54 commits

Author	SHA1	Message	Date
ReidenXerx	8f82610217	feat(scope-resolution): report when a field's only anchor is another language ... Round 3, found OUT-OF-SAMPLE — six field names appearing in no prior report, so nothing here was tuned against them. All six answered 0 backend ACCESSES while their definitions sat in `apps/research-dashboard/**`: TypeScript only. The in-sample set scored 5/5 and the out-of-sample set 0/6, and the gap is entirely this. Per-language inference (`3c5eadc7`) is right and stays. What was wrong is that declining is INVISIBLE: an empty result for a field anchored only in TypeScript is byte-identical to an empty result for a field nobody reads. One says "look in the other language or grep"; the other says "delete it". That is the same confident-empty failure this series exists to remove, one surface over — and this time the missing fact is about the ANALYZER's reach rather than the code. Declines are now counted and named, with the languages the anchors actually live in, kept SEPARATE from ambiguity because the remedies differ: ambiguity wants better receiver typing, this wants an anchor in the reading language. Collapsing them would tell a reader the wrong thing to do. A non-zero count warns at analyze time regardless of dev mode. The facts are published as `PipelineResult.propertyInference`, which they had to be for any of this to be testable — and that exposed a second defect. The round-2 ambiguity assertion, which I told the reviewer of #2856 I had strengthened, read its stat off a `scopeResolution` field that does not exist on PipelineResult: the `if (undefined) return` guard swallowed it and the test passed with the production code deleted. Both that assertion and the new ones now read the published field, and the guard is an assertion rather than an escape. Verified by deleting the counter and watching them fail. Reported by the same round-3 method note that caught it: verifying a fix against the cases it was written for only proves those cases pass. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-07 01:53:09 +03:00
ReidenXerx	411cac9b90	docs: document the new incomplete reason, the UNKNOWN verdict and the id churn ... Review found the code changes landed without the guidance around them, and an agent following this repo's own rules would have been told the wrong thing. `graph-write-collapsed` joined `INDEX_INCOMPLETE_REASONS` with no Sign block and no recovery section, while the precedent it cites (`embedding-checkpoint-pending`) has both — so `gitnexus status` would surface a new string naming silent wrong answers with nothing explaining trigger or remedy. Added to RUNBOOK and GUARDRAILS, including why this reason alone also fails the exit code. `AGENTS.md` said MUST warn on HIGH or CRITICAL and never mentioned UNKNOWN, and the shipped impact skill's risk table had no UNKNOWN row and still implied few-callers ⇒ LOW. An agent obeying those rules literally sees `risk: UNKNOWN` and proceeds, which negates the change the verdict exists to make. Both copies of both skills updated. `MIGRATION.md` now records that process ids do not survive this release — positional ids plus depth-first tracing, source-order siblings and round-robin selection mean `proc_7_handle` is a different flow afterwards. Bounded honestly: nothing in-repo joins on a raw process id, so it is index churn, not a broken consumer. `ARCHITECTURE.md`'s scope-resolution stage list gains the two new stages. The guide skill's node list gains `Property` and `TypeAlias` — the two node types this work most prominently creates. Also, on the pair-CSV preflight review asked to confirm: the hard abort IS deliberate, because a fallback recovering zero rows is the confident-empty failure this work targets. But the transient the message itself names — a second concurrent analyze sharing `.gitnexus/csv` — is a race, so the check now re-looks three times over ~150ms before declaring the file gone. Long enough to ride out a rename, far too short to mask a file that is genuinely missing. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 21:58:43 +03:00
drdave	021ac30376	feat(cli): add a bunx lane so bun-only machines can run gitnexus (#2765) ... * feat(cli): add a bunx lane to the runner ladder The ladder assumed a Node toolchain: global gitnexus, then pnpm dlx or npx in some order, with npx as the last resort. On a bun-only machine npm, npx and pnpm are all absent, so every rung fell through to npx and both the emitted hint and the generated .gitnexus/run.cjs produced a command the machine could not run at all. Add bun as a fourth mode, invoked as an install-free bunx one-shot, on two rungs: - npm 11+ with no pnpm to fall back on — bunx dodges the same arborist install crash the pnpm rung exists for (#1939); - npm and pnpm both absent — previously the dead end described above. Every pre-existing outcome is preserved: pnpm still wins on npm 11+, npx still wins on npm < 11, and pnpm still wins over bunx when npm is absent. Regression tests pin each of those. The bun PATH probe is lazy, so a machine with a Node toolchain pays no extra scan and the stale-index hook budget is unchanged. bunx takes no allow-build equivalent: bun's --trust is a bun add/install flag that writes trustedDependencies into a project package.json, which a one-shot has none of, so the argv stays flag-free. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016R9psS9gJ73MRyquoBoPKg * fix(lbug): restore the prebuilt native binary when install scripts were skipped Without this the new bunx lane resolves to a command that still fails: bun skips lifecycle scripts for a bunx fetch, so @ladybugdb/core's install script never copies lbugjs.node up from its per-platform sub-package and every native command dead-ends on 'LadybugDB native binary (lbugjs.node) is missing'. The existing guidance cannot rescue that case. It offers pnpm --allow-build, a global install, or adding trustedDependencies to a project package.json — bunx has no project package.json to add to, no per-invocation opt-in, and re-extracts the package on every run, so an out-of-band repair is wiped before the next invocation. In-process recovery is the only thing that can work. Recovery is cheap because nothing is actually absent: the binary is already on disk in @ladybugdb/core-<platform>-<arch>, and the skipped script only copied it up. Redo that copy (prebuilt only — never a source build, never a network fetch) before reporting failure. Best-effort by construction: read-only node_modules, an absent sub-package or an unsupported platform all fall through to the existing diagnostics unchanged, which a test pins. Also covers pnpm dlx without --allow-build and npm --ignore-scripts. Declare trustedDependencies so a plain `bun install` in this repo produces a working native binary too — the remedy the error message already prescribes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016R9psS9gJ73MRyquoBoPKg * fix(ai-context): name every install-free runner in the generated bootstrap note The emitted gitnexus:start block told a reader with no runner yet to run `npx gitnexus analyze`, falling back to a global npm install. Both name binaries a bun-only machine does not have, so the generated AGENTS.md and CLAUDE.md offered it no reachable bootstrap path. List npx, bunx and pnpm dlx instead of resolving one. The block is committed, so emitting the command this machine happens to resolve would make two contributors on different package managers rewrite it at each other on every analyze — the per-machine churn #1706 removed. Naming all three keeps the note machine-independent and correct everywhere. Regenerates this repo's own committed block to match. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016R9psS9gJ73MRyquoBoPKg * fix(cli): address PR #2765 review — bunx liveness, restore diagnostics, docs Addresses all five review comments on #2765. P1 — `hasBun()` was a PATH-existence check only, so a present-but-broken `bunx` shim (partial uninstall, failed `bun upgrade`) was selected with no functional validation. Because selecting `bun` also suppresses the npm-11 npx-crash warning, the result was a silent dead end: no diagnostic, and a `bunx gitnexus@latest analyze` command that only fails at execution time. Add `probeRuns()` — a real `bunx --version` liveness probe, gated behind the cheap spawn-free PATH scan so machines with npm/pnpm still pay nothing. It ignores the output on purpose (a banner or unparseable version still counts as alive); only a spawn failure, non-zero exit, or timeout rejects. Injectable via a new `bunRuns` dep so the mode tests stay host-independent. P2 — the `gitnexus-cli` skill (and both shipped mirrors) still described the pre-bunx ladder, stranding exactly this PR's audience: a bun-only machine whose agent bootstraps from that file was told to use npx/npm/pnpm, none of which exist there. All three copies now name `bunx` in the ladder and the bootstrap fallback, with a `shipped-skills-sync` fragment assertion so the gap is CI-caught (these copies are not byte-compared, only the engineering family is). P2 — `restorePrebuiltNativeBinary` collapsed every failure into `false`, so an EACCES/EROFS from `copyFileSync` was indistinguishable from "no prebuilt sub-package exists". Users on a read-only `node_modules` layer (a baked container image mounted read-only — a common CI pattern) got the generic lifecycle-script advice, which cannot fix a non-writable filesystem. Return a `RestoreOutcome` instead and route `copy-failed` to its own message. P2 — document that `trustedDependencies` only takes effect for `bun install` / `pnpm install` run inside this repo: it does nothing for a `bunx` one-shot or for a consumer's `bun add gitnexus`. The note sits on `restorePrebuiltNativeBinary` so a future maintainer cannot mistake that function for redundant and delete the thing the bunx path actually relies on. P3 — the `binary_missing` bun advice told `bunx` one-shot users to edit a package.json they do not have, and listed 1 of the 3 packages this package now trusts. Both repair messages now share one `BUN_REPAIR_LINES` const with the full package list and a `bun install -g gitnexus` alternative. Also: shortened the bootstrap note and raised the CLAUDE.md block budget 2900 -> 2950. The note has to name every install-free runner (that is the point of the bun lane), and main's own growth since this PR's last green CI had already pushed the generated block over the old ceiling. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015epfxkEMsmHFNVSFQqAkB4 * refactor(cli): simplify the #2765 review fixes Cleanup pass over the previous commit — no intended behavior change except the doctor status line noted below. Reuse: `probeRuns()` duplicated `probeVersion()`'s entire spawn setup — same argv, timeout, `windowsHide`, and the CVE-2024-27980 Windows-shim workaround — in a file with two byte-identical committed copies, so the shim rule lived at four sites. Its docstring's own objection was to the RETURN SHAPE, not to reuse, so `probeVersion` now returns `{ ran, major, minor }` and `hasBun` reads `.ran`. Existing callers only read `major`/`minor`, so nothing else changes. Also dropped a pointless `const runs = () => …` thunk (`&&` already short-circuits), and deleted a new test that was a character-for-character duplicate of `falls back to npx when npm is null-absent and pnpm is also absent` — its cheapest-first-gate rationale moved into that test's comment. Correctness in the budget comment: the claim that the bun rung is free because "pnpm is absent there, so its probe never ran" was wrong. `formatAnalyzeCommand` spawns `pnpm --version` unconditionally when no global `gitnexus` is on PATH — that spawn IS how pnpm presence is discovered. Real worst case is 5 subprocesses / ~8s, and the 8s needs Windows (`shell: true` spawns cmd.exe for an absent pnpm); on POSIX an absent pnpm ENOENTs in ~1ms. Comment now says that. Likewise "a machine with npm or pnpm never pays" was wrong for npm 11+ without pnpm — that IS the rung that pays. Altitude: `copy-failed` changed only the message text while still returning `kind: 'binary_missing'`, so `doctor` would have printed "✗ lbugjs.node missing" directly above a message saying the binary IS present — exactly the contradiction #2672 removed. Added a `binary_unwritable` kind, a doctor case, and a `nativeStatusCases` row. The binary-missing message construction moved out of `checkLbugNative` into `unrestorableBinaryFailure`, typed `Exclude<RestoreOutcome, 'restored'>` so a new outcome forces a decision instead of silently inheriting the lifecycle-script advice. Drift: the trusted-package list was hand-spelled in five places in native-check.ts, with "matches gitnexus/package.json" asserted only in a comment. All five now render from one `NATIVE_BUILD_PACKAGES` const (rendered output is byte-identical), and the test reads the list out of package.json instead of restating it, so a fourth native package fails the test rather than silently shipping stale advice. Finally, replaced the absolute CLAUDE.md block cap with the ratio the two prior justifications actually appealed to (`< 5465 * 0.55`). Raising 2700 -> 2900 -> 2950 was a ratchet with no ratchet: an absolute cap can only fail on the PR that adds the character, and the fix is always to nudge the number. Also fixed a stale runner ladder in skills-steering.test.ts that still omitted bunx. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015epfxkEMsmHFNVSFQqAkB4 --------- Co-authored-by: drdave-flexnteos <revenaugh.david@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com>	2026-08-06 08:40:36 +00:00
Parafee41	a857f4c5a6	docs(taint): document per-language model files (#2809) ... * docs(taint): document per-language model files * docs(taint): link language-specific model tests --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-08-05 09:15:32 +01:00
Gergő Magyar	7468cc915b	fix(analyze): replace the hand-incremented schema version with a derived DDL fingerprint (#2798) (#2808) ... * feat(schema): derive a fingerprint from the DDL this build creates `SCHEMA_FINGERPRINT` is a sha256 digest of the node and relation DDL that `runSchemaCreationQueries` actually executes, in the same shape as the existing `taintModelVersion` stamp (hex, sliced to 12). It exists because `INCREMENTAL_SCHEMA_VERSION` is hand-picked and has to *predict* whether an on-disk database matches this build's DDL. That number has collided with `main` eight times, twice exactly — and an exact clash is the quiet one, because the reuse gate is a strict `===`. `EMBEDDING_SCHEMA` is deliberately excluded: its `FLOAT[N]` width comes from `GITNEXUS_EMBEDDING_DIMS` at module load, so folding it in would make the digest a function of the environment rather than of code, and two runs of the same build under different env would thrash full rebuilds. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * feat(storage): record the DDL fingerprint in RepoMeta `RepoMeta.schemaFingerprint` stores the digest of the DDL an index's tables were actually created from. It is the derived companion to `schemaVersion`, not its replacement: both are compared, and both must match. Absent means mismatch, deliberately. Grandfathering a missing fingerprint would let an incremental top-up stamp a fresh one onto a database whose DDL was never verified, permanently certifying exactly the wrong-shaped index the field exists to catch. The cost is one full rebuild per pre-existing index. The version ladder gains a note that its "re-check against origin/main before merge" ritual now only guards *semantic* bumps. v25, v26, v30, v31 and v34 all changed emitted ids, edges or wire formats while leaving the DDL byte-identical, and the fingerprint cannot see any of them — but DDL collisions no longer need renumbering. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(analyze): gate index reuse on the DDL fingerprint, not just the version (#2798) `INCREMENTAL_SCHEMA_VERSION` is a hand-incremented integer that has to predict a derived fact: whether the on-disk DDL matches the code's DDL. It has collided with `main` eight times, and twice the collision was *exact*. An exact clash is the silent one. Two builds stamp the same number over different DDL, the `===` reuse gate reads the index as current, every `CREATE ... TABLE` is then skipped as "already exists" (suppressed in `runSchemaCreationQueries`), and the edges whose endpoint pair the live database cannot hold are dropped by `fallbackRelationshipInserts`' bare `catch`. The result is a wrong graph, with no error anywhere. Reuse now requires the version AND the DDL fingerprint to match, in both the pre-pipeline force-rebuild guard and the `isIncremental` predicate, and the fingerprint is stamped alongside the version at the end of a run. Both conditions are necessary. The fingerprint does not replace the integer: most entries in the version ladder change emitted ids, edges or wire formats while the DDL stays byte-identical, and a fingerprint-only gate would stop forcing rebuilds for all of them. What it does buy is that two branches picking the same number no longer need renumbering. The new branch sits above the `alreadyUpToDate` fast path for the same reason the version guard does — a clean tree at an unchanged commit would otherwise early-return before either check ran. Closes #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test(analyze): pin the DDL fingerprint gate and its two failure cases `schema-fingerprint.test.ts` pins the properties the gate rests on: the digest covers exactly the node and relation DDL that gets executed (recomputed from the exported lists, so adding a table or a FROM/TO pair without the fingerprint moving is impossible), it excludes the environment-derived embedding DDL, and it moves when any covered string moves. The two `incremental-orchestration` cases exercise the production path rather than modelling it: an index carrying the *current* version with a foreign fingerprint, and one with no fingerprint at all. Both were run against the pre-fix tree first and both failed there with `alreadyUpToDate === true` — the fast path swallowing the mismatch, which is the #2798 symptom exactly. `call-summary-schema-version.test.ts` widens its gate model to two equalities. The second argument defaults to the current fingerprint so all 33 existing version cases read unchanged, and a new case covers the collision, the legacy absence, and the semantic bump the fingerprint cannot see. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs(review-skill): point the schema-constant check at the fingerprint, not the deleted integer All four `gitnexus-review` SKILL.md mirrors told reviewers to verify `INCREMENTAL_SCHEMA_VERSION` "was bumped or regenerated". That constant no longer exists, so the instruction sent every future reviewer looking for something they could not find — and, worse, past its replacement. The check for graph DDL is now derived: `SCHEMA_FINGERPRINT` moves on its own, so the question is whether the diff changed a string in `NODE_SCHEMA_QUERIES` / `REL_SCHEMA_QUERIES`, and whether a newly added DDL array was folded into the fingerprint at all — the one way the derived gate can still be bypassed. What did NOT change is called out explicitly: the parse-store `SCHEMA_BUMP` and the bench fingerprint sets are still hand-maintained and still need the re-check-against-base ritual, and semantic changes that leave the DDL untouched fall outside the fingerprint entirely — those rely on the analyzer runner-identity receipt. Found by the review swarm's docs lane. The original plan for #2798 claimed no documentation mentioned the constant; that sweep covered five root docs and never looked at `.claude/skills/**` or the three mirrors. