37 commits

Author	SHA1	Message	Date
Gergő Magyar	6088d2e309	chore: release v1.6.10 (#3064) ... * chore: release v1.6.10 * fix(eval): derive the pinned runtime version from package.json The containment suite mounts a GitNexus runtime built from this checkout and asserts its version equals PINNED_GITNEXUS_VERSION, a constant hardcoded to "1.6.9" when the harness landed in #2566. The first release after that lands 1.6.10 in gitnexus/package.json, the built runtime reports 1.6.10, and `eval / containment (ubuntu)` fails on drift the release itself created. Read the version from gitnexus/package.json instead. The check keeps its real job -- proving the mounted runtime came from this checkout rather than a published package -- without a copy that only ever drifts on release day. 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>	2026-08-27 23:21:40 +01:00
dependabot[bot]	6ae35f1e71	chore(deps): bump aiohttp in /eval in the uv group across 1 directory (#2825) ... --- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.3 dependency-type: indirect dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-08-04 09:55:59 +00:00
Gergő Magyar	0ce7880290	fix(scope-resolution): a closure binding is a call SOURCE in every language, and function-local values carry their own identity (closes #2699) (#2718) ... * test(scope-resolution): audit the consumers of file-scoped node ids (#2699 part A) #2699 item 4 — "audit consumers that assume file-scoped ids" — after #2695/#2714 gave function-local CALLABLES position-bearing ids. Tests and findings only; no production change. That split is deliberate: `impact` reports `resolveDefGraphId` at CRITICAL with 23 DIRECT dependents across 7 modules (every language MRO builder, both Spring attachers, C++ member lookup, tryEmitEdge, emitReferencesViaLookup, buildGraphTargetIndex, emitFreeCallFallback, emitReceiverBoundCalls, preEmitInheritanceEdges, emitDetectedInterfaceImplementations, phpEmitUnresolvedReceiverEdges, emitRubyMixinEdges, emitRustTraitImplEdges, emitDartHeritageEdges), so changing that key chain is its own change, not a rider on an audit. A2 — detect_changes: CONCERN RESOLVED, now pinned. The worry was that an id containing `@row:col` re-keys whenever a declaration MOVES, making every edit look like symbol churn. It cannot: `local-backend.ts` maps diff hunks to symbols by LINE-RANGE OVERLAP (`n.startLine`/`n.endLine`) and merely REPORTS `n.id`. Node identity never participates in the match. New structural test asserts the WHERE clause never gains `n.id =` or `n.id IN`, keeps the one legitimate id-shaped predicate (the `BasicBlock:` prefix exclusion, #2082 U7), and confirms the id is returned rather than matched. Structural in the same idiom as `detect-changes-worktree.test.ts`, and labelled as not proving runtime behaviour. A1 — ANSWERED, and the answer is that #2699 is NOT fully closed by items 1-3. The fail-closed guard is gated on `isOverloadableCallable` (Function | Method | Constructor), so a function-local VALUE never reaches it. Measured on a fixture: a top-level `const handler` and a function-local `const handler` still produce ONE node, `Const:v.ts:handler`. That is the residual half of the issue's original complaint. Pinned as a KNOWN LIMIT with its reason (widening identity to values re-keys ~14,700 build-time nodes to change ~800 persisted ones — the decision recorded in `parse-worker.ts`), and deliberately NOT fixed here. A3 — id-persisting consumers, classified: - detect_changes ................ SAFE (position-keyed; pinned by A2) - MCP impact/context/trace ...... SAFE (resolve by name/uid at query time) - bench fingerprints ............ SAFE (digest capture shape, not node ids) - rust-captures golden .......... SAFE (digests captures, not ids) - cfg pipeline-pdg snapshot ..... AT RISK by design — pins exact edge ids, so it trips whenever attribution changes. That is the gate working; #2714 already exercised it. - wiki / group-contract links ... NOT id-keyed on locals (locals are never cross-file addressable, per the document-scoped contract of item 2). Verified: tsc clean; 14/14 across the two touched files; `detect_changes` reports 0 changed symbols (tests only). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(php): a closure binding is a call SOURCE, not only a TARGET (#2699 part B, S1) A call made inside a closure binding was attributed to the ENCLOSING scope, so the closure was a call TARGET but never a call SOURCE: impact(handler, direction:"downstream") reported nothing even though the closure calls out. Root cause, probe-measured rather than inferred. Instrumenting pickCallerCallableDef (graph-bridge/ids.ts) to log every rejection reason shows the closure's own scope EXISTS and its range DOES contain the call site, but its ownedDefs is EMPTY, so the ":94" owned-callable filter drops it and attribution falls through to the ":97" enclosing-scope fallback. The reason is one missing query rule. javascript/query.ts pairs the binding name with the closure via @declaration.function anchored on the INNER arrow node, so anchor.range equals the @scope.function range and pass2AttachDeclarations attaches the declaration to the CLOSURE's scope. No other language had that rule — PHP, Rust, Kotlin, Ruby and Dart all captured named function declarations only. That single omission is the entire empty-ownedDefs cause. This ports the rule to PHP with the same anchor discipline (@declaration.function on the inner anonymous_function / arrow_function, NOT on the assignment_expression wrapper). PHP needs nothing else: it already declares (anonymous_function) and (arrow_function) as @scope.function, so the rule alone completes it. Measured on a fixture: `$handler = function ($x) { return target($x); }` inside outer() now emits Function:src/a.php:outer.