14 commits

Author	SHA1	Message	Date
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
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	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
azizur100389	bdb824cfe4	feat(cli): add circular import cycle check (#2166)	2026-06-12 04:53:17 +01:00
Gergő Magyar	7eaeb0a0c4	feat: multi-branch indexing and branch-scoped querying (#2106) (#2137) ... * feat(git): add getCurrentBranch + resolveRefToCommit helpers (#2106) * feat(storage): branch-scoped getStoragePaths + branchSlug + resolveBranchPlacement (#2106) * feat(analyze): branch-aware indexing — per-branch slot, no overwrite (#2106) * feat(registry): nest non-primary branches under one path entry (#2106) * feat(mcp): optional branch scope on query tools + list_repos branches (#2106) * feat(cli): --branch on analyze + query/context/impact/cypher/detect-changes (#2106) * feat(cli): branch-aware list/status + per-branch staleness meta (#2106) * fix(review): apply autofix feedback - guard analyze against --branch != checked-out branch (prevents writing one branch's working tree into another branch's index slot) - fix branch-handle pool reinit thrash (track observed indexedAt by lbugPath, since applyBranchScope returns fresh handles) - remove dead resolveRefToCommit helper (staleness uses HEAD vs branch meta) - RepoListing.branches -> Omit<BranchSummary,'stats'> for type cohesion - add tests: branchSlug traversal containment, --branch mismatch reject, callTool branch threading, legacy-entry branch routing, status detached/stale * fix(review): address tri-review findings (#2106) - P1 data-loss: a detached-HEAD re-analyze (CI's actions/checkout default) no longer strips the primary's meta.branch stamp; preserve it so a later branch analyze cannot claim & overwrite the flat/primary index. +cascade integration test - P2: capture validateBranchName's trimmed return for --branch so a whitespace-padded value no longer false-rejects on-branch or ghosts an index - F1: on a lost/rebuilt registry, a branch run reconstructs the primary top-level entry from the flat meta, not the feature branch's meta * fix(storage): only trust a non-empty-string flatMeta.branch (#2106 R5) * fix(analyze): warn when the default branch is not the primary index (#2106 R8) * fix(mcp): resolve --branch <primary> on a legacy unstamped flat index (#2106 R4) * feat(cli): gitnexus clean --branch to remove a single branch index (#2106 R7) * fix(mcp): evict orphaned branch pools on unregister/clean (#2106 R3) * fix(analyze): union per-branch cache keys so a branch switch keeps shards (#2106 R6) * fix(analyze): normalize the auto-detected branch label via sanitizeDetectedBranch (#2106 R1) * fix(cli): skip AGENTS.md base_ref refresh for a non-primary branch fast path (#2106 R2) * fix(storage): atomic writeRegistry + re-read-before-write to narrow the registry race (#2106 R9) * refactor(storage): extract branch primitives to branch-index.ts (#2106 R10)	2026-06-10 10:24:40 +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	7d500390b9	fix: Use Ladybug native read-only enforcement and prepared statement execution for Cypher query paths (#1655)	2026-05-18 06:54:24 +01:00
Temirkhan	1fe3bf9399	feat(mcp): add tool safety annotations (#1127) ... * feat(mcp): add tool safety annotations * test(mcp): address PR #1127 review follow-ups - Replace private `_requestHandlers` SDK access in server.test.ts with `Client` + `InMemoryTransport.createLinkedPair()` for the tools/list annotation propagation test. The new path uses supported public APIs and surfaces SDK changes loudly instead of silently degrading. - Extract `OPEN_WORLD_READ_ONLY_TOOLS` set in tools.test.ts so future read-only open-world tools can be added without rewriting the invariant; preserves the current "only `query` is open-world" guard. - Add inline rationale on `group_sync` annotations explaining the conservative `idempotentHint: false` (writes contracts.json on every call even when output is deterministic). No runtime behavior change. Annotations themselves and tools/list shape are unchanged. --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>	2026-05-03 09:06:41 +01:00
ivkond	00966630c4	feat: cross-repo impact analysis (#794) — @repo MCP routing + group resources (#984)	2026-04-20 11:55:07 +01:00
ivkond	4fed097abb	feat(group): add sync pipeline, CLI, MCP tools, and monorepo fixture ... Wire extractors into the sync pipeline with service boundary detection. GroupService provides high-level API for all group operations. - Sync pipeline: orchestrates extraction (HTTP, gRPC, topics) with service boundary assignment and exact matching - GroupService: groupList, groupSync, groupContracts, groupQuery, groupStatus (groupImpact deferred to cross-repo follow-up PR) - CLI: group create/add/remove/list/sync/contracts/query/status - MCP tools: group_list, group_sync, group_contracts, group_query, group_status - Monorepo fixture: 3 services (auth/orders/gateway) connected via gRPC + Kafka + HTTP — all intra-repo cross-links discovered - Documentation: CLI commands and MCP tools added to both READMEs Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>	2026-04-02 00:40:31 +03:00
Gergő Magyar	acf6fbdd39	feat: configure eslint with unused import removal (#564) ... * feat: configure eslint with unused import removal Add ESLint v9 (flat config) for code quality: - eslint-plugin-unused-imports for auto-removing dead imports - @typescript-eslint for TypeScript-aware linting - eslint-plugin-react-hooks for React hooks rules - eslint-config-prettier to avoid formatting conflicts - lint-staged runs eslint --fix before prettier on .ts/.tsx - CI lint job added to ci-quality.yml * refactor: remove unused imports via eslint --fix Auto-fixed by eslint-plugin-unused-imports. No logic changes. * chore: add eslint fix commit to .git-blame-ignore-revs	2026-03-28 15:28:09 +00:00
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
marxo126	c437acf6bb	feat: deep flow detection — consumer access tracking, middleware chains, error shapes, api_impact tool (#482)	2026-03-23 22:13:48 +00:00
abhigyanpatwari	8a100a76d3	test: add test suite with vitest (unit + integration + fixtures) ... - 59 test files covering unit and integration tests - vitest config with coverage thresholds and fork pooling - Test fixtures (mini-repo + multi-language sample code) - Add vitest + coverage-v8 to devDependencies - Add test scripts (test, test:integration, test:all, test:watch, test:coverage) - Move typescript to devDependencies where it belongs Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-01 20:07:02 +05:30