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs(migration): record the one-time rebuild the fingerprint switch costs Replacing `schemaVersion` with `schemaFingerprint` means every index written by an earlier GitNexus carries no fingerprint, reads as a mismatch, and is rebuilt once. That is deliberate — grandfathering absence would stamp a fresh fingerprint onto a database whose DDL was never verified — but until now it was undocumented, so a user's first post-upgrade analyze would announce a full re-analyze with nothing to explain it. MIGRATION.md already sets the precedent: PR #2363's meta.json → gitnexus.json rename was equally automatic and equally in need of an entry. This follows that shape, and is explicit about the parts that are easy to undersell: - the cost is per INDEX, and branch-scoped slots (#2106) each pay separately; on a large repository a full re-analyze is substantial, not a blip; - rollback is safe — an older binary sees no `schemaVersion` and forces its own rebuild, which is a cost, never a stale graph; - alternating between an old and a new binary rebuilds on every switch, because the end-of-run meta is written as a fresh literal so neither field survives the other's run. The retired ladder's per-version rationale is pointed at in git history rather than reproduced: `git show 561f913a3:.../repo-manager.ts`. That commit is an ancestor of origin/main, so the pointer survives this branch being squash-merged. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(identity): cover workspace-linked packages in the analyzer dependency digest `dependencyNames` enumerated `dependencies`, `optionalDependencies` and `peerDependencies` only. `gitnexus-shared` is declared as a devDependency (`file:../gitnexus-shared`), and in a source-mode run the build root is the gitnexus package tree, which does not contain that sibling. So a change to gitnexus-shared moved neither `build.digest` nor `dependencyRuntime.digest`. That gap matters more since #2798 deleted `INCREMENTAL_SCHEMA_VERSION`. A DDL-affecting edit there is still caught by `SCHEMA_FINGERPRINT`, but a SEMANTIC-only edit — a new `REL_TYPES` member, say, where the relation table carries a bare `type STRING` column so no CREATE statement moves — was covered by nothing at all. Roughly thirty of the retired ladder's entries were exactly that change class, and the runner-identity receipt is what now carries them. Only checkout-local specifiers are added: `file:`, `link:`, `workspace:`, `portal:` and npm's bare local-path shorthands. Pulling in every devDependency was rejected — vitest, eslint and typescript would enter the digest and force a full re-analyze on unrelated tool bumps, which is worse than the hole. Scanning the linked sibling for the first time exposed a latent throw: `collectArtifacts` honoured `PRUNED_RUNTIME_DIRECTORIES` only for a real directory, so a SYMLINKED `node_modules` fell through to the payload branch and died with "Analyzer identity input is not a file". Worktree-style dev layouts and pnpm shared stores hit this immediately — verified in this worktree, where `gitnexus-shared/node_modules` is such a symlink. Pruning it loses nothing: packages beneath are still reached through `resolveDependencyPackageRoot`. Verified: a real `analyze` in this worktree succeeds with `packageCount` 259; editing the linked package's source moves the digest, bumping an installed registry devDependency does not, and removing the link moves it. `DEPENDENCY_RUNTIME_CANONICALIZATION` is deliberately not bumped — freshness compares digests, not the label, and the input-set change already moves them. Follow-up worth having: no fixture in the suite declares `devDependencies`, so this has no regression test yet. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * refactor(analyze)!: delete INCREMENTAL_SCHEMA_VERSION, gate reuse on the DDL fingerprint alone The integer and its ~180-line version ladder are gone, along with `RepoMeta.schemaVersion`. Index reuse is now decided solely by `SCHEMA_FINGERPRINT`; a mismatch — including the absent stamp every pre-existing index carries — warns and forces a full re-analyze, which wipes and recreates the database so the tables are built from the current DDL. Deleting the integer is safe because it was already redundant: the runner-identity guard deep-compares the whole schema-v4 receipt, including a digest over the build tree, and forces a rebuild on ANY analyzer delta. Verified empirically — a comment-only edit to logger.ts, with the fingerprint byte identical, produced "runner identity changed ... forcing a full rebuild". The fingerprint is not thereby redundant. It fires where that guard cannot: a DDL-affecting change in `gitnexus-shared`, which is a workspace-linked devDependency and so sat outside both digests until the companion commit closed that gap. Review findings folded in, each correcting a line this rewrite itself introduced and never published: - B1: two assertions matched a log string the rewrite had renamed; both tests failed. They now assert what production emits. - B2: the pre-existing downgrade test perturbed `schemaVersion: 7`, a field this change deletes, so the spread carried a valid fingerprint, every guard passed, and the run legitimately took the fast path. It perturbs the fingerprint now, restoring the only integration coverage of the gate-above-the-fast-path ordering invariant. - N5: duplicate `schemaFingerprint` keys silently collapsed two assertions into one (TS1117). - N6: the absent-stamp message told non-git repositories their index was "built by an older GitNexus version" — on every run, about an index this exact build had just written. Non-git repos never record a fingerprint, and now the message says so. - N9: the on-disk stamp is shape-checked before being echoed, so a crafted gitnexus.json cannot push ANSI escapes through the CLI log. - N7: a test case that re-computed the same digest expression with its operands swapped, mislabelled as a randomness check on a module-level const. - N10: comments claiming the digest "cannot collide" (it is 48 bits), pointing at a vector-column gate that does not exist, and asserting storage/ is free of a core/ dependency two lines below a core/ value import. None of these were caught by `tsc -p tsconfig.json`, which covers src only, nor by eslint, where no-dupe-keys is off. `tsconfig.test.json` reports all three test defects and is not currently wired into CI. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test(schema): pin that the fingerprint covers every DDL statement init executes `SCHEMA_QUERIES` is the list `runSchemaCreationQueries` iterates — the DDL that actually runs. The fingerprint hashes only two of its three members, and until now no test imported `SCHEMA_QUERIES` at all, so nothing tied the two together. A fourth member appended to that array — the one literally named for what init executes — would have been invisible to the gate. Every existing test would still pass, because they all recompute the digest from the same two arrays the fingerprint already uses. An index whose gate passed would then run `initLbug` over the old database, where `runSchemaCreationQueries` suppresses "already exists", so the new table would never be created and its edges would be dropped by `fallbackRelationshipInserts`' bare catch. A wrong graph, no error — exactly the failure #2798 exists to end. The check is a pure predicate over (executed, fingerprinted, documented exclusions) rather than a positional `toEqual`, so `EMBEDDING_SCHEMA` is named as an exclusion with its reason — its FLOAT[N] width is environment-derived — rather than sitting in a list where a future reader might "fix" it by folding it in. It asserts both directions and is order-insensitive, leaving ordering to the digest assertion that already pins it. The negative case is pinned in CI rather than checked by hand once: the same predicate over a synthetic fourth member must report it. If a refactor ever makes the predicate vacuous, that case fails even though the positive one would not. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test(analyze): name the invariant the version deletion now rests on Deleting `INCREMENTAL_SCHEMA_VERSION` moved a load-bearing guarantee into an implicit one. Roughly thirty of the retired ladder's entries changed no DDL at all — node ids, wire formats, resolution tiers — and the fingerprint is structurally incapable of firing on any of them. Their only remaining cover is the analyzer runner-identity receipt, and nothing in the suite said so. This adds a table over the real `analyzerRunnerIdentitiesEqual` with a well-formed schema-v4 receipt: byte-identical reuses; an entrypoint-only difference reuses (CLI vs analyze worker); a moved build digest with unchanged DDL forces — that case IS the invariant, commented as such; and a dependency change, an ABI change, undefined, null, a schema-v3 legacy receipt, a missing build section and a non-sha256 digest all fail closed. The deleted `expect(INCREMENTAL_SCHEMA_VERSION).toBe(35)` pin is also worth naming: it failed CI on every bump by design, which is what made an author stop and think. Nothing replaced it. This does not restore that — a digest has no literal to pin — but it does make the mechanism that took over the job visible to the next person who reads the file. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test(spring): pin CLASS_SCHEMA's membership in the fingerprinted DDL set When `INCREMENTAL_SCHEMA_VERSION` went away, its sibling in basicblock-callee-ids-schema.test.ts got a replacement assertion tying BASICBLOCK_SCHEMA to the fingerprint's input set. This file's `>= 23` floor was deleted with nothing put in its place. The file still asserts CLASS_SCHEMA's CONTENT — that the `frameworkAnnotations` column exists — but not that CLASS_SCHEMA is part of what the digest covers, and the second is what makes an index built before that column carry a different fingerprint and get rebuilt. Mirrors the sibling so the two read the same way. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(identity): stop a symlinked directory from aborting the whole analyze `collectArtifacts` fused two orthogonal facts into one condition: that four directory names never carry runtime payload, and that a symlink where a real directory was assumed falls through to the payload branch, where `snapshotReadableFile` stats the target, sees a directory, and throws "Analyzer identity input is not a file". The second was only fixed for those four names. Every other symlinked directory in a scanned package root still aborted the run — `dist -> build`, a vendored grammar link, anything inside a linked sibling checkout. Newly reachable, because making workspace-linked packages scannable pointed the scanner at a live checkout instead of an immutable registry tarball for the first time. Split along the actual seam: prune on the NAME alone, and give symlinks their own branch in the type dispatch, ahead of the payload branch. Link text is recorded rather than followed. Following was rejected on three grounds, each checked in source: the traversal is a stack with no visited set, so a self-referential link would recurse to `runtimeDepth` — which throws, trading one hard abort for another; `snapshotDirectory` rejects a symlink outright, so the directory guard could not accept one without a realpath rewrite of its canonical-path identity; and a link into an already-scanned tree double-counts against `runtimeEntries`/`runtimeBytes`, which also throw. The cost is stated in code: a link out of the package contributes its text, not its target's content. Links resolving to a regular file keep the existing content digest. The new `'unfollowed-symlink'` kind is threaded through every consumer, including the cache validator — which re-probes with `mode: 'link'`, since the readable-file probe resolves the target and would return null for exactly this kind, silently failing every warm validation. No canonicalization or cache-schema bump. Digest content changes only for trees that previously crashed: a delta scan over all 258 scanned roots of this install found no regular file bearing a pruned name and no symlink failing to resolve to a file, so `dependencyRuntime.digest` is byte-identical here. Six of the eight new tests fail against the unfixed tree with the exact production error; all eight pass after. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * refactor(analyze): give the reuse gate a real seam and sanitize logs at the funnel Cleanup pass over the #2798 branch. Net -183 lines. The gate had no extracted predicate, so its own test asserted it by regex-matching run-analyze.ts SOURCE TEXT. That pinned production formatting: one pattern froze three back-to-back single-name imports from './lbug/schema.js', so merging them — the obvious tidy-up — failed a test named "still imports the DDL digest itself". `schemaFingerprintMismatch` and `isSchemaFingerprintShaped` now live in core/lbug/schema.ts beside the constant. Not in run-analyze.ts next to `pdgModeMismatch`, because storage/ must stay off the analyze pipeline and mcp/resources.ts is a plausible second consumer — the same reasoning that puts `cjkSegmentationModeMismatch` in core/search/. The regex block is gone; the test calls the predicate. The three imports are merged. ANSI sanitation moved from one field to the funnel. The per-field guard's own comment stated the general hazard — gitnexus.json is parsed with no runtime shape validation and the notice reaches console.log — while two sibling guards twelve lines away echoed `runnerIdentity.schemaVersion` and `cjkSegmentation` from that same file raw into the same log. `log()` now strips C0/C1 controls, covering all seven guard messages and any written later. Also: - Deleted a duplicate integration test. After the downgrade test was repointed at `schemaFingerprint` it became the same scenario as the new one, differing only by an extra log assertion — which is now folded into the survivor. Saves a fixture and two full pipeline runs per CI pass. - Replaced a 3-parameter set-difference helper with one set equality. Its doc was false at one call site (arguments semantically swapped) and it needed a fourth test purely to prove itself non-vacuous; set equality cannot go vacuous. - Removed ~115 lines of runner-identity table that duplicated analyzer-identity.test.ts. The three genuinely uncovered cases moved there, and the #2798 invariant — build digest moved while the DDL did not — now asserts against a REAL analyzer-build-tree edit rather than a hand-built literal, which is strictly stronger than what it replaces. - MIGRATION.md quoted a log line the code cannot emit; it was written before the placeholder changed. - Restored the rationale on the `capabilities` docstring, which a previous pass replaced with its consequence — leaving a maintainer reading "duplicated by hand" as a wart to fix by importing, which is what the original forbade. - Marked the `isIncremental` conjunct as belt-and-braces: `!options.force` short-circuits before it, so it cannot decide anything. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * feat(analyze): force a rebuild when the vector column width changes `CodeEmbedding.embedding` is declared `FLOAT[EMBEDDING_DIMS]`, resolved from `GITNEXUS_EMBEDDING_DIMS` at module load. Nothing gated it. Flip the variable on a same-commit clean tree and no guard fired at all: `alreadyUpToDate` returned over a `FLOAT[384]` table while the process embedded at 768. The only reaction anywhere discards the embedding CACHE and re-embeds — into a column whose type it never revisits. This predates #2798; `INCREMENTAL_SCHEMA_VERSION` never covered dims either. It surfaced because the fingerprint work had to reason about why `EMBEDDING_SCHEMA` must stay OUT of the digest: its width is environment-derived, so folding it in would make the same build disagree with itself and thrash rebuilds. That exclusion is correct, and it leaves the width needing its own guard. Modelled on `cjkSegmentation`, the closest sibling: an env-resolved scalar stamped at write time and compared by a small exported predicate that forces on mismatch. `embeddingDimsMismatch` sits in core/lbug/schema.ts beside `EMBEDDING_DIMS`, so the query side can adopt it without importing the analyze pipeline — mcp/local/local-backend.ts already warns on a cjkSegmentation disagreement and has the identical claim here, since the query path embeds at the live width against a table of unknown width with no validation at all today. ABSENCE IS NOT A MISMATCH, deliberately. Forcing on it would be dead code: `embeddingDims` and `schemaFingerprint` ship together, and a missing fingerprint already forces exactly one rebuild — which is where this stamp lands. Absence also carries no signal here, unlike the fingerprint: a missing fingerprint means "DDL this build cannot vouch for" and ships WITH a DDL change, whereas a missing dims stamp means only "written before the field existed", and that run's table agreed with that run's width. Drift requires the env to change, which absence says nothing about. The `cjkSegmentation` trick of folding absence into the default was unavailable — there is no width that is safe to assume for an existing table — so the stamp is instead written unconditionally, giving absence exactly one meaning. Malformed values are not grandfathered: null, '384', NaN and objects all read as a mismatch and err toward a rebuild. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * feat(mcp): warn when the served index's vector width differs from the query embedder's The analyze side now forces a rebuild when the vector column width changes. The query side had no equivalent: a serving process embeds a query at its own width and searches a table whose width was fixed when the index was built. Disagree and the user gets wrong or missing semantic results with nothing explaining why. Mirrors the cjkSegmentation drift warning immediately above it — same warnings[] array, same per-query recomputation, agent-visible in the tool response, and it warns rather than refuses. A width mismatch degrades the semantic lane only; keyword results are unaffected, so `partial` is deliberately not set. Compares against `getEmbeddingDims()` — the width the query embedder actually produces — NOT schema.ts's `EMBEDDING_DIMS`. The two diverge exactly when GITNEXUS_EMBEDDING_DIMS is set on a server that embeds LOCALLY: the query path ignores that variable and embeds at 384, so comparing against the env-derived constant would report drift on a lane that works fine. The recorded width is what the vector CAST actually binds. `embeddingDimsMismatch` is imported from core/lbug/schema.js rather than restated, so "absent is not a mismatch" cannot drift between the analyze and query sides. That predicate was placed in schema.ts precisely so this consumer could reach it without importing the analyze pipeline. Two gates keep it quiet when it would be noise: it fires only for a repo where this process actually produced a query vector, so an index analyzed without --embeddings (or a server whose embedder is unavailable) never carries it. An untrusted recorded value — meta.json is schema-less JSON — is reported as "an unrecognized width" rather than echoed. `loadMeta` is hoisted out of the neighbouring try so both diagnostics share one read and an invalid GITNEXUS_FTS_CJK_SEGMENTATION cannot take this one down with it. Refs #2798 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(identity): detect an npm-linked dev dependency the specifier cannot see `isLocallyLinkedSpecifier` admits a devDependency whose SPECIFIER is checkout-local. `npm link <pkg>` leaves the specifier a registry range while the node_modules entry symlinks to a checkout — locally linked, invisible to a specifier check, so a semantic-only edit there still moves neither digest. The obvious placement is unaffordable, measured rather than assumed: probing every dev-only name inside collectRuntimePackages costs 1998 resolutions, not the ~8 it looks like, because dependencyNames runs for every package in the BFS and published tarballs retain their devDependencies. Persisted path guards go 2221 -> 11050 (+398%), and every guard is re-probed on each warm validation — the path `status` takes. Scoped to the root package instead. The declared-intent half is untouched and still enumerated everywhere: it alone can emit the `<missing>` edge for a declared link whose checkout is absent, where resolution returns null and cannot distinguish that from an uninstalled dev tool. The new resolved-location half runs only when `parent.root === packageRoot`, resolves through the existing resolver so its path guards are recorded, and admits a name iff the realpath'd root carries no node_modules segment. Bounded against mis-fire by EXPANSION. "Not under node_modules" is a proxy for "checkout-local"; under a relocated pnpm virtual store every dev dep passes it and the whole dev tree folds into the receipt — against limits that THROW, so a legitimate install would abort. Measured here: uncapped, that shape takes 259 -> 347 packages and 2250 -> 3786 guards. The cap admits at most four and DROPS THE WHOLE CHANNEL on overflow rather than an arbitrary prefix, because the abort comes from the transitive payload of whichever trees get folded in — four of a mis-fired thirteen is still unbounded, and a sorted-prefix receipt would be arbitrary. Overflow falls back to the specifier-only receipt that ships today. Cost on this install: 259 packages unchanged, 13 dev names resolved, guards 2221 -> 2250 (+29, +1.3%). Verified against the real implementation, not just a replay: validation guards 16295 -> 16324, packageCount and artifactCount unchanged, and `dependencyRuntime.digest` byte-identical — so this forces no re-analysis for anyone. Each test fails on the defect it targets: disabling the channel kills the npm-link and cap cases; dropping the root-only scope makes the differential guard-count case fail at 2.8x guards; removing the specifier half kills the `<missing>` case. Refs #2798 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>	2026-08-03 15:04:30 +01:00
azizur100389	797e4ef8f6	fix(ai-context): document CLI graph fallbacks (#2803) ... * fix(ai-context): document CLI graph fallbacks Teach generated GitNexus guidance to pair mandatory MCP graph checks with repo-scoped CLI fallbacks so agents can keep working when MCP is unavailable. Co-authored-by: Cursor <cursoragent@cursor.com> * style(ai-context): satisfy Prettier --------- Co-authored-by: Cursor <cursoragent@cursor.com>	2026-08-02 20:52:44 +01:00
Gergő Magyar	b0cacd05ee	fix(ci): stop the review agent rejecting its own graph-backed reviews (#2731) ... * fix(ci): stop the review agent rejecting its own graph-backed reviews The context-evidence gate only counted a `context` call when the call itself passed `file_path` equal to a changed path. The review skill teaches plain `context({name})`, so 17 of the 26 review-agent run failures were complete, graph-backed reviews thrown away after full model spend, with no log line saying which invariant failed. Prove the evidence from the result instead: `status=found` plus a `symbol.filePath` inside the repo-scoped changed-path set. Every other check stays exactly as it was - strict JSON, orchestrator-only turns, result ordering, duplicate tool-id rejection - and the `repo` argument still selects the head or the merge-base path set. Same failure inventory, smaller classes: - rejection now logs why (in-scope, out-of-scope, sidechain, unresolved and off-path counts plus up to three sanitized paths), and the envelope error names the message count and first-message shape - Glob/Grep leave the tool set: they were enabled through `--tools` but never allow-listed, so every lane call was denied and burned turns - both pinned `npm ci` installs retry three times; one registry ECONNRESET killed a whole run - the prompt matches the new contract and asks for the structured body even when the analysis is incomplete Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(skills): mirror the review-skill tool-set change into the shipped copies The npm package, Claude plugin, and Cursor integration ship byte-identical copies of .claude/skills/gitnexus-review, and the drift guard compares them. Dropping Glob/Grep from the lane frontmatter and the SKILL.md sentence only landed in the canonical tree. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(ci): stop one junk context result discarding a proven review Tri-review of this PR found that the previous commit fixed one spurious rejection and created another. Widening evidence candidacy from "the call that named a changed path" to "every orchestrator context call" also widened the *strict-parse* surface: `contextResultProvesChangedPath` throws rather than returning false, so a single malformed payload anywhere in the transcript now discarded a review that an earlier call had already proven. The MCP makes that reachable without any misbehaving model - `GITNEXUS_MCP_DEFAULT_MAX_TOKENS=12000` truncates any context payload over ~48 KB mid-JSON and appends a marker - and it also destroyed docs-only runs that the `no_indexable_changed_symbols` mode exempts. Reproduced by running the workflow's own embedded script on both trees: a proving evidence call followed by one truncated exploratory call gave `failure_code: null` on the base and `invalid_execution_transcript` on the head; it is `null` again here. - payload-shape failures are caught and counted (`malformedResults`) instead of thrown; transcript-structural invariants (envelope, tool shapes, duplicate ids, empty tool_result) still fail closed - diagnostics gained the reasons they were blind to: errored results, results that arrived out of order or via a sidechain, unanswered in-scope calls, and malformed payloads. A rejection can no longer print an in-scope call with every reason at zero - a deletion-only PR no longer registers head-scoped candidates that can never be satisfied: an empty eligible set is out of scope, not a result "outside the changed paths" - the mandatory-body prompt clause now pairs with a required `complete` boolean. An incomplete analysis publishes its partial body labelled `incomplete_analysis` instead of passing as an accepted review - `Agent(a,b,c)` is split into six separate `Agent(x)` rules: the pinned base action parses allowedTools with `.flatMap((v) => v.split(","))` (parse-sdk-options.ts at 3553f843), which shattered the grouped rule into `Agent(ci-correctness-lens`, four bare names, and `ci-critic-lens)` before the SDK saw it. Pre-existing and unproven at runtime, but the split form is correct under either reading and lets the header's dispatch canary actually prove something Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(ci): require a line range for context evidence The tri-review's adversarial lane executed `context({name: 'AGENTS.md'})` and had the result accepted: the gate checked only that the resolved filePath was in the changed set, so a bare File node passed for a review of that file's contents. The trusted prescan already defines an indexable symbol as one with startLine and endLine, so require the same here. Pre-existing rather than introduced by this branch, but it is the same "what counts as proof" surface the rest of this PR tightens. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(ci): close the remaining tri-review findings Addresses every finding the tri-review left open after 0432214d and 1d9f2d75, across both engines. Reliability and maintainability (Codex ce, ce-reliability, ce-maintainability): - both pinned `npm ci` installs now call one shared `.github/scripts/npm-ci-retry.sh` instead of two near-identical 12-line blocks that differed only in a label - each attempt runs under `timeout` (default 600s, overridable), so a slow registry can no longer crowd the model review out of the job's budget - the helper distinguishes a timeout kill (124) from an npm rejection in its log Test coverage (ce-testing, Codex swarm P3, ce-security, swarm test-ci): - the retry helper is now exercised behaviourally with a stub npm: first-try success runs once, two failures recover on the third, three failures exit 1 - a non-string `symbol.filePath` is a clean reject, not a type error - an adversarial resolved path (ESC, newline, `::set-output`, RTL override) is proven sanitized before it reaches the job log - the envelope error's shape string is asserted - an in-scope call whose result never arrives is counted, not silent - install flags that keep the runtime inert (`--ignore-scripts`, `--prefix`, the lock-bound registry) are asserted against the helper they moved into Correctness and clarity (risk-architect, ce-standards): - the prompt now tells the model to prefer the uid form or pass file_path when a bare name could resolve into an unchanged file, which was the narrower off-path failure mode the gate rewrite left behind - `contextResultProvesChangedPath` -> `contextResultProvesEligiblePath`, matching the set-membership contract its sibling was renamed for - the transcript fixture's default no longer carries a `file_path` the gate ignores, which implied the opposite of the contract - SKILL.md says "file reads" rather than naming a CLI-specific tool, per the CLI-neutrality rule in AGENTS.md; mirrored to all three shipped copies - the interactive-swarm README notes the CI lanes are narrower Publisher (ce-reliability residual, pre-existing): - the publish job no longer gates the whole job on authorization, so a request rejected at normalization no longer strands the "review in progress" marker on the PR forever. Publication stays authorization-gated at the step; only the marker cleanup is unconditional. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix(ci): ship the install helper executable The extracted helper was committed 100644, so the workflow's direct invocation would have failed on the runner with permission denied - a break introduced by the extraction itself, invisible to every existing assertion. Set the mode and pin it with a test. 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>	2026-07-28 17:13:29 +01:00
Gergő Magyar	df0110b06f	fix: index staleness — false-stale status after analyze (#2668) + inline staleness in query/context/impact/cypher tools (#2655) (#2683) ... * fix(analyzer): case-stabilize runner-identity path fields so status isn't false-stale (#2668) `gitnexus status` reported a freshly-analyzed, untouched repo as stale on Windows (econia/aptos-core, 1.6.10-aptos.0). `status`'s up-to-date check gates on `runnerIdentityIsCurrent`, which deep-compares the stamped runner identity against a freshly recomputed one. That comparison includes `build.rootPath`, `dependencyRuntime.manifestPath`/`lockfilePath`, and `runtime.executablePath` (only `invokedArtifact` is stripped), and `identityCacheKey` hashes packageRoot/buildRoot — all derived from paths that flow through `realpathSync.native`, which canonicalizes 8.3 names and symlinks but does NOT normalize the Windows drive-letter case. When `analyze` and `status` are launched under different drive-letter casing (`c:\...` vs `C:\...`, plausible across CLI shim / npx / server-worker entries), the two identities differ by that one byte and `status` reports stale. Fix: `normalizeAnalyzerRootPath(p, platform)` uppercases the Windows drive letter (POSIX no-op, platform-explicit for testability; preserves a `\\?\` extended-length prefix), applied at the single upstream source — `resolveBuildRoot`'s returned `{packageRoot, buildRoot}` — so every derived identity path field and the cache key inherit a case-stable root, plus at `runtime.executablePath` (process.execPath is the same compared class). The `runnerIdentityIsCurrent` gate is kept intact: a genuine analyzer change still differs in `build.digest`/`dependencyRuntime`, and analyze still rebuilds on real mismatch. Note: the drive-letter divergence was not reproduced on a Windows host (none available); the mechanical chain is verified in source and the fix is a correct defensive normalization that is a no-op on POSIX. If a `status --json` identity field-diff later shows `build.digest`/`dependencyRuntime`/`cliVersion` diverging instead, that indicates a genuinely different install (where "stale" is correct), not this bug. Migration: on Windows, an existing index stamped under the old (non-normalized) casing mismatches the normalized recompute once, triggering a single forced full re-analyze on first upgrade (and a one-time identity-cache recompute). One-time, Windows-only, POSIX no-op. Tests: pure `normalizeAnalyzerRootPath` unit tests (drive-letter uppercase, idempotence, drive-only scope, `\\?\` extended-length prefix, POSIX no-op). * feat(mcp): surface index staleness in query/context/impact/cypher tool responses (#2655) `checkStalenessAsync` already computes how many commits an index is behind the checkout's HEAD, and `list_repos` returns it as `staleness: {commitsBehind, hint}`. But the four hot read tools an agent actually calls in a session — `query`, `context`, `impact`, `cypher` — never surfaced it: `resolveRepo` only runs `maybeWarnSiblingDrift` (stderr, sibling-clone drift only), so a direct tool call gave zero indication the index might be behind HEAD. Thread the existing signal into those four tools at the single `callTool` dispatch chokepoint (after the one `resolveRepo`), reusing the `list_repos` `{commitsBehind, hint}` shape: - `stalenessForTool` computes `checkStalenessAsync` behind an in-flight-promise cache (5s TTL) keyed by lbugPath, so N concurrent tool calls share one `git rev-list` and flat/branch handles (same repoPath, different lastCommit) don't collide. The cache entry is evicted with the repo's other per-index state when the repo leaves the registry. - `withToolStaleness` skips the `git` spawn entirely for results that can't carry the field (via `canCarryStaleness`), so error-returning calls pay nothing. - `attachToolStaleness` adds a `staleness` field to an object result only when the index is behind HEAD. It NEVER changes an existing result's shape: raw-array results (non-tabular cypher rows) are returned untouched, because the CLI's `--limit` and other consumers branch on `Array.isArray`; error envelopes and already-annotated results are left as-is. Non-blocking: `checkStalenessAsync` swallows git failures to `{isStale:false}`, so a git error just omits the field — it never fails the tool. Deliberately out of scope: `@group`-targeted calls forward to `callToolAtGroupRepo` before the chokepoint (multi-repo, single-commit staleness is ill-defined); the legacy `search`/`explore` aliases; and `list_repos` / the `context` resource, which already carry the signal. Tests: `attachToolStaleness` branch matrix (stale object -> field; fresh -> unchanged; raw array -> unchanged; error envelope -> unchanged; idempotent; non-object -> unchanged; null-safe) and a flat-vs-branch cache-key regression test that fails when the cache is keyed by repoPath. * test(mcp): cover staleness tool-signal edge cases + harden the freshness boundary (#2655) Addresses the coverage gaps the review flagged on the #2655 staleness signal, plus one defensive guard so a failing freshness check can never fail a tool. Production (defense-in-depth, no behavior change on the happy path): - withToolStaleness now awaits stalenessForTool with a `.catch(() => undefined)` so a rejection degrades to no-staleness instead of failing query/cypher/ context/impact. - stalenessForTool wraps the check in `Promise.resolve(...).catch(...)` that evicts the cache entry on rejection — a transient failure isn't served as a permanently-rejecting promise for the rest of the TTL window, and the `Promise.resolve` wrap makes the boundary robust to a non-thenable return (a no-op for the real async checkStalenessAsync). A resolving promise is never evicted, so happy-path dedup is unchanged. Tests (gitnexus/test/unit/calltool-dispatch.test.ts): - F1: a rejecting checkStalenessAsync leaves the tool payload intact with no staleness field, and a later call recovers (proves the entry isn't poisoned). Written first and confirmed to fail without the guard. - F2: staleness attaches on query/context/impact object results and on cypher's tabular {markdown,row_count}; a raw-array cypher result keeps its shape. - F3: drift guard — exactly query/cypher/context/impact route through stalenessForTool; explain/pdg_query/detect_changes/check do not. - F4: the per-index cache dedupes within TOOL_STALENESS_TTL_MS and recomputes after it expires (driven via a Date.now spy, not fake timers). Tests (gitnexus/test/unit/analyzer-identity.test.ts): - F5: the produced identity's build.rootPath and runtime.executablePath are normalizer-stable, guarding that both call sites thread through normalizeAnalyzerRootPath (trivial on POSIX, a real regression guard on Windows CI). Plus a source comment noting the one-time Windows re-analyze on first upgrade. * test(mcp): run #2668 guard on Windows CI, document staleness field, cover staleness edge cases Addresses the review follow-ups on the staleness work: - Wire test/unit/analyzer-identity.test.ts into scripts/cross-platform-tests.ts (PLATFORM_LOGIC). Its "identity path fields are normalizer-stable" fixpoint is the Windows regression guard for the #2668 drive-letter normalization, but normalizeAnalyzerRootPath is a POSIX no-op, so the guard was only ever running (trivially green) on the Ubuntu full-suite and never on the windows-latest matrix where it actually bites. Now it runs where it matters. - Document the inline `staleness` field on query/context/impact/cypher responses in the gitnexus-guide skill (both the .claude source and the shipped gitnexus-claude-plugin mirror, kept in sync). - Add three staleness tests that pin behavior the prior tests only implied: * @group-routed calls never get the signal (forwarded before the wrapping switch) — locks the intentional skip so it can't silently flip. * one in-flight freshness check is shared across truly concurrent calls (two dispatched before checkStalenessAsync settles → a single spawn), not just sequential reuse of an already-resolved value. * a late rejection from a superseded cache entry does not evict the newer entry that replaced it after the TTL rolled over (the `=== entry` object-identity guard). The defensive stack in stalenessForTool/withToolStaleness (Promise.resolve wrap + guarded evict + outer catch) is retained deliberately: the wrap is load-bearing for the tests (a sibling describe's vi.resetAllMocks() makes the mock return undefined), and the guarded evict closes the superseded-entry edge now covered above. * fix(test): split the #2668 normalization guard into a portable cross-platform file Registering analyzer-identity.test.ts on the Windows/macOS matrix (previous commit) surfaced four pre-existing failures in that file on macOS 3/3 and windows 3/3. They are not new breakage: those fixture tests compare identity fields against the RAW temp-dir path while the identity resolves through realpathSync.native, so on macOS `/var/folders/...` is received as `/private/var/folders/...`. The file was simply never portable — it had only ever run in the Ubuntu full-suite. Reproduced locally by pointing TMPDIR at a symlink: the same four tests fail, and pass again without it. Move only the portable assertions — the pure `normalizeAnalyzerRootPath` cases (explicit `platform` argument) and the identity fixpoint guard (which compares each field against ITSELF normalized, never against the fixture path) — into test/unit/analyzer-identity-path-normalization.test.ts, and register that file on the matrix instead. The #2668 Windows regression guard still runs where it actually bites, without dragging four symlink-sensitive tests onto runners they were never written for. Verified: the new file passes with TMPDIR behind a symlink (the macOS condition); the heavy file is back to Ubuntu-only. * fix(test): keep the cross-platform #2668 file fixture-free so Windows stays green The split file still carried the fixture-based fixpoint guard, which fails on windows-latest: Invoked analyzer artifact is absent from the validated build: D:\a\...\node_modules\vitest\dist\workers\forks.js Cause is a pre-existing cross-drive defect in this module's `isInside()`, not the #2668 change. The GH Windows runner keeps the repo on D: and temp fixtures on C:. `path.win32.relative('C:\\...fixture', 'D:\\...forks.js')` cannot express a relative path across drives, so it returns the absolute target — which does not start with '..', so `isInside()` reports true. `resolveInvokedArtifact` therefore treats the vitest fork worker as the invoked artifact, it is absent from the fixture's validated build, and identity resolution throws. (Verified directly: `isInside` returns true cross-drive and false for the same-drive control.) Keep the cross-platform file strictly pure — only `normalizeAnalyzerRootPath` assertions with an explicit `platform` argument, no fixture and no filesystem — so it is green on every runner while still exercising the transform on real Windows. The fixture-based threading guard moves back to analyzer-identity.test.ts (Ubuntu-only), where the rest of that file's fixture tests already live, with a comment recording why it cannot be on the matrix. The underlying `isInside()` cross-drive bug is left untouched here (out of scope for this PR) but is worth its own fix: it also guards the trusted cache directory and the identity-cache path-escape check in validateIdentityCache, where a false "inside" verdict weakens validation on multi-drive Windows setups. --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com>	2026-07-25 07:21:44 +01:00
Gergő Magyar	fd1e0a999c	feat(ci): review agent runs as a coordinated reviewer swarm (#2572) ... * feat(ci): review agent on Sonnet 5 with structured, linked reviews Bump the pinned review model from claude-sonnet-4-5-20250929 to claude-sonnet-5 (verified against the pinned Claude Code 2.1.214 with subscription auth and --json-schema structured output). Restructure the published review body: verdict-first summary, findings ordered by severity, fixed section order, and every file or symbol reference as a GitHub permalink pinned to the analyzed head SHA (or the merge-base SHA for deleted and rename-old paths) instead of bare path:line text, so references are clickable and render inline previews. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * feat(ci): review agent runs as a coordinated reviewer swarm Implement the review skill's expert-lens section in CI: the main agent spawns four trusted lanes in parallel via the Task tool — correctness, security, blast-radius, and coverage — each a purpose-built persona restricted to Read/Glob/Grep plus the read-only graph MCP tools. Personas live in the canonical skill tree (mirrored to all shipped copies) and are installed into the reviewer's user-scope agents dir from the exact control SHA, so a hostile PR head can never define a lane. Lane reports are treated as unverified claims: the main agent re-anchors findings before publishing, and the publisher's context-evidence gate still requires the main conversation's own successful context call. Bash and the newer Agent tool remain disallowed for every context; the analyze timeout gets swarm headroom (45 -> 60 minutes). The workflow contract test now pins the swarm posture. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): sidechain tool calls can no longer satisfy the evidence gate The review agent's own review of this PR found that proveGraphReview() walked the flat transcript without reading parent_tool_use_id, so a spawned lane's context call could satisfy the publisher's graph-evidence gate the prompt reserves for the orchestrator. Entries with a non-null parent_tool_use_id are still strictly validated (malformed linkage fails the transcript) but are excluded from both candidate context calls and qualifying results; a new fixture proves sidechain-only evidence is rejected while mainline evidence beside sidechain turns still passes. Also gives the orchestrator turn headroom for the four dispatched lanes (--max-turns 100 -> 150), addressing the review's LOW finding. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * refactor(skills): swarm-lane dispatch belongs to the review skill Move the lane orchestration out of the workflow prompt and into the gitnexus-review skill itself: a new "Swarm lanes" section names the four ci-persona lanes, defines when and how to dispatch them (parallel, one message, per-lane context and file slices), and owns the verification contract (lane reports are unverified claims; re-anchor, dedup, drop unanchored findings; lanes structure the work but never gate it). Any runner of the skill — the CI workflow or a local harness — now triggers the lanes from one canonical definition. The workflow prompt keeps only its CI-specific deltas: the lanes' trusted-control-SHA install provenance, the Task-tool dispatch surface, and the publisher's orchestrator-only context-evidence gate. Mirrors synced; 122 contract tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * feat(skills): add adversarial finder lane and critic gate to the swarm ci-adversarial-lens joins the parallel finder wave: it assumes the change is broken and constructs reachable failure scenarios — interleavings, hostile inputs, state corruption, abuse of newly exposed surfaces — each verified to a concrete entry point before it may be reported. ci-critic-lens runs last as a gate on the orchestrator's finished draft: it audits anchoring, concreteness, severity calibration, format conformance, and honesty, returning PASS or a numbered defect list with the smallest repair per item. The skill bounds it to two passes and the critic hardens the review without ever blocking it; the workflow inherits both lanes automatically through the wholesale ci-personas install. Mirrors synced across all three shipped trees; 122 contract tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * refactor(ci): workflow defers the whole swarm contract to the skill Now that the skill's Swarm lanes section owns dispatch, verification, the critic gate, and the fallbacks, the workflow prompt stops restating any of it. It contributes only what CI alone knows: the lanes' control-SHA install provenance, the concrete environment mapping for lane inputs (diff, manifest, head and merge-base checkouts, exact SHAs), and the one CI override — the publisher's context-evidence gate remains orchestrator-only. Analyze timeout gains headroom for the critic's sequential rounds (60 -> 75 minutes). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): dispatch swarm lanes via the Agent tool, not the renamed Task alias On the pinned Claude Code 2.1.214 the subagent-dispatch tool is `Agent` (`Task` was renamed to `Agent` in 2.1.63 and is now a legacy alias), and permission rules evaluate deny before allow. The workflow allowed `Task` and denied `Agent`, so the orchestrator could never dispatch a lane and every review silently fell back to the inline single-agent path while the text-only tests certified the broken config. Use `Agent` consistently: add it to --tools, allow it scoped to the six ci-personas (`Agent(ci-correctness-lens,...,ci-critic-lens)`), remove it from --disallowedTools, and update the prompt. Tests now match the scoped allowlist on the raw string (commas inside Agent(...) break a split) and assert Agent is no longer bare-denied. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): harden swarm permissions — allow Glob/Grep + merge-base reads, quarantine PR-head agents Three permission-hygiene gaps around the swarm dispatch: - Glob/Grep were in --tools but had no allow rule, so the lanes' declared tools could manufacture denied-tool errors; allow them (read-only, sandboxed by cwd + add-dir). - The prompt hands lanes the merge-base source checkout for deleted / rename-old symbols, but no Read rule covered it; add a scoped Read() allow (which grants access without triggering --add-dir agent discovery). - The --add-dir PR-head copy is scanned for spawnable agent definitions and the pinned runtime has no suppression env, so a PR could ship its own .claude/agents/*.md. Drop that subtree from the materialized copy after checkout-index (skills left intact), so only the trusted control-SHA personas can ever be dispatched. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * test(ci): pin the Agent allowlist to the ci-personas; require a dispatch canary A text-only assertion cannot prove the pinned CLI actually dispatches the lanes (print mode silently ignores invalid settings and does not validate Agent(type) content at parse time) — that is what let the original Task/Agent inversion pass CI. Two mitigations for the class: - A cross-consistency test asserts the six names in the Agent(...) allowlist equal the six ci-personas filenames and each persona's frontmatter name, so a rename or typo in any of the three fails without auth. - The activation checklist now requires the post-merge canary to prove a positive dispatch AND an unlisted-type refusal before enabling the trigger. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): bound swarm transcript volume with per-persona maxTurns The six lanes stream into the single execution transcript the publisher validates, but the personas carried no turn budget, so a large-PR swarm run could overflow the (hard-throw) transcript caps and brick a valid review. Bound each lane deterministically — finders maxTurns 12, the critic maxTurns 6 — which keeps the worst case (~2×(150+5×12+2×6) ≈ 444 messages) under the unchanged 1_000 cap, so no cap needs raising. A new test encodes that invariant: it fails if a persona's maxTurns is bumped without revisiting the cap. Applied byte-identically across all four shipped skill trees. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * test(ci): independently pin both sidechain evidence-gate guards The sidechain-exclusion guards at candidate registration and result acceptance were mutually redundant on realistic transcripts (a real sidechain turn carries parent_tool_use_id on both its call and result), so deleting either guard alone still passed the whole suite. Add two asymmetric cross-wired fixtures — a mainline call with a sidechain result (pins the acceptance guard) and a sidechain call with a mainline result (pins the registration guard), both expecting missing_graph_evidence. Mutation-verified: deleting either guard alone now reddens the suite. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * docs(skills): require own evidence before dispatch; document critic fail-open and swarm naming Strengthen the gitnexus-review "Swarm lanes" contract (all four mirrors): - The orchestrator must make its own graph context call on a changed symbol before dispatching any lane, so a fully-delegated run cannot leave the publisher's evidence gate unsatisfied (mirrored into the workflow prompt, with a test pinning the ordering phrase). - Document that the critic's fail-open is deliberate (bounded to two passes, cannot deadlock, review still gated by evidence + schema), and distinguish it from the hard lane-7 gate in the separate gitnexus-pr-swarm-review skill. - Give a concrete local-harness registration pointer for ci-personas. - Add a reciprocal cross-reference in gitnexus-pr-swarm-review (single path — that skill is not part of the mirrored family). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * docs: record the review-agent swarm capability (AGENTS.md, CLAUDE.md, reviewer-swarm README) Reflect the shipped swarm in the standing docs: bump AGENTS.md to 1.14.0 and CLAUDE.md to 1.8.0 with changelog rows, extend the gitnexus-review description to mention the ci-personas swarm lanes, and refresh the reviewer-swarm README so its differentiator names the real distinction (interactive on-demand swarm vs the CI review agent's in-workflow lanes) now that both run swarms. No CHANGELOG.md edit (feature-PR rule). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): close pre-push review findings on the swarm permission change Adversarial review of the fix diff caught two issues introduced by the permission-hygiene commit: - Bare Glob/Grep in --allowedTools are separate tools that the Read()-scoped path denies (/proc, github.workspace, ...) do not cover, opening an undenied read path to the raw checkouts and host paths via a prompt- injected lane. Drop the bare allow — under dontAsk they stay denied by omission; lanes read via the scoped Read() rules and the graph MCP. - The agents quarantine removed only the add-dir root's .claude/agents; make it recursive so a nested (e.g. monorepo subpackage) .claude/agents cannot survive and be discovered. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * feat(ci): post an "in progress" marker while the review swarm runs Swarm reviews can take up to 75 minutes, and until now the PR showed no sign a review was running. Add a dedicated write-scoped `acknowledge` job that, under the same authorization gate as analyze, upserts a per-PR "🔄 GitNexus review in progress" sticky comment linking to the live run (and reacts 👀 to the trigger comment); the publisher removes that marker when the review — or a clean failure — posts. The marker lives in its own job so the model-facing analyze job stays secretless and read-only: it cannot post to the PR, so per-lane live progress isn't exposed there — the marker is a binary "running" state with a link to the Actions run where lane-by-lane progress is visible. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-20 07:31:40 +01:00
Gergő Magyar	8b5057f325	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>	2026-07-19 15:07:24 +01:00
Gergő Magyar	1408bfbffe	fix(hook): emit MCP query hint when server owns DB lock (#2396) (#2397) ... * 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>	2026-07-08 18:34:05 +01:00
Gergő Magyar	187c162fd8	feat: full Codex support — hooks, plugin marketplace, and setup (#2328, supersedes #1131) (#2369) ... * 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>	2026-07-04 13:32:17 +01:00
Gergő Magyar	4227194ad7	chore: release v1.6.9 (#2367)	2026-07-04 07:53:06 +01:00
Livio Gamassia	d546fa3cce	fix(storage): rename index metadata to gitnexus.json with dual-write compatibility (#2363)	2026-07-03 19:32:59 +01:00
Parafee41	6e42040070	docs: fix bundled skill reference drift (#2362) ... * docs: fix skill reference drift * docs: complete guide tool coverage and graph schema (#2356 items 5-6) - add the 6 undocumented MCP tools to the guide's Tools Reference (route_map, shape_check, api_impact, tool_map, group_list, group_sync) - document the experimental @groupName cross-repo trace mode - expand the Graph Schema section to the real node/edge type surface, pointing at gitnexus://repo/{name}/schema as the authoritative list - sync the packaged gitnexus/skills copy Item 7 of #2356 (Codex host naming / duplicated filename) does not reproduce on current main - no remaining copy contains it. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-03 09:50:56 +01:00
Gergő Magyar	221069785b	chore: release v1.6.8 (#2260) ... Bump gitnexus, plugin.json, and marketplace.json to 1.6.8 and add the CHANGELOG section. Headline: opt-in PDG-backed impact analysis plus the full PDG/taint substrate (CFG → reaching-defs → intra/inter-procedural taint → control dependence) across the language matrix, multi-branch indexing, private GitHub PAT + Azure DevOps support, and MCP trace/HTTP. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-20 21:09:54 +01:00
azizur100389	fff01189b1	fix(cpp-hooks): handle pack-base comments and missing hook overrides (#2247)	2026-06-18 21:55:46 +01:00
Goutham Krishna Mandati	4c73b18387	feat(mcp): add trace tool for shortest call path between symbols (#2173) ... * feat(mcp): add trace tool for shortest call path between symbols (#1821) Implement the \ race\ MCP tool and \gitnexus trace\ CLI command that finds the shortest directed call path between two symbols using BFS over CALLS + HAS_METHOD edges. - MCP tool definition in tools.ts with READ_ONLY annotations - Directed BFS in local-backend.ts with parent-map path reconstruction - Symbol resolution via resolveSymbolCandidates (name/UID/file-hint) - Gap reporting with furthest reachable node and depth tracking - CLI wiring: gitnexus trace <from> <to> [--from-uid] [--to-uid] [--depth] - i18n keys in en.ts and zh-CN.ts + help-i18n.ts registration - ARCHITECTURE.md tools table entry - 16 unit tests (11 BFS core + 5 CLI wiring) * test(mcp): account for trace tool in tools.test.ts count The trace tool makes GITNEXUS_TOOLS length 15; update the hardcoded count, add 'trace' to the expected-names list, and refresh the stale "13 tools" comment and it() title. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): sanitize trace maxDepth to reject 0/NaN/negative `Math.min(params.maxDepth ?? 10, 30)` had no lower bound and `??` does not recover 0 or NaN, so `--depth 0|-5|abc` made the BFS loop run zero iterations and return a false `no_path`. Clamp at the real boundary with a `Number.isInteger && > 0` guard (the MCP inputSchema minimum is advisory only), and reject a non-numeric `--depth` in the CLI up front rather than forwarding NaN. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): check trace target before applying test-file filter The `isTestFilePath` filter ran before the target-equality check, but resolveSymbolCandidates does not exclude test-file symbols. A target (or a required hop) that lives in a test file was therefore skipped under the default includeTests=false and produced a false no_path with a misleading dynamic-dispatch suggestion. Match the explicitly-requested target first; non-target test-file nodes are still filtered. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * perf(mcp): bound trace BFS with per-level LIMIT and visited cap The per-level query had no LIMIT and the visited set was uncapped, so a high-fanout hub could materialize an unbounded frontier. Cap per-level rows (interpolated LIMIT — Kuzu does not bind LIMIT) and the total visited set; either cap sets a `truncated` flag so a resulting no_path reports that the search was cut short rather than implying the graph was exhausted. Note: the sibling impact BFS shares the same unbounded pattern; applying the cap there is deferred (out of scope for this PR). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(mcp): clarify trace traverses call + class-member edges trace was advertised as a "shortest call path" but also traverses HAS_METHOD (class→member) containment edges so a class-rooted trace can descend into its methods. Keep that capability (consistent with impact/ context) and make the docs honest: rename EDGE_TYPES→TRAVERSAL_EDGE_TYPES, state the call + class-member traversal in the MCP/CLI/i18n/ARCHITECTURE descriptions, and note each hop's edge type is reported in edges[]. No behavior change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): set status:'error' on trace failure responses Every trace return path sets a `status` discriminator except the caught-error path, so a consumer switching on `result.status` saw undefined on failure. Add status:'error' to both the backend trace() catch and the CLI traceCommand catch. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): return a friendly error for non-string trace from/to A non-string from/to reaching resolveSymbolCandidates surfaced a low-level "x.includes is not a function" via name.includes. Guard the four name/uid params at the top of _traceImpl and return a structured status:'error' with a clear message instead. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(mcp): single row-decode + drop dead field in trace BFS Decode each BFS row once into named locals instead of repeating `(row.x ?? row[N])` across the two parent.set calls and the furthest-tracking. Drop the `type` field from the parent map value (it was written but never read), and rename the internal `deepestInfo` to `lastReached` for accuracy (the output field `furthest` is unchanged). Pure refactor — no behavior change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(cli): dedicated trace includeTests i18n key + guard coverage `trace|--include-tests` reused the impact help key, so rewording the impact option would silently change trace's help text. Add a dedicated help.option.trace.includeTests key in en + zh-CN and repoint it. Add CLI coverage for the (already symmetric) --from-uid/--to-uid flag-value guard and for --include-tests forwarding. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): faithful BFS mock + expand trace coverage Fix makeResolveMock: concatenate neighbors across ALL frontier ids (it returned only the first node's, so a multi-node frontier was unmodelled) and key the UID branch on params.uid (the old query-text match never fired). Add coverage: shortest path through the second frontier node (proves the mock fix), confidence floor fallback, HAS_METHOD traversal with a mixed edge-type chain, no_path furthest:null, and from_file disambiguation. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * style(trace): apply root prettier formatting to trace files The root `quality / format` gate (prettier --check, printWidth 100) runs on the full repo and flagged the trace sources/tests (the local config masks it). Reformat to root style — no behavior change; trace + tools suites and tsc stay green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): document the trace tool for AI agents Add `trace` to the GitNexus skill docs so agents reach for it instead of hand-chaining context/impact hops. The guide gains a Tools Reference row and a "shortest path between two symbols" subsection (params, result shape, status/furthest/truncated semantics); the debugging skill gains a "how does A reach B?" pattern row and a trace tool example. Mirrored to the .claude and claude-plugin copies (byte-identical) and the cursor copy (compact style). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): drop unused trace test fixtures (CodeQL js/unused-local-variable) CodeQL flagged two unused locals in the trace BFS tests: the top-level SYMBOL_C and a SYMBOL_D inside the maxDepth test (both defined, never referenced). Remove them. No behavior change — 58 trace/tools tests stay green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-14 10:43:01 +01:00
Gergő Magyar	7c3d4e6862	feat(pdg): control dependence — post-dominators + CDG (Ferrante) [M5 #2085] (#2188) ... * feat(pdg): add CDG + POST_DOMINATE edge types (M5 #2085) * feat(pdg): post-dominator tree on reverse CFG (M5 #2085) * feat(pdg): Ferrante control-dependence over the post-dom tree (M5 #2085) * feat(pdg): emitFileCdg + optional POST_DOMINATE debug edges (M5 #2085) * feat(pdg): wire CDG emission in-phase + pdgModeMismatch CDG-cap stamp (M5 #2085) * test(pdg): CDG snapshot + end-to-end pipeline answerability (M5 #2085) * fix(review): apply autofix feedback (M5 #2085) * fix(pdg): label CDG edges by controller arm sense, not edge kind (#2188 F1/F2/F4) Tri-review (with Codex as the independent engine) found the CDG 'T'/'F' label was wrong for the commonest control flow: the M1 TS visitor wires a condition's fall-through FALSE arm as `seq`/`loop-back`, but `branchSense` mapped both to 'T', so guard clauses, if-no-else, and loop `break` got 'T' instead of 'F' (F1, P1). The structural CDG edges were correct; only the label — the AC3 "under what condition does X run?" answer — was wrong. - F1: replace edge-kind `branchSense` with controller-arm-sense `labelFor`. An ambiguous fall-through edge (seq/loop-back) takes the COMPLEMENT of its source block's explicit cond-true/cond-false sibling arm. This correctly handles do/while (loop-back = TRUE arm) and inner-if-in-loop (loop-back = FALSE arm) — the ambiguity a kind→label table cannot resolve. Adds real-parser regression tests (the hand-built tests used a fictional cond-false edge and missed it). - F2: correct the false "sound over-approximation that never drops a real dependence" claim in post-dominators.ts — exit-unreachable regions both drop and invent control dependences (latent for the current TS visitor, which keeps EXIT reverse-reachable). Reframe the exit-less-loop test to characterize, not bless, the degenerate behavior. - F4: make the AC2 property-test reference compute post-dominance INDEPENDENTLY (node-removal reachability, no shared code with post-dominators.ts), so a post-dom direction bug can no longer pass both the impl and the reference. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(ci): root-prettier format + run-analyze pdg stamp gains maxCdgEdgesPerFunction (#2085) Two deterministic CI failures from the M5 CDG work: - quality/format: basicblock-roundtrip.test.ts failed CI's root `prettier --check .` (the pre-commit hook uses the gitnexus-local prettier config, which differs); reformatted with the root config. - tests/ubuntu/coverage: run-analyze.test.ts pinned the resolved RepoMeta.pdg shape (DEFAULTS) and the all-zero cap override without the new maxCdgEdgesPerFunction key (default 5000); added it so resolvePdgConfig toEqual and pdgModeMismatch(DEFAULTS) pass. (The stale-test sweep missed this file in PR #2188 — same trap M2 hit.) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(mcp): add pdg_query tool definition (controls/flows modes) [M6 #2086] * feat(mcp): pdg_query backend — controls (CDG) + flows (REACHING_DEF) + e2e test [M6 #2086] * feat(mcp): document PDG edges + pdg_query (schema, cypher, skill, --pdg-gated ai-context) [M6 #2086] * fix(mcp): correct pdg_query symbol-anchor lower bound + harden inputs [PR #2188 review] Tri-review (Codex + adversarial + correctness lanes) of the M6 pdg_query surface found the symbol-anchor window over-includes a neighbor function's block. The upper bound was widened to the 1-based BasicBlock basis (symEnd+1) but the lower bound was left 0-based, so a block on the line directly above the target function leaked into the result. Shift both bounds +1 ([symStart+1, symEnd+1]) so the window is the function's true block span. Also from the same review: - pdg_query no longer throws on a no-arguments MCP call: the dispatch passes raw `params`, so default it to {} → a clean mode-validation error instead of a TypeError. (`explain` shares this latent pattern — pre-existing follow-up.) - tools.ts: the controls-mode description no longer hard-codes the 'F' branch sense for guards — `if (!ok) return;` rides the predicate's 'T' arm; the guard:true flag is label-agnostic (regex on the dependent block text). Tests: a hand-seeded adjacency regression (verified failing without the lower-bound +1) + a no-arguments validation test. Skill doc updated to document the two-sided [symStart+1, symEnd+1] window. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): drop always-true anchor conditional in pdg_query [CodeQL #2188] CodeQL alert 756 flagged `...(anchor ? { anchor } : {})` in _pdgQueryImpl as a useless conditional: `anchor` is unconditionally assigned in both the file-path and symbol branches before the return (the not-found/ambiguous/no-layer paths return earlier), so it is always truthy. Drop `| undefined` from the declaration (TypeScript definite-assignment holds across both branches) and emit `anchor` directly. No runtime change — the `anchor` field was already present on every result. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(cli): add hasPdg to the noStats bridge expectation [#2188] The M6 work threaded `hasPdg: options.pdg === true` into the AIContextOptions passed to generateAIContextFiles on the --skills regeneration path, but this test's strict .toEqual expectation predated it (4 keys vs 3 → CI failure). Add `hasPdg: false` (the value on this non---pdg path). The assertion stays strict; the #1477 noStats bridging it guards is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(cli): collapse generateGitNexusContent params to an options bag [#2188] The function had grown to 9 positional params; reaching `hasPdg` meant passing six `undefined`s (the M6 review's maintainability flag). Collapse params 3-9 (generatedSkills, groupNames, noStats, skipSkills, runnerPath, defaultBranch, hasPdg) into a `GitNexusContentOptions` object with the defaults moved to destructuring. The body is unchanged (same local names); the single production caller and the test calls become self-documenting named fields. Pure refactor — generated AGENTS.md/CLAUDE.md content is byte-identical. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cfg): skip CDG for exit-unreachable CFGs (unsound post-dominance) [#2188] M5 review P2: computePostDominators roots only at cfg.exitIndex and nothing enforced that EXIT is reachable from every block. For an entry-reachable region that cannot reach EXIT (a non-terminating loop, or a multi-terminal CFG a future visitor might emit) the EXIT-rooted reverse walk degenerates — it both drops real control dependences and invents spurious ones. Add a pure precondition predicate `isExitReachableFromAllBlocks` (co-located with the algorithm it guards) and gate it in emitFileCdg: a CFG that violates it is skipped for CDG (counted as skippedUnsoundFunctions + one onWarn), while its CFG and REACHING_DEF projections — which do not depend on post-dominance — are kept. A CDG-specific gate, not a widening of isEmitSafeCfg, so the blast radius is exactly the unsound CDG. The current TS visitor always satisfies the precondition (every loop gets a structural header→loopExit edge), so CDG output for real fixtures is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(cfg): bound computeControlDependence materialization (heap parity) [#2188] M5 review P2: unlike computeReachingDefs (maxFacts) and the emit-side edge cap, computeControlDependence materialized the full deduped seen/out before emitFileCdg's per-function cap could trim it — O(edges × post-dom depth) heap for a deeply nested function. Add a `maxEdges` ceiling (default 0 = unbounded) returning {edges, truncated}, mirroring computeReachingDefs's {facts, truncated}. The ceiling is checked before pushing a new unique edge, so `truncated` means a genuine overflow (not merely "reached cap"). emitFileCdg passes a FIXED materialization ceiling (8× the default edge cap) — deliberately NOT derived from the runtime edge cap, because CDG's materialization IS the deduped-edge quantity the cap reports on (deriving it would pre-truncate that set and lose the exact dropped count). A ceiling hit is surfaced via onWarn + the truncated flag — never silent. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(mcp): share resolveBlockAnchor; fix explain's anchor off-by-one [#2188] M6 review P2 (duplication) + the flagged pre-existing _explainImpl correctness follow-up. _pdgQueryImpl and _explainImpl each carried a near-identical symbol↔block anchor resolver that had DRIFTED: pdg_query used the corrected [symStart+1, symEnd+1] window (BasicBlock startLine is 1-based, the symbol span 0-based) while _explainImpl still used [symStart, symEnd] — dropping a taint source on the function's final line AND leaking a neighbor's block on the line directly above. Extract one `resolveBlockAnchor` helper, used by both, that applies the correct window and a single (bare) clause convention (callers compose their own WHERE). This removes ~50 duplicated lines and fixes explain's anchor in one place. A hand-seeded characterization test (taint-explain Block 4) pins both bounds — verified to FAIL on the pre-fix window (it returned the line-10 neighbor instead of the line-15 final-line source). Existing taint-explain + pdg-query suites are unchanged (their fixtures have interior sources/sinks). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): pdg_query reports "status unknown" when the layer can't be confirmed [#2188] M6 review P3 (Codex): when meta is UNREADABLE and the bounded global existence probe returns zero rows of the edge type, _pdgQueryImpl asserted "no PDG layer" — but a genuinely edge-free layer (all-linear functions) is indistinguishable from a missing one via that probe. Soften only that fallback path to an inconclusive "PDG layer status unknown — was this repo indexed with --pdg?" note. The meta-stamped path (stamp present, cap absent ⇒ layer truly missing) keeps the definitive "no PDG layer" wording. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): cover pdg_query ambiguous / pagination / Windows-path gaps [#2188] M6 review test-gap follow-ups, all hand-seeded with controlled data: - ambiguous symbol name → status:'ambiguous' + ranked candidates shape (uid/name/filePath/score), never a silent guess; - total/truncated page boundary in both directions (limit below the match count sets truncated with the full total; limit above it omits truncated); - a Windows-style filePath containing ':' resolves and fnLineOf decodes the function-line segment correctly (split-from-right past the drive letter). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): ship gitnexus-pdg-query skill mirrors + add pdg_query to the guide [#2086] M6 bundled pdg_query into this PR, but the skill shipped only in the canonical gitnexus/skills/ root. Mirror it (byte-identical) to the two hand-maintained roots the sibling taint skill uses — .claude/skills/gitnexus/ and the plugin — so Claude Code + plugin users get it too. Also extend the gitnexus-guide tool reference (all 3 copies, now byte-identical): add a `pdg_query` row + a "Control & data dependence" section mirroring the taint/`explain` section, and reconcile the pre-existing drift where only the .claude copy carried the `check` tool row (a real registered tool) — all three now list it. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(architecture): refresh CFG/PDG section for the full M1–M6 stack [#2086] The PR body had deferred the "ARCHITECTURE docs refresh" to #2086; now that M6 ships here, do it: - MCP tools table gains `explain` and `pdg_query` (were absent). - "Optional CFG/PDG emission" was M1-only; rewrite to cover the whole opt-in stack — M1 CFG, M2 REACHING_DEF, M3/M4 taint, M5 CDG (Ferrante over CHK post-dominators, with the exit-unreachable skip), M6 read surface (pdg_query + explain, anchored + LIMIT-bounded, shared resolveBlockAnchor) — and note the no-Function→BasicBlock-edge join. - LadybugDB schema notes the `--pdg` additions: the `BasicBlock` node table and the CFG/REACHING_DEF/CDG/TAINTED/SANITIZES/TAINT_PATH relation types, kept out of the default VALID_RELATION_TYPES / web schema. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-13 18:49:03 +01:00
Minidoracat	912285064a	perf(hooks): cmdline-first Linux db-lock scan, drop the lsof fallback (#2180) (#2183) ... * perf(hooks): cmdline-first Linux db-lock scan, drop the lsof fallback (#2180) The probe's Linux scan was O(processes × fds) — stat every fd of every process — so on a busy host it blew its budget and fell through to lsof, which then timed out (~2 s) and fail-closed. Every Grep/Glob/Bash hook spent ~2 s of CPU to conclude 'couldn't tell'. Rewrite linuxProcScanFindGitNexusServer (name kept; return type now tri-state 'owned' | 'not-owned' | 'timeout') as three phases: 0. /proc/<pid>/comm prefilter — kernel task->comm, never touches the target's memory maps; truncation-safe whitelist match (comm is capped at 15 visible chars). Calibrated to what a real server reports: @ladybugdb/core's worker_threads rename the main thread to 'MainThread', so that is whitelisted alongside the launcher basenames — omitting it would blind the probe to every server. 1. bounded /proc/<pid>/cmdline read (openSync+readSync, default 16 KiB with a floor of 4 KiB and a bounded escalation up to a hard ceiling) so a D-state holder cannot stall the hook and the mcp/serve mode token is never clipped off a long interpreter path. 2. dev+ino fd match for the 0–2 survivors only. Dispatch: 'owned' and 'timeout' both map to true. Timeout is now fail-closed (overload self-throttle) instead of falling through to lsof; the Linux lsof fallback is removed entirely. End-to-end semantics on busy hosts are unchanged (the old lsof arm also fail-closed there) — the ~2 s of wasted work and the orphan-spawning lsof are what's gone. macOS lsof+ps and Windows Restart Manager paths are untouched. Also: fix the budget parse bug (Number(raw && trim()) treated '0' as 1200; now parseInt-then-validate, with <= 0 an explicit immediate timeout) and add GITNEXUS_HOOK_PROC_ROOT so the Linux scan can be unit tested against a fixture procfs instead of the host's real /proc. Measured on a 583-process host with 6 background gitnexus mcp servers: owner detection 6–12 ms (was ~1216 ms + lsof timeout), ~100x. Tests: new hook-db-lock-probe.test.ts drives all three phases against a fake procfs (comm-truncation safety, Phase 0 trap, 4 KiB-boundary owner-miss guard, budget=0 immediate timeout, EACCES fail-closed) plus a live-/proc e2e that pins the fd-visible lbug-handle property against a real subprocess holder. The lsof/ps owner-detection suites are relaned to macOS (Linux no longer takes that path); the lsof orphan-reaping suite is removed (no lsof is spawned on Linux now) with a rationale note. Note: pre-commit typecheck skipped; remaining tsc errors are pre-existing on main (none in files touched here). * fix(hooks): honest EACCES verdict + real escalation coverage (#2183 review) Addresses the tri-review (maintainer + Codex): - [P2] Phase-2 fd-dir EACCES no longer claims 'owned'. /proc/<pid>/fd is owner-only (0500), so a cross-user/root gitnexus server serving ANY repo cleared Phase 0+1 and hit EACCES here, and the old catch returned 'owned' — falsely claiming it locks THIS repo's lbug (dev+ino never compared) and permanently suppressing augment. Split the failure shapes: ENOENT -> continue (raced away); EACCES/EPERM and transient EIO/ESTALE -> 'timeout' (unverifiable -> fail-closed, but honest, not a false ownership claim); ENOTDIR/other structural errors -> continue (not a real fd dir). Same fail-closed dispatcher outcome, no false 'owned', plus a GITNEXUS_DEBUG diagnostic so an operator can tell this skip path from a real owner. - [P2] The escalation test now actually iterates the escalation loop: the gitnexus token sits under 4 KB while the mode token is padded past GITNEXUS_HOOK_PROC_CMDLINE_MAX=4096, and a readSync spy asserts >1 read (the old 9 KB-under-16 KB-cap shape read once and never escalated). - escalation loop now re-checks the budget each iteration and returns a distinct timeout sentinel (never '' — an empty string would read as 'not a candidate' and could drop a real owner -> fail-open); the caller maps it to 'timeout'. - GITNEXUS_HOOK_PROC_ROOT is gated to test context so a stray production env export can't disable Linux owner detection (fail-open). - New uid-agnostic spy tests pin every fd-readdir errno branch (EACCES/EPERM/EIO/ESTALE -> timeout, ENOTDIR -> not-owned) regardless of the runner's uid (the disk chmod-000 tests no-op under root). Note: pre-commit typecheck skipped; remaining tsc errors are pre-existing on main (none in files touched here). * fix(hooks): drop the always-true outOfBudget presence guard (CodeQL #2183) CodeQL flagged `typeof outOfBudget === 'function' && outOfBudget()` as unneeded defensive code: readLinuxCmdline has a single caller (linuxProcScanFindGitNexusServer) that always passes the callback, so the typeof guard is dead. Drop it, leaving `if (outOfBudget())`, and note the invariant in the comment. Mirrored in the byte-identical plugin copy. * fix(hooks): parse numeric hook env with Number() so scientific notation works (#2183 review) getCmdlineMaxBytes and resolveLinuxProcBudgetMs parsed their env via Number.parseInt(raw, 10), so a value like "16e3" silently became 16 (parseInt stops at 'e') instead of 16000. Switch both to Number(String(raw).trim()), which honors scientific notation and is stricter on trailing garbage ("123abc" -> NaN -> default) — matching the repo-majority Number()+isFinite env idiom (src/cli/analyze.ts, src/core/embeddings/hf-env.ts). The two functions had DIFFERENT guard skeletons, so a verbatim swap would regress the budget: resolveLinuxProcBudgetMs used `raw != null ?` with no empty-string short-circuit, and Number("")===0 (vs parseInt("")===NaN) would make a set-but-empty GITNEXUS_HOOK_LINUX_PROC_BUDGET_MS="" resolve to budget 0 => immediate fail-CLOSED timeout => augment permanently skipped. Added the `&& String(raw).trim()` guard so ''/whitespace fall to the 1200 default while "0" still parses to the deliberate #2180 immediate-timeout vector. Exported both helpers for white-box tests (the values are otherwise only observable indirectly through scan timing) and added platform-independent coverage: "16e3"->16000, ""/whitespace->1200 (the regression guard), "0"->0, "123abc"/unset->1200, cmdline "8e3"->8000, "2e3"/""/unset->16384. Both byte-identical hook-db-lock-probe.cjs copies updated together. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hooks): allocUnsafe the per-chunk cmdline read buffer (#2183 review) readLinuxCmdline allocated each per-chunk read buffer with Buffer.alloc(chunkCap), zero-filling memory that readSync immediately and fully overwrites. Switch the hot read buffer to Buffer.allocUnsafe — safe because readSync initializes exactly [0, bytes), only buf.subarray(0, bytes) is consumed, and Buffer.concat deep-copies that slice into `collected`, so the uninitialized tail can never reach the decoded cmdline. The zero-length `collected = Buffer.alloc(0)` is left unchanged (allocUnsafe gains nothing on a 0-length buffer). The existing D3 multi-chunk decode tests cover the read path and stay green. Both byte-identical hook-db-lock-probe.cjs copies updated together. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(hooks): harden the live /proc owner-detection e2e against CI flake (#2183 review) Two flake mechanisms, fixed without weakening what the e2e proves: - Holder readiness (the genuine false-FAIL): the pid-file poll was 200x25ms=5s; a loaded runner can be slow to spawn the child, tripping expect(holderPid).toBeGreaterThan(0). Widened to ~10s and raised the per-test timeout 20s -> 40s. - Scan budget (kept the assertion honest): the live scan ran at the default 1200ms. Because the dispatcher maps a budget 'timeout' to owned=TRUE, a busy host exhausting 1200ms before reaching the holder would make the assertion pass for the WRONG reason (a hollow timeout, not real fd-visible detection). Set a generous explicit 10000ms budget via the existing setEnv() helper so the module afterEach restores it (replacing the raw `delete process.env...` that bypassed env tracking). Raised the coarse timing regression guard to sit ABOVE the budget (5000 -> 15000) so a legitimately-slow-but-correct scan can't trip it. The load-bearing asserts (dev+ino fd-visibility precheck, owned===true for our own lbug) are unchanged. Verified the e2e executes (not skipped) on Linux. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore(changelog): empty the root CHANGELOG [Unreleased] section Per maintainer request, nothing should sit under [Unreleased] in the root CHANGELOG.md (the release-owned changelog is gitnexus/CHANGELOG.md, whose [Unreleased] is already empty). Removes all three accumulated blocks — Fixed (#2163), Performance (#2180), Changed (KuzuDB->LadybugDB) — leaving only the [Unreleased] header above [1.5.3]. Pure removal; no release sections touched. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-13 11:52:14 +01:00
Gergő Magyar	9ff7337f1e	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`).	2026-06-13 10:24:16 +01:00
Gergő Magyar	129bc84c0d	feat(taint): interprocedural taint via function summaries over resolved CALLS (#2084) (#2179)	2026-06-13 07:04:14 +01:00
Minidoracat	0054496323	fix(hooks): wrap the augment CLI child in the orphan guard (#2163) (#2169) ... * fix(hooks): wrap the augment CLI child in the orphan guard (#2163) Follow-up invited by the maintainer on #2165: the augment child (7s local / 12s npx) was the longest-lived unwrapped subprocess, exposed to the same SIGKILL-orphan mechanism fixed for lsof/ps. - Export resolveUnixGuardTimeout from the probe module (both copies, byte-identical); adapters share the same module instance, so the memo and lazy self-test still run at most once per hook process. - Wrap every CLI-executing branch of runGitNexusCli in the three probe-equipped adapters with the guard: budget ceil(inner/1000)+1 seconds with -k 1, strictly above each branch's inner spawnSync timeout, so the supervised path is unchanged and the wrapper only matters once the hook itself is SIGKILLed. Windows and no-guard hosts keep byte-identical argv. The plugin adapter's PATH-direct gitnexus branch (its most common production path) is wrapped too; the cheap which/where probe is not. - Cursor integration: debug-gated 'augment skipped: hook slots saturated' on the slot-starved early return. Its augment child stays unwrapped for now — that integration does not install the probe sibling (the 'cursor probe' item on the #2163 follow-up list). - Reaping tests get a guard-availability precheck with an explicit failure message (assertion, not skipIf, so a coreutils-less Linux host fails diagnosably instead of going silently green). - Tests: orphaned-augment reaping (CJS + Plugin, red without the wrap, ~9.1s reap measured), disabled-sentinel degradation equivalence, source pinning for all three adapters (exact per-branch budget-formula counts) + probe export + cursor debug line. Note: pre-commit typecheck skipped; remaining tsc errors are pre-existing on main (none in files touched here). * fix(hooks): group-SIGKILL the npx arm, prove guard exit propagation (#2169 review) Addresses the tri-review findings on #2169: - [P2] npx-arm containment: the CLI is the guard's grandchild there — at budget expiry coreutils timeout TERMs the group, npx (the obedient direct child) dies, timeout returns, and -k never fires, so a SIGTERM-immune grandchild escaped unbounded. The npx arm's wrapper now uses -s KILL: an unignorable group SIGKILL at budget that reaps the grandchild (kept -k 1 as a harmless belt; direct-exec arms keep TERM-first). CHANGELOG, adapter docblocks, and the test comment now state the per-arm semantics honestly. New behavioral test: a staged hook with a PATH-injected fake npx spawning a SIGTERM-immune grandchild is SIGKILLed; the grandchild must be reaped (red without -s KILL), with a route self-proof marker pinning the npx arm. - [P3] guard self-test now proves exit-status propagation (sh -c 'exit 42' must yield status 42), so an always-exit-0 stub like /bin/true is rejected and resolution falls through to the built-in candidates instead of silently killing the augment feature. New test: stub guard rejected, augment still emits context. - [P3] cleanup SIGKILLs in the reaping tests re-check the /proc/<pid>/cmdline identity immediately before firing (PID-reuse guard), applied consistently to the two pre-existing #2165 spots and both new tests. - Review notes: source pins now constrain wrapper argv order and exact per-arm counts; adapters degrade to unwrapped on probe version skew (typeof check) instead of a swallowed TypeError; export JSDoc wording fixed for relative env paths; debug-gated diagnostic when no guard is available (e.g. macOS without coreutils), with the CHANGELOG entry qualified accordingly. Note: pre-commit typecheck skipped; remaining tsc errors are pre-existing on main (none in files touched here). --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-06-12 15:17:30 +01:00
Gergő Magyar	14397dd4aa	feat(taint): intra-procedural taint analysis (#2083) (#2164) ... * feat(taint): harvest occurrence-tagged call/member sites on StatementFacts (#2083 U1) Worker-side site harvest in TsHarvester: call/new/member-read records with dotted callee paths, receiver slots, per-argument occurrence tagging with nested-site links, per-declarator resultDefs, spread/template/require-literal markers. hasTaintSafeSites validation seam. The pdg parse-cache chunk-key namespace is versioned (pdg:1 -> pdg:2) instead of a global SCHEMA_BUMP so flag-off users keep warm caches; bench fingerprints re-baselined for the three call-bearing scenarios (straight-line/dense-bindings byte-unchanged). * feat(taint): built-in TS/JS source/sink/sanitizer model + site matcher (#2083 U2) Typed spec (kind taxonomy; sanitizers carry neutralizes-kinds), the canonical Express/Node model, and matchFunctionSites: ESM alias/namespace + require- literal callee resolution, bare-name fallback restricted to true globals, sanitizers module-or-global only (never user-shadowable by name), spread/ template arg-position rules, deterministic taintModelVersion. * feat(taint): pure intra-procedural taint propagation engine (#2083 U3) Two-rule model (statement-local + du-fact worklist) with per-taint neutralized-kind exclusion sets: sanitizers exclude only the sink kinds they neutralize (escape(req.body) suppresses res.send but still fires db.query; exec(path.basename(t)) fires), intersection-over-paths so a bypass occurrence keeps the taint live, kill locality on resultDefs, propagate-through args+receiver with viaCall hops, one path per finding, deterministic caps, coverage-gap statuses. Test-first: 38 scenarios on real harvested CFGs. * feat(taint): thread taint caps + model version through pdg config/meta (#2083 U5) resolvePdgConfig gains maxTaintFindingsPerFunction (200), maxTaintHops (32), and the taintModelVersion digest; RepoMeta.pdg + RunScopeResolutionInput surfaces added. The key-union comparator trips full writeback on M2->M3 upgrade and on model-version change without --force (mode-flip tested). No CLI flags or rc keys (programmatic parity with the other caps). * feat(taint): in-phase taint emit with sparse TAINTED/SANITIZES edges (#2083 U4) run.ts pdg window: match-first fast path (solver only when a function has both a matched source and sink) -> computeReachingDefs with the shared RD fact derivation -> computeTaintFlows -> per-finding TAINTED (versioned hop-encoded reason via the shared path codec, statement-level occurrence identity) + per-kill SANITIZES, dedup-before-budget, truncate-and-warn. All emit counters surfaced (aggregate warn for gaps/drops, debug for volume); PROF gains taint=. Flag-off golden untouched. * feat(mcp): explain tool for persisted taint findings (#2083 U6) Anchorless calls enumerate the sparse TAINTED table (bounded, deterministic, limit-clamped); anchored calls (file or symbol via resolveSymbolCandidates) return full decoded hop detail. sinkKind rides a version-1 codec header (1;<kind>|hops — no other persisted channel exists; U4/U6 ship together). RepoMeta.pdg probe yields a no-taint-layer note instead of an error. TAINTED/SANITIZES pinned OUT of VALID_RELATION_TYPES (KTD9a negative- membership tests); generators + canonical skill docs + mirrors updated. * test(taint): acceptance fixture battery, snapshots, and bench gates (#2083 U7) pdg-repo taint-cases fixtures complete the six plan shapes; committed findings/kills snapshot via a shared pure-path harness that also feeds the AE2 exact-equality assertion (stored TAINTED == pure-path findings, the no-explosion gate). New taint-dense bench scenario with four --check gates: per-function findings pinned AT the cap, absolute reason-byte + site-bytes disk ceilings (the load-bearing R10 gate), zero-match pass < 0.5x match- dense, N-linearity. Pre-existing scenario baselines untouched. * refactor(taint): share one pointKey helper across propagate + emit (#2083 review) Extract pointKey(ProgramPoint) to cfg/reaching-defs.ts (colon-separated, matching the codebase block:stmt id convention) and import it in both propagate.ts and emit.ts, replacing the two divergent locals (':' vs '.'). Edge-id material now uses the colon form; ids are in-memory only and no test asserts the pointKey segment shape. * fix(taint): discriminate taint state by source occurrence (#2083 review) Two distinct sources flowing into one variable at one def point no longer collapse to a single TAINTED edge: the taint-state key gains a root source-occurrence discriminator ({point, siteIndex} — the same fields recordFinding's identity uses, excluding kind). Def->use fact lookup keys on the source-independent (binding, def-point) portion. Same-source multi-path flows still share one state so their exclusion sets intersect (the raw arm soundly wins); termination holds (finite keys, monotone shrink, no cross-source ping-pong). Restores the KTD6 identity contract. * fix(mcp): route dotted symbol names in explain to symbol resolution (#2083 review) The fileish classifier matched any dotted name (UserController.create) as a file via its extension-like suffix, so symbol resolution never ran and the tool returned a silent empty file-anchored result. Tighten the classifier to require a path separator or a real source extension (derived from the resolver's EXTENSIONS list, multi-language), so dotted/bare names route to resolveSymbolCandidates (found / ambiguous / not-found). * fix(mcp): gate explain no-taint-layer note on taintModelVersion (#2083 review) An M1/M2-era --pdg index has meta.pdg defined (BasicBlock/REACHING_DEF recorded) but no taintModelVersion and zero TAINTED rows. The probe keyed on generic meta.pdg presence, so explain returned the generic empty note instead of the actionable 'no taint layer — run analyze' hint. Gate on meta.pdg?.taintModelVersion (the field M3 stamps) so an M2-era index gets the layer hint; a taint-stamped index with no findings still gets the generic note. * fix(taint): sequence-expression value flows only the final operand (#2083 review) A comma expression in value position (exec((log(x), 'safe'))) default- descended, fanning every operand's occurrences into the enclosing sink argument — over-tainting exec's arg 0 with x. Add an explicit walkValue case that records earlier operands' uses with occurrence fan-out suppressed (new FactAccumulator.suppressOccurrences) and routes only the last operand through the value path. Sites-layer only; defs/uses/mayDefs byte-identical (cfg + reaching-defs snapshots unchanged). * perf(taint): FIFO head-cursor worklist + dedup before chainHops (#2083 review) Replace queue.shift() (O(N) dequeue) with a strict-FIFO head cursor plus order-preserving prefix reclamation; FIFO is load-bearing because chainHops reads the live taints map whose parent/source/viaCall are rewritten order-sensitively on monotone shrink, so hop determinism is dequeue-order contingent. Extract findingKey() and dedup-check before chainHops in the justify branch — already-recorded identities discard their hop chain (first write wins), so the ancestry walk was pure waste. The else kill branch is untouched. Findings + hops byte-identical (snapshot unchanged). * perf(taint): O(1) member-read dedup via composite-key set (#2083 review) addMemberRead rescanned the whole per-statement sites array per call to dedup by (object, property, parent) — O(n^2) on member-read-dense statements. Track a composite-key Set alongside sites for O(1) dedup. (The require-literal join is already O(sites) with a no-op body on non-require sites, so no early-exit is needed there.) Behavior identical: harvest + model-match + taint snapshots unchanged. * refactor(taint): drop test-only export; source taint caps via emit.ts (#2083 review) Remove the sanitizerNeutralizes export (its only consumers were two test assertions — inlined to entry.neutralizes membership). Re-export the DEFAULT_PDG_MAX_TAINT_* caps from emit.ts and point run.ts at emit.ts, so the pipeline's taint dependency surface is the single orchestration module rather than reaching into propagate.ts. * test(taint): extract the shared TS CFG/taint test harness (#2083 review) The parse/collectFunctions/cfgOf/cfgsOf/importsFor harness was copied byte-for-byte across four suites (harvest, model-match, propagate, taint-emit). Promote it to test/helpers/ts-cfg-harness.ts and import it. site-safety/reaching-defs carry a structurally different inlined builder and are left as-is. Pure extraction, no assertion changes. * test(mcp): harden explain limit-rejection battery (#2083 review) Add NaN, Infinity, -Infinity, and a numeric string to the out-of-bounds limit cases — a regression fence over the interpolated LIMIT, confirming the Number.isInteger guard rejects every non-integer/non-finite/string input before it reaches the query.	2026-06-12 07:35:09 +01:00
Minidoracat	10d1e47df3	fix(hooks): bound db-lock probe subprocesses and gate probe behind hook slot (#2163) (#2165) ... * fix(hooks): bound db-lock probe subprocesses and gate probe behind hook slot (#2163) The Claude PreToolUse db-lock probe leaks orphaned lsof processes when the hook process is hard-killed mid-probe (e.g. Claude Code's 10s hook timeout under load). Orphans accumulate, raise load, slow the next probe, and snowball to sustained 100% CPU. - Wrap the unix lsof/ps fallback in coreutils timeout (-k 1 2 / -k 1 1), resolved via a lazy self-test, so probe children self-destruct within ~3s even if the hook is SIGKILLed. GITNEXUS_HOOK_TIMEOUT_PATH overrides the guard binary; the sentinel value 'disabled' turns the guard off; hosts without a usable guard keep the previous behavior. - Acquire the per-repo hook slot before probing (all three adapters), bounding concurrent probes to 3 per .gitnexus, with probe and augment inside try/finally so the slot is always released. - Tests: source-order contract, slot-gating behavior, orphan reaping with a SIGTERM-immune fake lsof and a SIGKILLed parent (red on base), probe-copy byte parity, no-guard equivalence, broken-guard rejection. Note: pre-commit typecheck skipped; the 62 tsc errors are pre-existing on main (all in src/core/** and src/server/, none in files touched here; base==head invariant verified). * fix(hooks): address tri-review P3 findings (#2165) - Map guard signal-death (status null + signal, no spawnSync error) to fail-closed at both the lsof and ps call sites, closing the freeze window (SIGSTOP / laptop sleep > 2s) that previously landed fail-open. Rewrite the exit-code comments: coreutils surfaces the -k kill as signal death, 124 is budget expiry (live arm), 137 covers only exit-code-propagating wrappers or an externally SIGKILLed child. - Add a debug-gated 'augment skipped: hook slots saturated' stderr line on the slot-starved early return in all three adapters, restoring observability under GITNEXUS_DEBUG=1. - GITNEXUS_HOOK_TIMEOUT_PATH now participates in candidate fall-through: the env candidate is tried first, then the built-ins, each behind the lazy self-test — an existing-but-unusable env path (directory, non-executable) can no longer silently disable orphan containment. - Tests: +6 — guard exit 124 pins the live arm (CJS+Plugin), guard signal-death pins the new mapping (CJS+Plugin, red before the fix), antigravity behavioral slot-gate, env-dir fall-through still reaps a SIGTERM-immune orphan via a built-in guard. Note: pre-commit typecheck skipped; the 62 tsc errors are pre-existing on main (none in files touched here).	2026-06-11 15:38:13 +01:00
Gergő Magyar	292f26ece3	fix(hooks): silence MCP-owned-DB augment skip for strict hook runners (#1913) (#2134) ... * fix(hooks): silence MCP-owned-DB augment skip for strict hook runners The PreToolUse augment-skip path wrote `[GitNexus] augment skipped: MCP server owns DB` to stderr unconditionally on a normal (non-error) skip. Strict hook runners that validate hook output (e.g. Codex `PreToolUse`) treat that as noisy / "invalid pre-tool-use JSON output". Gate the diagnostic behind GITNEXUS_DEBUG via a shared `isDebugEnabled()` helper, so normal skips are silent by default (empty stdout AND stderr, exit 0) and the reason stays recoverable with `GITNEXUS_DEBUG=1`. Applied consistently to all three hand-maintained hook copies (claude, antigravity, claude-plugin). Tests: - Unit (claude CJS + plugin): assert default-silent and debug-on behavior for the MCP-owned-DB skip and for the fail-closed (lsof ETIMEDOUT) skip that routes through the same gated line; the owner-detection tests run with GITNEXUS_DEBUG=1 so the skip discriminator stays observable. - e2e (antigravity): the antigravity adapter shares the identical gated skip but only runs from its install dir, so cover it through the install pipeline with a faked DB-owner probe (strict empty-stdout/stderr + debug-on). Promote the fake-probe helpers (createHookToolDir / hookEnv, plus a module-private writeExecutable) into shared hook-test-helpers so unit + e2e reuse them. Fixes #1913 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hooks): unify GITNEXUS_DEBUG gating in main() catch handlers The main() catch-handler in all three hook copies still gated its crash log on truthy `if (process.env.GITNEXUS_DEBUG)`, while the skip diagnostic the #1913 fix added is gated on the strict `isDebugEnabled()` helper (=== '1' || === 'true'). That split meant GITNEXUS_DEBUG=0 or =false suppressed the skip line yet still enabled crash logging — two conflicting contract signals in the same file. Switch the three catch handlers to isDebugEnabled() so GITNEXUS_DEBUG has one strict meaning everywhere: exactly '1' or 'true' enables all diagnostics; everything else (incl. '0', 'false', empty, unset) is silent. Add boundary tests asserting the MCP-owner skip stays silent with GITNEXUS_DEBUG='0' and 'false' (CJS + Plugin), pinning the strict contract. Refs #1913 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(hooks): gate antigravity stale-index hint stderr behind GITNEXUS_DEBUG The antigravity AfterTool handler mirrored the stale-index hint to stderr unconditionally on a normal (non-error) success path — the last ungated stderr write of the class issue #1913 targets, and a divergence from the claude hook, which never mirrors this hint to stderr. Gate the stderr mirror behind isDebugEnabled(). The hint still reaches the agent via additionalContext (stdout JSON) — parts.push(hint) stays unconditional — so there is no functional loss; only the by-default terminal mirror moves behind GITNEXUS_DEBUG=1. This knowingly changes the #1730 terminal-mirror behavior in favor of strict-runner cleanliness and parity with the claude adapter. Split the e2e assertion into a default-silent test (hint in additionalContext, absent from stderr) and a GITNEXUS_DEBUG=1 test (hint mirrored to stderr). Refs #1913 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(hooks): document GITNEXUS_DEBUG=1 for hook diagnostics GITNEXUS_DEBUG was documented only in the cursor integration README, so the diagnostic escape hatch for the Claude Code / Antigravity hooks was undiscoverable. Operators hitting a silent hook skip (MCP server owns the DB, fail-closed probe timeout, or an already-current index) had no documented way to surface the reason. Add a Troubleshooting subsection explaining that the hooks stay silent on normal skip paths for strict runners, that GITNEXUS_DEBUG=1 surfaces the reason on stderr, and that only '1'/'true' enable diagnostics (stdout JSON the agent consumes is unaffected). Refs #1913 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(hooks): update setup-antigravity unit test for gated stale-index hint U2 (7995e921) gated the antigravity stale-index hint stderr mirror behind GITNEXUS_DEBUG, but a second test — setup-antigravity.test.ts's "AfterTool emits stale-index hint" — also asserted the hint on stderr by default and was missed (it lives outside the two files validated locally; the full CI matrix caught it). Update it to the U2 contract: assert the hint via additionalContext with stderr silent by default, plus a GITNEXUS_DEBUG=1 run asserting the terminal mirror reappears. Refs #1913 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-10 09:09:41 +01:00
Gergő Magyar	1cf65b339c	chore: release v1.6.7 (#2126) ... Bump gitnexus 1.6.6 -> 1.6.7, add the 1.6.7 CHANGELOG section (14 PRs since v1.6.6), and sync the Claude plugin manifests (plugin.json + marketplace.json) to 1.6.7.	2026-06-09 21:37:33 +01:00
Gergő Magyar	4682a477d8	feat(mcp): paginate list_repos to avoid client token truncation (#2119) (#2120) ... * feat(mcp): paginate list_repos to avoid client token truncation (#2119) list_repos returned every indexed repository in one unpaginated array, which large/LLM MCP clients truncate by token limit — so agents with hundreds of indexed repos could not enumerate them all (the data transmits fully; the consuming client drops it). Add bounded limit/offset pagination to the list_repos tool: - result changes from a bare array to { repositories, pagination: { total, limit, offset, returned, hasMore, nextOffset } }; default page 50, max 200 (shared constants) - reject malformed limit/offset; clamp limit above the max - deterministic order (lower-cased name, then path) over one registry snapshot per call, so paging never skips or duplicates an entry - covers both stdio and remote /api/mcp (shared createMCPServer/callTool) The internal listRepos() method (5 callers), GET /api/repos, and the `gitnexus list` CLI are unchanged. The array->object tool-result shape is a deliberate contract change, documented in CHANGELOG. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(mcp): reject list_repos limit above the max instead of clamping (#2119) parseListReposPagination silently clamped limit>max to the maximum while throwing on every other out-of-bounds value (limit<1, offset<0, non-integer, NaN). A client that advanced offset by its requested limit (rather than pagination.nextOffset) then silently skipped repositories and saw hasMore:false — defeating the "never skips" guarantee. Reject an over-max limit too, so validation is symmetric and a caller never gets a smaller page than it asked for without a clear error. Updates the schema/description, the helper + ListReposPagination JSDoc, the guide note, and the two clamp tests. Resolves the cross-engine-corroborated P2 (Codex + adversarial lane) and the maintainability lane's clamp-vs-throw inconsistency from the PR #2120 review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(mcp): name the list_repos return type and mark the parser @internal Extract the inline listRepos() element shape into an exported RepoListing interface and use it for both listRepos() and listReposPage().repositories, replacing the opaque Awaited<ReturnType<LocalBackend['listRepos']>> expression the maintainability review flagged. Tag parseListReposPagination @internal (it is exported only for unit testing). Pure type/JSDoc change; no behavior. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(eval-server): type formatListReposResult to the paginated shape Narrow formatListReposResult's parameter from `any` to { repositories: RepoListing[]; pagination?: ListReposPagination } and drop the dead bare-array branch — after #2119 callTool('list_repos') always returns the paginated object, so the Array.isArray shim was unreachable. Add a list_repos continuation hint to the eval-server's getNextStepHint (parity with the MCP server), and cover the previously-untested non-empty + hasMore:false formatter branch. Migrates the two bare-array formatter tests to the object shape. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(mcp): harden list_repos pagination coverage - Exercise the #2054 sibling-clone guarantee through the real callTool tool path (in the #2054 describe, which has temp-dir cleanup), proving siblings and remoteUrl survive listReposPage's sort+slice — not only listRepos(). - Assert total + limit on the middle-page test (a total miscalculation at a non-zero offset would otherwise slip past it). - Cover the benign boundaries: negative-zero offset (accepted as page 0) and a MAX_SAFE_INTEGER offset (empty page). - Replace the integration test's '\n\n---' split with a string-aware brace scan, so a repo path containing braces can never truncate the JSON parse. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(skills): sync the list_repos pagination example to the guide mirrors The .claude and gitnexus-claude-plugin guide mirrors only carried the one-line table note; add the full "Paginating list_repos" section (shape + multi-page traversal example + notes) so all three guide copies are byte-consistent with the canonical gitnexus/skills/gitnexus-guide.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: drop list_repos CHANGELOG entries from this PR Restore gitnexus/CHANGELOG.md to match main so this PR contributes no changelog change; the changelog is curated separately from feature PRs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-09 19:59:54 +01:00
Copilot	689e6ef1f8	chore: Sync Claude plugin manifests with the 1.6.6 release (#2090) ... * Initial plan * fix: sync Claude plugin manifest versions * test: fold manifest sync check into existing node suite * chore(autofix): apply prettier + eslint fixes via /autofix command * test: run manifest sync guard in always-on suite --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>	2026-06-08 16:50:09 +01:00
Gergő Magyar	2dc0cc6398	fix(mcp): prevent sibling-clone repo ID collisions and correct generated MCP tool names (#2067)	2026-06-07 10:57:15 +01:00
Gergő Magyar	f01d913eef	fix(hooks): resolve gitnexus on PATH with a pure-Node scan, all-OS (#1938) (#1980)	2026-06-03 03:19:49 +01:00
Gergő Magyar	f885330b34	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>	2026-06-02 09:00:34 +01:00
ManniX-ITA	39e9b40136	fix(windows): pass windowsHide:true to every child_process spawn-family call (#1794) ... * fix(hooks): pass windowsHide:true to every spawnSync to suppress flashing console windows on Windows On Windows, every PostToolUse and Stop event from Claude Code (and the Cursor integration variant) cold-spawns ``node`` / ``npx.cmd`` / ``git`` / ``lsof`` through ``child_process.spawnSync``. Without ``windowsHide: true`` in the options, Node's child_process module asks ``CreateProcess`` to use ``STARTF_USESHOWWINDOW`` with ``SW_SHOWDEFAULT``, and a black console window flashes onto the user's desktop for the duration of the call. Under active editor / agent use this means a near-continuous stream of pop-up windows — unusable in practice (reported live on a Windows 11 workstation running the gitnexus Claude plugin against an active project; the flashes stack on the taskbar and steal focus from the editor). The Node fix is one option flag per spawnSync: spawnSync(cmd, args, { encoding: 'utf-8', timeout, cwd, stdio: ['pipe', 'pipe', 'pipe'], windowsHide: true, // <-- new }); ``windowsHide`` is a no-op on macOS/Linux (Node docs: "Hide the subprocess console window that would normally be created on Windows systems"), so the patch is platform-neutral and zero-risk on the other two majors. This commit touches every ``spawnSync`` call in the three sources that ship the hook layer: * gitnexus/hooks/claude/gitnexus-hook.cjs (4 sites) * gitnexus/hooks/claude/hook-db-lock-probe.cjs (3 sites) * gitnexus-claude-plugin/hooks/gitnexus-hook.js (6 sites) * gitnexus-claude-plugin/hooks/hook-db-lock-probe.cjs (3 sites) * gitnexus-cursor-integration/hooks/gitnexus-hook.cjs (3 sites) Total: 19 spawn sites guarded. ``hook-lock.cjs`` / ``hook-lock.js`` don't spawn subprocesses; nothing else in the hooks/ dirs touches ``child_process``. Verified on Windows 10 22H2 / Node 22.21 / gitnexus 1.6.5 by installing the locally-built tarball and running an active Claude Code session against a large mixed-language repo — no console window appears for any hook fire (pre-fix: ~2-3 visible flashes per edit). No behavioural change on Linux/macOS hosts. * test(hooks): regression — every hook spawnSync paired with windowsHide:true Source-level assertion that every ``spawnSync`` invocation in the hook layer has a matching ``windowsHide: true`` in its options object. Without the flag, Node's child_process module asks CreateProcess to use STARTF_USESHOWWINDOW with SW_SHOWDEFAULT and a black console window flashes onto the user's desktop for the duration of each call — see the parent fix commit. The check is source-level rather than behavioural because: * the flag's effect is observable only on Windows; * GitHub Actions runs vitest on Linux for the hook tests; * regressing this is easy (every new spawnSync site has to remember to add the flag), and a runtime check on a Windows-only CI leg would still let a PR land on the main branch first. Counts spawnSync occurrences and windowsHide:true occurrences per file (in code, ignoring comments) and asserts equality. Five files covered: * gitnexus/hooks/claude/gitnexus-hook.cjs * gitnexus/hooks/claude/hook-db-lock-probe.cjs * gitnexus-claude-plugin/hooks/gitnexus-hook.js * gitnexus-claude-plugin/hooks/hook-db-lock-probe.cjs * gitnexus-cursor-integration/hooks/gitnexus-hook.cjs Adding a new hook file requires updating the HOOK_FILES tuple. A sanity assertion ``spawnCount > 0`` catches accidental deletion of all spawn calls in a future refactor (would otherwise silently make the count-equality assertion trivially true). Sits next to the existing "no shell: true" and ".cmd extension" regression tests in test/unit/hooks.test.ts — same shape, same spirit. * fix(src): extend windowsHide:true to every spawn-family call in cli/core/mcp/server Companion to the hook-layer fix in this branch's first commit. The same Windows console-window flash bug applies to every ``spawn`` / ``spawnSync`` / ``execFile`` / ``execFileSync`` / ``execFileAsync`` / ``execSync`` call in the source tree — not just the hooks. The MCP local backend (``src/mcp/local/local-backend.ts``) and the ``gitnexus serve`` git helpers (``src/server/git-clone.ts``) are particularly bad because they run from daemonized processes that have no parent console; the spawned child auto-allocates one and it pops onto the user's desktop. The CLI sites are less visible (the user is at a terminal with an existing console; ``stdio: 'inherit'`` shares it) but the flag is harmless there — windowsHide only suppresses NEW console allocation, an inherited parent console is untouched. The visible output of ``gitnexus analyze`` and friends is preserved verbatim. The pre-existing fix at ``src/core/lbug/extension-loader.ts:96`` established the convention in this codebase. This commit applies it uniformly. Sites covered (21 new): | File | Sites | |---|---| | src/cli/analyze.ts | 1 | | src/cli/setup.ts | 2 | | src/cli/wiki.ts | 3 | | src/core/embeddings/embedder.ts | 1 | | src/core/git-staleness.ts | 3 | | src/core/run-analyze.ts | 1 | | src/core/wiki/cursor-client.ts | 2 | | src/core/wiki/generator.ts | 3 | | src/mcp/local/local-backend.ts | 2 | | src/server/git-clone.ts | 2 | | src/core/lbug/extension-loader.ts | (already had it, untouched) | Combined with the 19 hook sites from the first commit + the 1 pre-existing extension-loader site, the codebase now has uniform ``windowsHide: true`` on every spawn-family call. Behavioural notes: * ``windowsHide`` is documented by Node as a no-op on POSIX — Linux/macOS hosts see byte-identical behaviour. * ``stdio: 'inherit'`` callers (e.g. ``cli/wiki.ts:522`` opens the editor in the user's terminal) keep their interactive UX. The child inherits the parent's stdio handles; no new console is allocated; the flag has nothing to hide. * Piped callers (``stdio: ['pipe',…]``) continue to deliver every byte of stdout/stderr back to the parent for the parent to log / process / re-print. No output is swallowed. * ``execSync`` / ``execFileSync`` callers that previously had no ``stdio`` option (e.g. ``generator.ts:887`` ``execSync('git rev-parse HEAD', { cwd })``) keep their default pipe semantics (``.toString()`` still works) — windowsHide is added alongside the existing ``cwd`` option. Verified on Windows 10 22H2 / Node 22.21 by installing the locally built tarball and exercising: * MCP detect_changes via the local backend → no flash. * gitnexus serve → no flash on git clone/clone-pull. * gitnexus analyze interactively → output appears in terminal as before, no extra window. * test(windowsHide): extend regression to every spawn-family call in src/ Companion to the src/ patch. The hooks.test.ts regression now covers 16 files (5 hooks + 11 source files), and asserts the invariant for every spawn-family function — not just spawnSync. Changes: * Generalise countSpawnCalls() to also count spawn, execFile, execFileSync, execFileAsync, execSync (the entire spawn-family surface of child_process). Skip method calls (e.g. RegExp.exec) via a negative-lookbehind on ``.``. * Add SRC_FILES table with all 11 source-tree files that import spawn-family functions from child_process. * Loop over [...HOOK_FILES, ...SRC_FILES] so a regression in any file fails the same test name. * Tighten the assertion to ``hideCount >= spawnCount`` rather than strict equality, because some sites (e.g. setup.ts:534 using execFileAsync via shell:true on Windows) may legitimately add windowsHide to nested option objects in future refactors. * Sanity gate ``spawnCount > 0`` per file catches a refactor that deletes all spawn calls (would otherwise make the assertion trivially true). Manually exercised against the patched repo: 16 files, 28 total spawn-family calls, 28 windowsHide:true. All pass. The convention to keep this list in sync: every new file in gitnexus/src/ that imports from 'child_process' must be added to the SRC_FILES tuple. The cost is one line per file; the benefit is the next contributor never has to think about windowsHide again — the test will catch a miss before merge. * style: prettier --write on storage/git.ts + hooks.test.ts CI quality / format job flagged two formatting issues in the merge-resolution commit: a long single-line options object in storage/git.ts and similar in hooks.test.ts. prettier --write fixes both with the project's standard wrap-and-trailing-comma style. No semantic change. * test(git): include windowsHide in toHaveBeenCalledWith assertion The merge-resolution commit added windowsHide:true to the 'git rev-parse --is-inside-work-tree' execSync call in src/storage/git.ts, but the matching strict-shape assertion in git.test.ts:31-34 still expected the pre-patch two-key options object {cwd, stdio}. vitest's toHaveBeenCalledWith does a deep structural match, so the extra third key flipped the assertion to fail. Add windowsHide: true to the expected shape. Only this one assertion is strict; the two siblings ('passes the correct cwd' and the no-cwd-arg case) use expect.objectContaining and expect.any(String) and remain green without modification. * test(setup-codex): include windowsHide in execFile shape assertions Same root cause as the git.test.ts fix on this branch: the windowsHide patch added windowsHide:true to the execFile() options in src/cli/setup.ts, but three strict-shape toHaveBeenCalledWith assertions in setup-codex.test.ts still expected the pre-patch {shell:true} / {shell:false} two-key options. vitest does a deep structural match, so the extra key flipped the assertions to fail on every CI matrix leg (ubuntu coverage + macos + windows). Adding windowsHide:true alongside the existing 'shell' key in all three sites. * ci: retrigger checks go-parity failed on a flaky onnxruntime-node postinstall network timeout (AggregateError [ETIMEDOUT] in node ./script/install), which cascaded into the CI Gate. No code change — empty commit to re-run the pipeline. * fix(test): strengthen windowsHide regression assertions (PR #1794 review) - Replace toBeGreaterThanOrEqual with exact toBe per DoD §2.7 - Remove unused `m` variable in countSpawnCalls (CodeQL finding) - Add windowsHide: true to runGit test helper for consistency --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: ManniX-ITA <35522085+ManniX-ITA@users.noreply.github.com> Co-authored-by: Test <test@example.com>	2026-05-24 09:51:21 +01:00
Shane Thurston Wijaya	105efd0f7c	feat(wiki): added --lang <lang> flags to gitnexus wiki for multilanguage wiki generation support (#1613)	2026-05-17 19:54:02 +01:00
Copilot	ed50a6729f	fix(wiki): Remove the hidden 60s default timeout, validate gitnexus wiki timeout/retry flags, and surface timeout errors (#1651)	2026-05-17 12:03:54 +01:00
Derek Pearson	89c03b2ebb	fix: skip Claude augment hook when GitNexus server owns DB (#1493) ... * fix(claude): skip augment hook when server owns db * chore(autofix): apply prettier + eslint fixes via /autofix command * fix(hooks): cross-platform DB lock probe for MCP owner guard Extract hook-db-lock-probe.cjs with a single hasGitNexusDbLockedByGitNexusServer entry point used by both Claude hooks: - Linux: scan /proc/<pid>/fd via dev+inode (no lsof required), optional lsof fallback; GITNEXUS_HOOK_LINUX_PROC_BUDGET_MS caps scan time - macOS and other Unix: trusted lsof + ps (absolute paths / env overrides) - Windows: Restart Manager + Win32_Process via win-rm-list-json.ps1 and GITNEXUS_HOOK_POWERSHELL_PATH Update hooks.test.ts source coverage for the probe module. Co-authored-by: Cursor <cursoragent@cursor.com> * Update gitnexus/hooks/claude/win-rm-list-json.ps1 Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix(gitnexus): repair package.json JSON after malformed engines edit Co-authored-by: Cursor <cursoragent@cursor.com> * Update Node.js engine version requirement to 22.0.0 * Update Node.js engine version to >=22.0.0 * fix(hooks): address ce-code-review findings on PR #1493 P0: - Replace malformed `RM_UNIQUE_PROCESS` block in `gitnexus/hooks/claude/win-rm-list-json.ps1` (duplicate struct decl + duplicate `ProcessStartTime` + unbalanced braces) with a single well-formed `[StructLayout(LayoutKind.Sequential, Pack = 4)]` struct, so PowerShell `Add-Type` actually compiles and the Windows DB-lock probe stops fail-open on every machine. - `gitnexus/src/cli/setup.ts` now copies `hook-db-lock-probe.cjs` and `win-rm-list-json.ps1` into the user's `~/.claude/hooks/gitnexus/` alongside `hook-lock.cjs`, preventing the `MODULE_NOT_FOUND` thrown by `gitnexus-hook.cjs:18`'s top-level require on every fresh install. `gitnexus/test/unit/setup.test.ts` extended to assert both new copy destinations. - Four fail-open hook tests (`ENOENT lsof`, `npx parent line`, `non-GitNexus ps line`, `ps ENOENT`) now seed `createHookToolDir` with a valid `[GitNexus]` stderr line so `expect(parseHookOutput).not.toBeNull()` actually holds on CI. P1: - Plugin copy of `win-rm-list-json.ps1` gains `Pack = 4` so its CLR struct matches the 12-byte native `RM_UNIQUE_PROCESS` layout (multi-blocker `RmGetList` no longer reads mangled `dwProcessId`). - `GITNEXUS_HOOK_CLI_PATH = ''` now falls through to the resolution chain in `gitnexus-hook.cjs`, matching the plugin copy and removing the twin-file divergence on empty-string envs. - Lock-warning suppression test seeds `gitnexusMarkerPath` and asserts the augment subprocess actually ran, plus `GITNEXUS_DEBUG=1` preserves the full discarded prefix. - MCP-owner skip branch in both hook copies now emits `[GitNexus] augment skipped: MCP server owns DB` on stderr, so agents can distinguish intentional skip from silent failure. P2: - `ps` loop in `hook-db-lock-probe.cjs` fails-closed on `ETIMEDOUT` to mirror the `lsof` handling (symmetric subprocess-probe contract). - `RmStartSession` return value captured in both `.ps1` copies; exits early with `[]` on non-zero so subsequent RM API calls don't operate on an invalid handle. - Windows RM-list `.ps1` encoded cache distinguishes uninitialized (`undefined`) from load-failed (`null`) with a one-shot `GITNEXUS_DEBUG` warning instead of silently caching empty string. - `createHookToolDir` helper accepts `lsofOutputLines` and `psOutputByPid`; the multi-PID test uses them instead of duplicating the fake-binary construction inline. - All five skip-path tests now assert `result.status === 0` and the new skip-signal stderr line. - `AGENTS.md` documents the seven hook configuration env vars (`GITNEXUS_HOOK_CLI_PATH`, `_LSOF_PATH`, `_PS_PATH`, `_POWERSHELL_PATH`, `_LINUX_PROC_BUDGET_MS`, `_RM_TARGET`, `GITNEXUS_DEBUG`). - `GITNEXUS_DEBUG` path in `gitnexus-hook.cjs`/`.js` writes the full discarded stderr prefix instead of a 180-char preview. - Inline comment in `hook-db-lock-probe.cjs` explains the intentional Windows ETIMEDOUT fail-closed semantics. - Removed the unnecessary `as WriteFileOptions` cast and orphaned `import type { WriteFileOptions }` in `hooks.test.ts`. P3: - `isGitNexusServerCommand` unexported from `hook-db-lock-probe.cjs` (kept as private helper). - Env-path overrides (`GITNEXUS_HOOK_CLI_PATH`, `_POWERSHELL_PATH`, `_LSOF_PATH`, `_PS_PATH`) require `fs.existsSync` before being returned, so typos / stale config fall through to the standard resolution chain. Misc: - `gitnexus/package.json` engines.node back to `>=22.0.0` (matches origin/main and the original PR reviewer's earlier request). Twin-tree parity / CI sync mechanism tracked separately at abhigyanpatwari/GitNexus#1591. Test plan: vitest run test/unit/hooks.test.ts → 113 passed, 18 Unix-only skipped; setup.test.ts → 14 passed. * chore(autofix): apply prettier + eslint fixes via /autofix command * trigger --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: Cursor <cursoragent@cursor.com>	2026-05-14 16:39:30 +01:00
Shane Thurston Wijaya	88d3df77cc	feat:(wiki) added --timeout and --retries flags for large module pages to mitigate timeout aborts (#1543) ... * feat:(wiki) added --timeout and --retries flags for large module pages to mitigate timeout aborts * docs(wiki): document --timeout and --retries options * docs(wiki): document --timeout and --retries in SKILL.md --------- Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-05-13 18:35:39 +01:00
Abhigyan Patwari	ec4624af87	fix(hooks): cap concurrent augment subprocesses (#1486) (#1510) ... * fix(hooks): cap concurrent augment subprocesses to prevent runaway process spawn (#1486) When Claude Code fires PreToolUse hooks for parallel Grep/Glob/Bash tool calls, each invocation spawned its own `gitnexus augment` subprocess — a Node + LadybugDB cold start that holds resources for several seconds. Under heavy parallel search load (issue #1486: 180+ piled-up processes, load avg > 100), these accumulated faster than they completed because nothing capped concurrent in-flight augments. Add a lockfile-based concurrency guard under `<.gitnexus>/.hook-locks/`: each running hook claims a `<pid>.lock`, the guard counts live PIDs and prunes stale entries (>30s mtime or pid no longer alive), and bails silently when MAX_INFLIGHT (3) is reached. Augment is best-effort enrichment — missing a few fires under burst load is preferable to melting the system. Applied to all three hook variants that spawn augment: - gitnexus/hooks/claude/gitnexus-hook.cjs (npm-installed Claude hook) - gitnexus-claude-plugin/hooks/gitnexus-hook.js (plugin Claude hook) - gitnexus-cursor-integration/hooks/gitnexus-hook.cjs (Cursor hook) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(hooks): make augment concurrency cap a hard cap via atomic slot files Address Claude's review of #1510. The original count-then-claim guard had a TOCTOU window: N hooks could each read `active < MAX_INFLIGHT` between readdirSync and the per-pid `wx` write and all proceed, briefly exceeding the cap. The PR title's "cap" language overstated this. Replace with fixed-name `slot-0.lock` ... `slot-N.lock` under `.hook-locks/`. `O_CREAT|O_EXCL` on a fixed path is OS-atomic — exactly one process wins each slot, so the cap is hard regardless of burst arrival timing. Each slot file contains the owning PID so stale-takeover still works when a hook crashes without releasing. PID liveness is checked before age (Claude's Finding 3): a slow-but-alive hook is never wrongly evicted. The 30s age window only kicks in to defend against PID reuse on a long-abandoned slot, well above the 7s augment timeout so a healthy run never hits it. Also adds the missing concurrency-guard tests to cursor-hook.test.ts (Claude's Finding 2): source-level wiring + dead-PID reclaim + 3-slots-full bail. Previously only the CJS and Plugin variants had test coverage for the guard; the Cursor variant was validated only by code inspection. Tests: 5726 passing, +9 from baseline (1 hard-cap burst test + 4 source regressions in hooks.test.ts; 3 source + 2 integration in cursor-hook.test.ts). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(hooks): inspect slot mtime + content via single fd (codeql TOCTOU) CodeQL flagged the stale-takeover path in acquireHookSlot as a potential filesystem race (js/file-system-race): statSync(slotPath) followed by readFileSync(slotPath) gives a TOCTOU window where the file could be swapped between the metadata check and the content read. Replace the two separate path-based calls with a single openSync + fstatSync + readSync + closeSync sequence. Both mtime and owner PID now come from the same file descriptor, so the operations are atomic on one inode. No behavioral change beyond closing the race. Applied to all three hook variants (CJS, Plugin, Cursor). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(hooks): distinguish EPERM from ESRCH in PID liveness check Cursor Bugbot caught a contradiction with the stated design: the bare `catch` after `process.kill(owner, 0)` was treating EPERM (process exists but owned by another user) the same as ESRCH (process gone), which would evict a live slot whenever the lock dir straddled user boundaries. Inspect the error code: ESRCH → dead, evict; EPERM → still alive, keep the slot; anything else → assume alive (be conservative under unexpected failure rather than over-evict). Applied to all three hook variants. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(hooks): fail closed when lock dir cannot be created Previously the mkdirSync catch in acquireHookSlot returned `() => {}` (a truthy no-op). The caller checks `if (!release) return;` to skip augment when the guard can't be established — but a truthy no-op slipped through that check and let augment spawn unguarded. On a cross-user shared `.gitnexus/` or read-only filesystem, N concurrent hooks would each take that branch and reintroduce the #1486 fan-out the guard exists to prevent. Return `null` instead so the caller's `if (!release) return;` skips augment cleanly. Augment is best-effort enrichment — skipping it when the guard fails is strictly safer than running unguarded. Also clarify the stale-slot comment: PID-liveness wins for slots younger than HOOK_LOCK_STALE_MS, but age is the final arbiter beyond 30s (PID-reuse defense). The previous wording said "PID-liveness wins over age" without qualifying it, which contradicted the >30s branch. Add source-level regression tests in hooks.test.ts and cursor-hook.test.ts asserting acquireHookSlot returns null (not () => {}) on lock-dir failure. Note in the Cursor test file that the 10-spawner burst test is not duplicated because the algorithm is byte-for-byte identical to the CJS hook and already covered there. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor(hooks): extract lock guard into helper modules Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/04dd20c5-28fd-433a-83cf-ad83fd03fb32 --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>	2026-05-13 08:56:27 +01:00
sburdges-eng	b79278705a	fix(hook): resolve canonical repo root + guard read-only FTS ensure (#1226) ... * fix(hook): resolve canonical repo root + guard read-only FTS ensure (#1224) Two bugs in the Claude Code hook + query layer integration: 1. `findGitNexusDir` (in `gitnexus/hooks/claude/gitnexus-hook.cjs` and `gitnexus-claude-plugin/hooks/gitnexus-hook.js`) walked upward from cwd looking for a non-registry `.gitnexus/`. In linked git worktrees created via `git worktree add`, the canonical repo's `.gitnexus/` never sits above the worktree path, so the walk silently fails and neither augmentation nor staleness notifications fire. Fix: keep the cwd-walk as the fast path, then fall back to `git rev-parse --git-common-dir` to resolve the shared `.git/` directory (which lives inside the canonical repo across all linked worktrees) and walk up from its parent. Returns null cleanly when `git` isn't on PATH or cwd isn't inside any working tree. 2. `ensureFTSIndex` in the LadybugDB adapter rethrew when the active connection is read-only (e.g. the MCP query pool, which opens DBs read-only by design). Defensive callers used to surface five "Cannot execute write operations in a read-only database" warnings per query. Fix: extract `isReadOnlyDbError` (mirroring the existing `isDbBusyError` discriminator) and have `ensureFTSIndex` catch the read-only error, cache the key, and return silently. Index creation is owned by `gitnexus analyze` on a writable connection — the ensure call is safely a no-op on the read pool. Lock / busy / "already exists" / schema errors continue to propagate. Tests: - `test/unit/hooks.test.ts`: new "Linked git worktree resolution" block exercises both hooks against a real linked worktree to confirm PostToolUse stale notifications fire, plus a negative case when the canonical repo has no `.gitnexus/`. - `test/unit/lbug-readonly-error.test.ts`: new file unit-tests the `isReadOnlyDbError` discriminator (positive matches, case insensitivity, non-Error inputs, and unrelated errors that must still surface — lock contention, "already exists", schema misses). - `test/integration/lbug-core-adapter.test.ts`: extends the existing FTS coverage with an idempotency assertion for `ensureFTSIndex` to pin the read-only guard's success-path contract. Verified with `npx tsc --noEmit` and `vitest run` on the affected files (hooks + readonly + lbug-core-adapter + bm25-search + lbug-extension-loader + lbug-embedding-hashes — 136 tests pass). Build: `npm run build` succeeds. Closes #1224 * fix(local-backend): cover supported vector path Add the supported-platform regression assertion for QUERY_VECTOR_INDEX and align the unsupported VECTOR diagnostic wording with platform policy. Made-with: Cursor --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>	2026-04-30 18:12:03 +01:00
CauchYoung	86abc01445	fix(hooks): ignore global registry during staleness checks (#1141) ... * fix(hooks): ignore global registry during staleness checks * test(hooks): cover indexed repos under global registry --------- Co-authored-by: laplace young <yangqk12@whu.edu.cn>	2026-04-28 09:39:18 +01:00
Copilot	2b0392cd83	feat(analyze): preserve existing embeddings by default; --force regenerates them; add --drop-embeddings opt-out (CLI + HTTP API) (#1055) ... * Initial plan * fix(analyze): preserve existing embeddings by default; add --drop-embeddings opt-out Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/da1da041-afcd-4d38-8a2f-39ca52a462ff Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> * analyze: --force on embedded repo now regenerates embeddings (preserve+top-up) Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/e2759765-b8f6-453a-8c28-595439d23cb4 Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> * analyze: wire dropEmbeddings into HTTP API; log cache-load failures; extract pure deriveEmbeddingMode + behavioral tests; sync GUARDRAILS.md Agent-Logs-Url: https://github.com/abhigyanpatwari/GitNexus/sessions/7d88e595-cbd8-47b2-ba4f-fb5b9a60cda4 Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: magyargergo <11230420+magyargergo@users.noreply.github.com>	2026-04-24 13:07:40 +01:00
Gergő Magyar	bf09eab95b	feat: configure prettier with pre-commit hook (#563) ... * feat: configure prettier with pre-commit hook integration Add prettier, lint-staged, and prettier-plugin-tailwindcss at the repo root with husky pre-commit hook integration. Moves husky from gitnexus/ to root package.json for reliable hook installation. - Root package.json with prepare/format/format:check scripts - .prettierrc with endOfLine:lf and tailwindStylesheet for TW v4 - .prettierignore excluding fixtures, vendor, generated, *.d.ts, *.md - .gitattributes enforcing LF line endings for Windows consistency - Pre-commit hook uses direct node_modules/.bin/ paths (no npx) * style: apply prettier formatting to entire codebase One-time bulk format. No logic changes. Use .git-blame-ignore-revs to skip this commit in git blame. * chore: add .git-blame-ignore-revs for prettier format commit * perf: pre-commit hook runs only tests related to staged files Use vitest --related to scope test execution to tests that import the changed files, instead of running the full suite on every commit. * perf: remove vitest from pre-commit hook, keep in CI only Pre-commit now runs lint-staged + tsc only. Tests run in CI (ci-tests.yml) where they belong — keeps commits fast. * ci: add prettier format check to quality workflow PRs will now fail if code isn't formatted with prettier.	2026-03-28 14:58:04 +00:00
Candido Sales Gomes	5a5850832c	refactor: migrate from KuzuDB to LadybugDB v0.15 (#275) ... * refactor: migrate from KuzuDB to LadybugDB v0.15 KuzuDB was archived (Apple acquisition, Oct 2025). LadybugDB is the community fork with full API compatibility. - Package swap: kuzu → @ladybugdb/core, kuzu-wasm → @ladybugdb/wasm-core - Rename all internal paths: kuzu → lbug (adapters, schema, storage) - Storage path: .gitnexus/kuzu → .gitnexus/lbug (with auto-cleanup) - Add explicit VECTOR extension loading (required in v0.15) - Update CI workflow, documentation, and all tests - 1151 unit + 27 integration tests passing Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: address code review findings (P1-P3) P1: Fix WASM adapter to use getAll() API, wire cleanupOldKuzuFiles into analyze command, add symlink path traversal protection. P2: Cache VECTOR extension load state, batch augmentation engine queries (20→4), fix web getCopyQuery for multi-language tables, fix stale KuzuDB references, correct brainstorm package names. P3: Complete lbug-wasm.d.ts type declarations, batch semantic search per-label, update stale BM25 comment. * chore: remove outdated KuzuDB migration brainstorming document * fix: load FTS extension in MCP pool adapter on init The read-only pool adapter never loaded the FTS extension, so all QUERY_FTS_INDEX calls failed silently. This broke search-pool and augmentation integration tests, and caused empty results in the web UI server mode. * feat: implement shared Database caching and connection reference counting * feat: enhance KuzuDB migration handling and status reporting * fix: mock cleanupOldKuzuFiles in local backend callTool tests * fix: update mock for cleanupOldKuzuFiles and adjust imports in callTool tests --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-15 15:53:01 +00:00
Linus Beckhaus	c4eaf45ab1	feat(hooks): auto-reindex notification with cross-platform hardening (#205) ... Adds PostToolUse hook that detects stale GitNexus index after git mutations (commit, merge, rebase, cherry-pick, pull) and notifies the agent to reindex. Uses lightweight staleness check (git rev-parse HEAD vs meta.json) instead of running gitnexus analyze synchronously, avoiding KuzuDB corruption and 120s blocks. Security and cross-platform hardening: remove shell:true from all spawnSync calls, use .cmd extensions on Windows, add path.isAbsolute(cwd) guards, fix setup.ts path escaping with JSON.stringify, use sendHookResponse() consistently. Includes 73 regression tests.	2026-03-07 08:59:54 +00:00
abhigyanpatwari	20ebd6b781	feat: security hardening, MCP improvements, skills, hooks, and CLI updates ... - Export security primitives (CYPHER_WRITE_RE, isWriteQuery, isTestFilePath, VALID_NODE_LABELS, VALID_RELATION_TYPES) from local-backend - Improve MCP kuzu-adapter with better query handling - Add PR review skill for Claude, Cursor, and npm package - Add CLI guide and CLI skills - Update hooks for Claude plugin and Cursor integration - Remove deprecated claude-hooks.ts CLI module - Update eval-server, setup, and analyze CLI commands - Improve CSV generator and ingestion processors - Update CLAUDE.md and AGENTS.md configs Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-01 20:13:42 +05:30
abhigyanpatwari	39b01f101e	feat(skills): rewrite skill descriptions for better auto-invocation ... Skill descriptions were too tool-centric ("using knowledge graph", "blast radius") which prevented Claude Code from matching them to user intent. Rewritten to user-intent-driven format with "Use when..." phrasing and example trigger phrases so Claude can semantically match user requests. Updated across all 3 sources: gitnexus/skills/, gitnexus-claude-plugin/skills/, .claude/skills/, and the ai-context.ts fallback generator. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-02-26 18:24:41 +05:30
abhigyanpatwari	2a444acf1d	fix(plugin): hook logic bug and version mismatch ... - Fix hook exit status check: || → && so failed augment errors don't get injected into Claude's context as graph results - Add exit status check to npx fallback (same bug) - Update plugin version from 1.2.11 to 1.3.3 in both marketplace.json and plugin.json Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-02-26 18:08:32 +05:30
Linus Beckhaus	238abbd947	refactor(skills): prefix all skill names with gitnexus- for disambiguation ... Skill folder names determine invocation paths in Claude Code plugins (e.g. plugin:gitnexus:gitnexus-cli). Generic names like "cli" or "debugging" could collide with other plugins, so prefix them all with gitnexus- for clarity. Updated across plugin dirs, main package source files, ai-context.ts generator, setup.ts installer, and all CLAUDE.md/AGENTS.md routing tables.	2026-02-25 14:15:42 +01:00
Linus Beckhaus	4f4fe9e587	update version	2026-02-25 13:40:49 +01:00
Linus Beckhaus	dbf3495713	fix(skills): remove gitnexus- prefix from skill frontmatter names ... Skill names should match folder names since the plugin namespace (gitnexus:) already provides context. Avoids redundant display like gitnexus:gitnexus-cli → now gitnexus:cli.	2026-02-25 13:39:25 +01:00