$handler@3:2 -> Function:src/a.php:target where it previously emitted `outer -> target`. The pinned test in closure-binding-labels.test.ts asserted the OLD, wrong behaviour by design ("to catch that asymmetry changing in EITHER direction"), so it is INVERTED here rather than deleted, per its own instruction. Its block comment is corrected to record the measured root cause, including that Kotlin and Ruby will need BOTH this rule AND a relaxed kind gate (their lambda_literal / do_block is @scope.block deliberately, #1757), and that Dart has no closure scope at all. Verification: closure-binding-labels 50/50; PHP resolver suites 221/221 (php, php-coverage, php-response-shapes). detect_changes {staged}: 1 changed symbol (PHP_SCOPE_QUERY), 0 affected processes, risk LOW. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(rust): emit a node for a closure binding and make it a call SOURCE (#2699 part B, S3) Rust was the one exception to #2687's "a closure bound to a name is a Function node in every language": `let handler = || target(1);` produced NO graph node at all, so the closure could be neither a call target nor a call source. Needed BOTH query channels, which is the finding worth recording. Porting only the scope-resolution rule (as S1 did for PHP) changed nothing measurable here, because there was no node to attribute anything to: - languages/rust/query.ts — closure-binding declaration, @declaration.function on the INNER closure_expression so anchor.range aligns with the existing (closure_expression) @scope.function. This is what gives the closure's own scope a callable in ownedDefs, which is what stops pickCallerCallableDef falling through to the enclosing fn. - tree-sitter-queries.ts — @definition.function on the OUTER let_declaration. This emits the Function NODE that Rust never had. Note the deliberate anchor asymmetry between the two channels: the graph-node channel anchors the WRAPPER (matching the existing (lexical_declaration (variable_declarator ... (arrow_function))) rule), while the scope-resolution channel anchors the INNER closure (to align with @scope.function). Getting these backwards silently produces either no node or an unattributable one, so both sites carry a comment saying so. Measured on a fixture — `let handler = || target(1);` inside outer(): Function:src/a.rs:outer CALLS Function:src/a.rs:outer.handler@2:4 Function:src/a.rs:outer.handler@2:4 CALLS Function:src/a.rs:target Previously the whole binding was absent and the call read as `outer -> target`. The rule also covers `move` closures: the closure_expression node spans the `move` keyword. Verification: closure-binding-labels 50/50; rust.test.ts 192/192; rust-coverage, rust-f70, rust-scope all pass; rust-captures-golden passes UNCHANGED, so no golden regeneration was required. detect_changes {staged}: 2 changed symbols (RUST_SCOPE_QUERY, RUST_QUERIES), 0 affected processes, risk LOW. One caveat on the suite runs: this host times out `beforeAll` hooks at the default 60s under load — rust.test.ts needed --hookTimeout=600000 to complete, and a concurrent second vitest run starves worker startup entirely (every test fails at ~5001ms). Both are host artifacts, not signal. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(kotlin,ruby): a closure binding is a call SOURCE, via a Block-scope callable boundary (#2699 part B, S2) Kotlin and Ruby anchor a closure on a Block-kind scope — Kotlin lambda_literal and Ruby do_block/block are @scope.block DELIBERATELY (#1757 smart casts), so they must not be re-kinded. pickCallerCallableDef gated its child-scope walk on kind === 'Function', so a closure there could never become a call SOURCE. Both halves are required; neither alone changes anything: 1. kotlin/query.ts and ruby/query.ts gain the closure-binding declaration rule, with @declaration.function on the INNER lambda_literal / block so its range aligns with the @scope.block range (the anchor discipline documented in javascript/query.ts). Without this the closure scope owns no callable def. 2. pickCallerCallableDef accepts a Block-kind child as a callable boundary when the scope IS that callable's body. Without this the kind gate still rejects. The alignment test in (2) is the part worth scrutiny. Relaxing the kind gate to accept ANY Block owning a callable would be a real regression: a nested `fun foo()` declared inside a block is owned by that block, so a call made at BLOCK level — outside foo — would be misattributed to foo. Comparing the def's declaration position against the scope's start position discriminates them: for a closure the declaration and the scope sit on the SAME node, so the positions match; for a nested function the block starts at `{` while the def starts at the declaration, so they do not. Existing Function-kind behaviour is untouched, so every already-working language is unaffected by construction. The comparison is base-safe: scope-extractor.ts builds a def id as `def:<filePath>#<startLine>:<startCol>:<type>:<name>` from the same Range a scope carries, so both sides share one coordinate base. This is called out in the helper's docblock because `defStartLine` nearby documents its own output as 1-based, which invites a wrong "fix" (#2377 is exactly this class of hazard). Ruby's call forms are restricted to lambda/proc by name: an unrestricted (call block: (block)) would match ANY method call taking a block, so `mapped = items.map { |i| ... }` would wrongly declare `mapped` a callable. Verified against the parser: 3 matches (->, lambda, proc), map excluded. Separate #eq? patterns rather than one #match? alternation, which is a known hazard on this tree-sitter line. Measured on fixtures: Kotlin Function:src/A.kt:outer.handler@2:4 CALLS Function:src/A.kt:target Ruby Function:src/a.rb:outer.handler@4:2 CALLS Method:src/a.rb:target#1 previously `outer -> target` and `outer#0 -> target#1`. The pinned Kotlin test asserted the old behaviour by design and is INVERTED, not deleted. Ruby had NO pinned case, so a new one is added rather than inverted. The describe title no longer claimed something false ("not yet a call SOURCE" now holds only for Dart) and was retitled. Verification: closure-binding-labels 51/51; kotlin.test.ts, kotlin-coverage, ruby.test.ts, ruby-scope, ruby-namespaced all pass (478 passed / 1 expected inversion before the test was flipped). impact on pickCallerCallableDef: CRITICAL, 191 impacted, ONE d=1 (resolveCallerGraphId) — the return contract is unchanged, so that dependent is unaffected. detect_changes {staged}: 5 changed symbols, 2 affected processes (both EmitReferencesViaLookup, one of them the new ScopeIsCallableBody step), risk medium. Dart remains the last failing language: dart/query.ts declares no @scope.function at all, and dart/captures.ts synthesizes one only from a declaration WITH a body node, which an expression-bodied closure lacks. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(dart): give a closure binding a scope and a distinct identity (#2699 part B, S4) Dart was the last language where a closure binding could not be a call SOURCE, and fixing only that would have made the graph WORSE, not better. This lands both halves together for that reason. ## The attribution half A Dart closure had no scope at all. `dart/query.ts` declares no @scope.function anywhere — Dart's function scopes are SYNTHESIZED in `dart/captures.ts` from `declNode` + `findFunctionBody(declNode)`, and `findFunctionBody` looked only at the next named SIBLING for a `function_body`. A closure literal carries its body as a CHILD (`function_expression_body`), so it matched nothing and no scope was produced. `query.ts` gains the closure-binding declaration rule and `findFunctionBody` understands the child form. Deliberately NO @scope.function is added to the query: it would collide at identical range with the synthesized one, and duplicate scope ids make `buildScopeTree` throw, which DROPS THE WHOLE FILE. ## The identity half, and why it is not optional With attribution alone, two same-named closures in one file both keyed to the bare `Function:a.dart:handler`. One node then appeared to call BOTH targets — a CALLS edge present nowhere in the source. That is worse than the missing edge it replaced, so S4 could not ship without this. Root cause is not Dart-specific. `enclosingCallablePrefix` derives a SEMANTIC relation — what encloses this callable — by SYNTACTIC ancestor walk. Dart parses `int outer() { … }` as `function_signature` followed by `function_body` as SIBLINGS, so the enclosing callable is never an ancestor of code inside it and no membership set can fix that; the walk looks in the wrong direction. This is what SCIP and real compilers avoid by construction. SCIP keeps a local symbol opaque (`local <id>` — no name, no position, no chain) and models containment as a SEPARATE `enclosing_symbol` field; its spec says the local/global choice should follow ACCESSIBILITY, not the ability to name an enclosure. Dart's own analyzer answers this from `Element.enclosingElement` in the element model, never from AST ancestry. clang uses `name@offset` for a function-local; Kythe uses a document-scoped VName plus a `childof` edge. Identity is positional and opaque; enclosure is a relation. `findSplitBodyCallableAncestor` is the narrow fix at that seam: a fallback used ONLY when the ancestor walk finds nothing, recovering the callable from the body's preceding sibling. The sibling must be a BARE SIGNATURE, and that restriction is load-bearing — "any preceding callable sibling" is WRONG and was caught regressing PHP during this work. In `<?php function target($x) {…} $handler = function ($x) {…};` the closure is at FILE level, so the ancestor walk correctly finds nothing, the fallback runs, and an unrestricted version mis-qualified the file-level `$handler` as `target.$handler`. A preceding sibling is only an ENCLOSING callable when it cannot hold its own body. `SPLIT_SIGNATURE_NODE_TYPES` is exactly that set and is DERIVED, not listed: `LOCAL_SCOPE_BODY_NODE_TYPES` is already `FUNCTION_NODE_TYPES` minus the bare signature types, so the difference between them IS the split-signature set (`function_signature`, `method_signature` — verified at runtime). PHP's `function_definition` carries a body and is in both, so it is excluded. No language is named in shared code, and any future split-grammar language is covered for free. ## Verification Full resolver sweep — the gate that caught #2714's Rust regression — 2926 passed / 1 skipped / 0 failed across 51 files. closure-binding-labels 52/52; dart.test.ts, dart-coverage, callable-id-lockstep, function-local-identity, caller-identity-regression all pass (156/156 across 6 files). impact on `enclosingCallablePrefix`: LOW, 5 impacted, 3 d=1 all inside parse-worker. detect_changes {staged}: 5 changed symbols, 0 affected processes, risk LOW. Three existing Dart expectations FLIPPED rather than being deleted: Dart locals now carry the same enclosing-callable + position identity every other language got in #2695, so `local.dart:handler` became `local.dart:caller.handler@1:2`. A new test pins the actual defect — two same-named closures staying DISTINCT nodes — because the qualification assertions alone would not fail if the fabricated edge returned. One note for future work: an id-shape assertion here carries a call-site suffix on indirect invocations (`…handler@3:2:5:9`) but not on direct calls. That is the callable-value-flow pass keying its edge by invocation position, not part of the node id. Part B is now complete: PHP (S1), Rust (S3), Kotlin + Ruby (S2), Dart (S4). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(scope-resolution): close every deferred item on #2699 (A1 values, twin-list guard, schema bumps) Clears the limitations this PR had been carrying rather than leaving them as follow-ups. ## A1 — function-local VALUES now carry their own identity This was #2699's ORIGINAL complaint and the one a callable-only gate could never reach: a top-level `const handler` and a function-local `const handler` collapsed onto ONE `Const:v.ts:handler`. #2695 restricted position-qualified identity to Function|Method|Constructor because the collision that produced wrong CALLS edges was between callables, and widening churned ids for symbols the pruner mostly deletes. The churn is real and is accepted here deliberately. Widening needed THREE gates aligned, not one: - id-building — `parse-worker.ts` nestedCallablePrefix - resolution — `ids.ts` position key - registration — `node-lookup.ts` position-key registration Missing the third would register no position key for values, so every lookup misses and falls through silently. That is the #2714 failure mode: the caller attaches to a node that does not exist and the edge is DROPPED, which looks like "zero dangling edges" from outside. All three now route through ONE predicate, `isPositionQualifiedLocalLabel`, rather than repeating the label set a third time. Only LOCALS move. The prefix comes from `enclosingCallablePrefix`, which returns undefined when nothing encloses the declaration, so top-level and class-member ids are untouched — verified by the full resolver sweep, where a leak onto class members would have broken assertions in every language. `Property` is included on purpose: a class field stays unqualified because the prefix walk boundaries on class-likes, while an object-literal property inside a function is genuinely local and would otherwise keep the old collision. Measured: `Const:v.ts:handler` + `Const:v.ts:run.handler@3:2`, two distinct nodes. The KNOWN LIMIT test is FLIPPED per its own former instruction ("this test should be updated as part of it rather than deleted"). ## Schema bumps — required by Part B, not just by A1 INCREMENTAL_SCHEMA_VERSION 20 -> 21, parse-cache SCHEMA_BUMP 27 -> 29. SCHEMA_BUMP is 29, not 28, and that is the point of re-checking it against origin/main at MERGE time rather than branch time. This branch cut at 27 and bumped to 28; #2415 also bumped 27 -> 28 and merged first. The automated main-merge onto this branch surfaced the collision — leaving it at 28 would have shipped this whole change with NO parse-cache invalidation, so every warm cache keeps replaying the pre-fix captures and ids. This is the third instance of that collision recorded in parse-cache.ts (#2632/#2653 hit it at v21, and #2653/#2654 hit INCREMENTAL_SCHEMA_VERSION the same way). Part B already changed emitted node ids AND edges on files that did not themselves change (Dart locals re-keyed, Rust gained a node it never emitted, five languages gained closure-source attribution). A v20 index topped up incrementally keeps serving the old attribution, and a warm parse cache replays the old captures and ids verbatim. Shipping S1-S4 without these would have let every existing index silently keep the pre-fix graph. ## Twin-list drift guard — the sixth instance in this family `IMPLICIT_RECEIVERS` (gitnexus-shared lookup-core.ts) and `THIS_RECEIVERS` (type-env.ts) spell the same concept in two packages, and nothing enforced agreement — `$this` was added to the shared list in #2714 only because it was already in the other. New structural test asserts set equality plus the ONE deliberate asymmetry (`Me`, Visual Basic spelling, absent from the shared list because no SupportedLanguages entry uses it) in BOTH directions, so re-adding it there or dropping it here each fail loudly. Structural rather than value-imported: both constants are module-private, and exporting them purely to be testable would widen two public surfaces to satisfy a test. ## Two false comments corrected - `lookup-core.ts` said "see the drift guard noted in #2714", implying a guard existed when it was only a deferred follow-up. It exists now, and the comment points at it. - `callable-id-lockstep.test.ts` claimed its regex "fails if any site reconstructs the id". It matches ONE template spelling; a hand-rolled concatenation still slips past. Now stated as a tripwire for the known shape, not a proof. ## Skill learnings Four entries appended to eval/workflow_bench/learnings.jsonl from this run: the v9fs safe-writer failure, backticks silently terminating a query template literal (hit three times), a module-level TDZ const that passes tsc and then presents as N file failures with ZERO failing assertions, and concurrent vitest runs starving worker startup so a whole suite fails at ~5001ms. ## Verification Full resolver sweep 2926 passed / 1 skipped / 0 failed (51 files) — identical to pre-A1, which is the evidence that only locals moved. All EIGHT bench gates PASS with fingerprints UNCHANGED, so no regeneration was needed. function-local-identity, callable-id-lockstep, receiver-twin-list-drift and closure-binding-labels 71/71. tsc --noEmit clean. detect_changes {staged}: 9 changed symbols, 14 affected processes, risk HIGH — expected, and the reason the sweep above is the gate rather than a targeted list. Every affected process routes through `resolveDefGraphId`, the key chain Part A measured at CRITICAL with 23 direct dependents. Deliberately NOT done: the SCIP end state (opaque `local <id>` plus an explicit enclosure EDGE instead of containment encoded in the id string). It is a design direction, not a limitation of this work, and it is INCOMPATIBLE with A1 — A1 widens chain-encoded identity, that removes chain encoding entirely. Bundling both would re-key every local twice. Written up in the research notes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * test: update two assertions the #2699 changes correctly invalidated Both failed on CI at da3d8397 and are fixed here. Neither is a behaviour regression; both pinned values that this PR deliberately changed. 1. this-boundary.test.ts — "a Kotlin lambda still sees the receiver" The `this.m()` edge still exists and `this` still resolves to the enclosing receiver, which is the ONLY property this test exists to guard (its own comment said so: "what matters here is only that the `this.m()` edge still exists at all"). Only the SOURCE moved, from `run` to the lambda: Method:K.kt:K.run#0 -> Method:K.kt:K.run.f@2:16 Method:K.kt:K.run.f@2:16 -> Method:K.kt:K.m#0 The comment justifying the old expectation is now false and is corrected rather than left: it said the lambda "is not its own caller anchor" because Kotlin scopes `lambda_literal` as a BLOCK. Kotlin still scopes it as a block (#1757 is unchanged) — what changed in S2 is that a Block-kind scope is accepted as a caller anchor when the scope IS the callable's body. 2. call-summary-schema-version.test.ts — INCREMENTAL_SCHEMA_VERSION pin Moves 20 -> 21 with the bump, which is the point of pinning it: a change that alters emitted ids or edges without bumping would otherwise ship silently. Also adds the missing reuse-gate case. `passesReuseGate(20)` now asserts FALSE — a v20 index predates closure bindings becoming call SOURCES, the Rust node for `let f = || …`, the Dart closure scope + enclosing-callable identity, and position-qualified function-local values. Topping such an index up incrementally keeps serving the old attribution, including the Dart case where two same-named closures collapsed onto one node and asserted a CALLS edge present nowhere in the source. Why CI found these and local verification did not: the verification set was `test/integration/resolvers/` plus a hand-picked list, and both failures sat outside it — one integration test about `this` (which a caller-attribution change obviously touches) and one unit test pinning the exact constant that was bumped. Grepping for the changed constant, and for tests asserting closure attribution, would have found both. All 8 suites that reference the schema constants were then run: 177/177, no third pin. Verification: this-boundary + call-summary-schema-version 17/17; the 8 schema-referencing suites 177/177. detect_changes {staged}: 0 changed symbols, 0 affected processes, risk LOW (assertion-only edits). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR * fix(scope-resolution): resolve every finding from the multi-engine review of #2699 part B The first cut of Part B shipped four P1 defects. A two-engine review (Claude swarm + ce personas; Codex gpt-5.6-sol swarm + ce + adversarial) found all four, three of them because an independent engine disagreed with the authoring one. Each is fixed here and pinned in test/integration/closure-review-findings.test.ts. ## P1-1 — a multi-line closure binding fabricated a CALLS edge The worst of the four, because it reintroduced the exact defect class #2699 exists to remove. The two query channels anchor on DIFFERENT nodes by design (graph-node on the outer wrapper, scope-resolution on the inner closure) and the bridge joins them on line only. Same line, the join matches. Split across lines: $multi = function ($x) { return target($x); }; the join missed, `resolveDefGraphId` failed closed, and `resolveCallerGraphId` then CLIMBED to the parent scope — emitting `outer -> target` although `outer` calls nothing, while the real `outer.$multi` node sat with zero outgoing edges. `resolveCallerGraphId` now fails closed at the owning callable instead of climbing. If we have identified the callable that owns a call site and cannot name its graph node, crediting an ancestor is not graceful degradation — it invents a relationship. A missing edge is the correct failure direction for a graph whose consumers include `impact`. Getting there took two attempts, worth recording: the first guard keyed on the def's qualifiedName carrying the `@line:col` local marker, but that suffix is added by parse-worker for GRAPH NODE ids and scope-resolution defs do not have it, so the guard never fired. `pickCallerCallableDef` now reports whether the callable came from a child scope, and the fail-closed applies to the owning callable either way. ## P1-2 — TS constructor parameter properties were re-keyed as locals A REGRESSION against the base, not merely an incomplete fix. Admitting `Property` to the position-qualified set made the enclosing-callable walk reach the constructor's `method_definition` THROUGH the parameter list — a LOCAL_SCOPE_BODY hit that lands before any class boundary — so `constructor(private readonly port: Port)` produced `Property:svc.ts:Service.constructor.port@2:14` instead of `Service.port`. That silently empties the slot `impact`, `rename` and FTS address while the class still asserts HAS_PROPERTY against it, and it is the Angular/NestJS DI idiom. A real instance exists in this repo at src/core/group/service.ts:304. parse-worker.ts already computed the correct exemption (`isFunctionLocalProperty`, lines 2245-2257) two lines above; the new ternary discarded it. Now reused, so the owner-edge decision and the id decision cannot disagree. ## P1-3 — Dart top-level and `final` closures were never call sources The rule matched only `initialized_variable_definition`, Dart's FUNCTION-LOCAL shape. A top-level `var` is `initialized_identifier` and a top-level `final`/`const` is `static_final_declaration`; the second declarator of `var f = ..., g = ...` is also `initialized_identifier`. None got a declaration capture, so `findFunctionBody` never synthesized their scope. dart/captures.ts ALREADY listed all three in bindingNodeTypes for callable-flow — the declaration rule simply did not mirror it. It does now. ## P1-4 — Ruby `do ... end` and `Proc.new` closures were uncovered `do ... end` is the dominant MULTI-LINE Ruby style and produces `(do_block)`; all three patterns matched `(block)` only. The scope channel already covered both, so these closures got a Block scope owning nothing and their calls fell through to the enclosing method. The PR's own Ruby test used the brace form, so it passed. Fixing it needed BOTH channels — tree-sitter-queries.ts had no graph-node rule for the `(call)` forms either, exactly as Rust did. Verified: brace, do/end and Proc.new are now all sources. ## Also from the review - The split-signature fallback could fire on VALID TypeScript: a `declare namespace` containing a bodyless overload made the next declaration's `export_statement` a sibling of a `function_signature`, so `send` became `internalHelper.send@2:9`. The fallback now requires the matched node to be the signature's BODY (a body holds statements; a declaration wrapper holds another signature), which separates the two without naming a grammar. - `isCallableDef` re-spelled `Function | Method | Constructor` in the same file that imports `isOverloadableCallable` and calls it three times — a NEW twin list, in the PR whose headline is a twin-list drift guard. It now delegates. - A partial edit had left a self-contradictory comment in parse-worker.ts ("Restricted to CALLABLE labels: the / Applies to VALUES as well as callables"). - eval/workflow_bench/learnings.jsonl carried a "skill": "gitnexus-plan" entry, but that skill's SKILL.md:347 states feedback is chat-only and forbids appending learnings during a planning task. Dropped; the three gitnexus-work entries are sanctioned and stay. - Ruby's lambda/proc patterns tested the method NAME only, so `MyMod.lambda { }` was captured as a closure binding. `!receiver` now constrains them. - Rust's closure work (S3) had ZERO test coverage anywhere — verified once by a throwaway fixture and never pinned. Now covered. ## Verification Full resolver sweep plus the identity/closure suites: 3017 passed / 1 skipped / 0 failed across 58 files (up from 2997 — the new tests). This is the gate that mattered for P1-1: failing closed instead of climbing could have silently deleted real edges in any language, and ~2900 resolver assertions say it did not. All EIGHT bench fingerprint gates PASS with fingerprints UNCHANGED. tsc --noEmit clean. detect_changes {staged}: 14 changed symbols, 18 affected processes, risk CRITICAL — expected, since P1-1 changes the fallthrough of `resolveCallerGraphId`, the key chain Part A measured at CRITICAL with 23 direct dependents. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 18:25:19 +01:00
Gergő Magyar	89bbdcf566	fix(ingestion): stop double-indexing const X = () => {} as Function + edgeless Const twin (#2687) (#2691)	2026-07-25 16:56:17 +01:00
Abhigyan Patwari	a84e029066	fix(eval): give vitest a writable .vite-temp inside read-only dependency mounts (#2630) ... * fix(eval): give vitest a writable .vite-temp inside read-only dependency mounts Every task verify command and every hidden oracle ends in `npx vitest run <test>`, and both run through run_verify with read_only_workspace=True. Vite transpiles a TypeScript config by writing <node_modules>/.vite-temp/<config>.timestamp-*.mjs before it loads anything, so against a read-only dependency mount vitest dies with EROFS before a single test executes: EROFS ... /workspace/gitnexus/node_modules/.vite-temp/vitest.config.ts.timestamp-*.mjs This is pre-existing and was masked: until #2627 the verify command died at `npx: not found`, short-circuiting the `&&` chain before vitest ran. Confirmed by reproducing it at that merge base with npx bypassed entirely (`./node_modules/.bin/vitest`), so it is independent of the node-prefix mount. Because it blocks the oracle as well as the authored-test verify, `resolved` stays 0/N without this. bwrap cannot create a mount point inside an already-read-only bind -- the same constraint that put SANDBOX_NODE under /opt/claude -- so overlaying a tmpfs only works if the directory already exists in the mounted bytes. It cannot be mkdir'd into the dependency snapshot after capture either: the snapshot is digest-bound and validate_dependency_binding fails closed on drift. So the empty directory is captured during dependency capture, before the manifest and both dependency digests are computed, making it part of the snapshot rather than an untracked mutation of it. The sandbox then overlays a tmpfs on exactly that path; everything else in the mount, and the whole workspace, stays read-only, and the overlay never reaches the host clone the credited patch comes from. Scoped to dependency mounts whose target basename is node_modules, so hidden oracle and skill mounts stay wholly read-only with no writable island. Note: this shifts sandbox_dependency_content_digest and sandbox_dependency_manifest_digest, so promotion evidence recorded before this change is no longer comparable. That is already true of any harness fix that changes what the sandbox exposes. Verified on the self-hosted runner through the real path -- TaskAssetCache .prepare -> stage_task_assets -> prepare_sandbox -> run_verify with the actual trivial-version-alias verify string: passed, 15/15 tests, no EROFS. Full eval suite there with GITNEXUS_REQUIRE_BWRAP_CANARY=1: 337 passed, 4 skipped. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(eval): only overlay .vite-temp where the mount source actually carries it The tmpfs overlay keyed purely on the mount target basename being node_modules, which also matched the trusted GitNexus runtime mount at /opt/gitnexus/node_modules. That mount's source is the built runtime and does not carry a .vite-temp, and bwrap cannot create a mount point inside an already-read-only bind, so the containment CI job failed: bwrap: Can't mkdir /opt/gitnexus/node_modules/.vite-temp: Read-only file system FAILED test_real_bubblewrap_runtime_mount_imports_cli_without_exposing_checkout My runner probe only exercised the dependency-mount path, so it missed this. Gate the overlay on the mount SOURCE actually containing the directory rather than on the target name. task_assets.py captures .vite-temp only into dependency-snapshot node_modules, so the overlay now fires exactly there and never on the runtime mount -- and the gate is correct by construction, since a tmpfs can only overlay a mount point that already exists in the bound bytes. Adds a regression test for a node_modules mount whose source has no captured .vite-temp (the runtime-mount shape) getting no overlay, and updates the positive test to create the directory in its mount source. Verified on the self-hosted runner: the exact failing test now passes, and the full containment selection is 124 passed, 4 skipped. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-22 10:16:25 +01:00
Abhigyan Patwari	13095bc4bc	fix(eval): mount the node prefix for npx and catch nested Claude Code bootstrap noise (#2627) ... * fix(eval): ignore Claude Code bootstrap noise nested below the workspace root The planning-phase boundary check excluded Claude Code's own sandbox-bootstrap paths only at the workspace root: workspace_snapshot tested relative.parts[0] against WORKSPACE_SNAPSHOT_BOOTSTRAP_NOISE. But Claude Code bootstraps into whatever directory it is running in, and the benchmark's task prompts cd into gitnexus/, so the same noise landed one level down as gitnexus/.claude/.cc-writes -- whose parts[0] is "gitnexus", so it was never excluded. In skill-evolution run 29861768554 that accounted for 13 of 18 sessions, each failing with error_kind plan-evidence-invalid and the identical error_detail "phase changed unauthorized workspace path(s): gitnexus/.claude/.cc-writes". The same code path also guards the review phase (runner.py:499), so review arms hit it as review-evidence-invalid. Widening the whole set to match at any depth would be wrong: it also contains package.json, package-lock.json, node_modules and the .env family, and both gitnexus/package.json and gitnexus/.claude/settings.local.json are real tracked files whose edits must still be caught. So the root-anchored rule is unchanged, and a second narrow rule matches only the entries Claude Code itself creates inside a .claude directory (.cc-writes, agents, commands) at any depth -- never .claude itself. The predicate moves into _is_bootstrap_noise so it is directly testable. It is still evaluated before pending.append, so an excluded directory is never descended into. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(eval): mount the node install prefix so npx and npm resolve in the sandbox _runtime_mount_args bound only the `node` binary itself to SANDBOX_NODE. npm and npx are not standalone binaries -- they are symlinks into ../lib/node_modules/npm/bin/*-cli.js -- so the install prefix carrying both bin/ and lib/node_modules has to be mounted for them to resolve at all. On GitHub-hosted images node lives in /usr/local/bin, whose prefix (/usr/local) is already inside the wholesale /usr read-only bind, so npm and npx came along for free and the gap stayed invisible. A self-hosted runner's actions/setup-node installs into its own tool cache, outside /usr, so only the single node file was bound. Every task's verify command is "cd gitnexus && npx tsc --noEmit && npx vitest run <test>", so in skill-evolution run 29861768554 all 18 of 18 result records carried the identical verify_output "/bin/sh: 1: npx: not found" -- no run could resolve regardless of model output. It reached the model too: the session transcripts show 12 "npm: not found" failures, with gitnexus/scripts/build.js dying on `npm ci` with status 127. Binds Path(node_bin).resolve().parent.parent read-only at /opt/claude/nodejs, a fresh target outside the already-read-only trees (same constraint that put SANDBOX_NODE under /opt/claude), and adds its bin/ to SANDBOX_PATH. The bind is skipped when the prefix already sits inside /usr, /bin, /lib or /lib64, so the already-covered case does not widen the mount surface redundantly. SANDBOX_NODE is deliberately unchanged -- sanitized_graph.py and runner_sessions.py invoke it directly. SANDBOX_PATH is now derived from SANDBOX_NODE_PREFIX so the two cannot drift, and the minimal-mounts probe asserts against the constant instead of a duplicated literal. The real-Bubblewrap npx canary lives in test_proposer_sandbox.py deliberately: test_workflow_bench.py pins the set of files carrying the canary marker, and it runs in the eval-containment-linux job, where actions/setup-node also installs into the tool cache -- so the canary exercises the real failure shape. Combines plan steps 3-5 into one commit: the mount, SANDBOX_PATH and the pinned probe assertion are one behavioural change, and splitting them would leave a commit whose asserted PATH disagrees with the mounted reality. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(eval): only bind a verified node prefix, and stop excluding .claude/agents Addresses two findings from the branch review of the two preceding commits. 1. The prefix was derived as Path(node_bin).resolve().parent.parent with no check that the layout is really <prefix>/bin/node. Probed: /opt/bin/node bound ALL of /opt (every tool cache on a hosted runner), /mnt/tools/node bound /mnt, and a bare <dir>/node bound <dir>'s parent. That last shape is not hypothetical -- the pre-existing real-Bubblewrap node canary builds exactly it (tmp_path/toolcache/node), so eval-containment-linux would have silently read-only mounted the whole pytest tmp_path inside a containment test, passing while doing it. This function exists to keep the sandbox surface minimal, so an unrecognized layout now binds nothing extra and simply leaves npx unavailable, exactly as before the mount was added. 2. CLAUDE_BOOTSTRAP_ENTRIES also excluded "agents" and "commands" on the theory that they might appear nested too; only .cc-writes ever was observed. Every excluded name is a blind spot: once a .claude directory exists (gitnexus/.claude/settings.local.json is tracked) anything written under an excluded entry is invisible to the phase-boundary check, and Claude Code loads .claude/agents relative to its cwd -- which these tasks point at gitnexus/. Probed: a planning phase could plant gitnexus/.claude/agents/planted.md with the check reporting nothing, then the work phase reads it. Narrowed to .cc-writes alone; extend the set from an observed failure, never pre-emptively. