4 commits

Author	SHA1	Message	Date
mengkaka	79543c8f83	feat(storage): add configurable index storage and content retention tiers (#3060) ... * feat(storage): add configurable index storage and content retention tiers Rebase #3060 onto current origin/main. Keep GITNEXUS_STORAGE_PATH, GITNEXUS_STORAGE_ROOT, and GITNEXUS_CONTENT_RETENTION, and fold in main's FTS skip, embed-session, and help-text updates. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Keep legacy registry rows on the local storage fallback, resolve symlinks before the destructive-path guard, and align hook lookup with CLI branch slugs, branch-slot metadata, and longest-path match. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Only list swept upload directories after a successful removal so callers cannot treat a permission or transient rm failure as gone. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Document that getStoragePath may consult registered storage while this module still does not mutate the global registry. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(storage): close review findings for external indexes and retention Re-inspect ownership under the analyze lock, fail-closed when the registry file is missing, and keep skip-git hook discovery plus retention fields on HTTP/MCP list surfaces. /api/file stays 410 unless contentRetention is full. Co-authored-by: Cursor <cursoragent@cursor.com> * chore(autofix): apply prettier + eslint fixes via /autofix command * Address PR review feedback (#3060) Treat lock-only index dirs as empty, honor HTTP --force storage policy, and prefer registered plus branch-aware slots in hooks and augment. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Keep hook fallbacks inside the current worktree, compare foreign-local slots canonically, and make storage fixtures survive ownership validation. Co-authored-by: Cursor <cursoragent@cursor.com> * Fix macOS hook test expecting realpath'd registry paths. resolveHookRepo returns the written registry path, not a filesystem realpath, so the assertion must match that. * Address gitnexus-check warnings on hook install docs and slot tests. The Cursor troubleshooting list omitted registry-query.cjs, and the writable-slot test only checked that isDirectory exists instead of that the path is a directory. * Align the HTTP catalog source-scan with skippable resolveRepo validation. resolveRepo lists fresh repos with validate: options.validateStorage !== false so DELETE can skip prune; the test still required a literal validate: true. * Harden storage path sinks so CodeQL path-injection and ReDoS alerts clear. Contain every filesystem probe inside the resolved storage slot with the inline path.relative idiom, reject filesystem-root slots, and trim slot basenames in linear time. * Settle bridge stamps before writing so CI size/mtime matches stay stable. LadybugDB can still flush into bridge.lbug after close+rename; persist whole-millisecond mtimes and wait for consecutive stats to agree so a freshly written pair matches. * Type the settled bridge stat as fs.Stats so tsc does not see bigint. Awaited<ReturnType<typeof fsp.stat>> collapsed the bigint overload and broke prepare/typecheck on CI. * Keep the bridge mtime stamp exact so same-size swaps still fail the pair check. Co-authored-by: Cursor <cursoragent@cursor.com> * Wrap the bridge stamp predicate so prettier --check stays green. Co-authored-by: Cursor <cursoragent@cursor.com> * Require a quiet interval before stamping a settled bridge file. Co-authored-by: Cursor <cursoragent@cursor.com> * Reuse shared storage and settle helpers instead of local copies. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Cursor <cursoragent@cursor.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>	2026-09-12 20:31:55 +00:00
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
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	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