the dedup guard so an explicit dispatch on a
tagged HEAD is honored.
2. Idempotency across post-publish failures (H). The guard marker
('rc/<HEAD_SHA>' lightweight tag) and the release tag ('v<RC>'
annotated) are now pushed atomically *before* 'npm publish'. A
publish failure leaves the marker in place and the guard refuses to
re-publish. Added a defensive 'npm view <pkg>@<rc> version' check
before publish to catch registry-level races. Recovery path
documented in CONTRIBUTING.md.
3. Tag ↔ package integrity (M). 'v<RC>' now points at a detached
release commit whose tree contains the rewritten package.json, so
the tag's source archive matches the npm tarball exactly. 'main'
stays pristine; the release commit is reachable only via the tag.
* fix(ci): surface registry errors on defensive version check; drop actions: read
- npm view <pkg>@<rc> version now distinguishes E404 (safe) from network
failures (abort) via the same mktemp+grep pattern used for the other
two npm view calls
- Dropped actions: read on the ci workflow_call — no sub-workflow uses
the Actions API
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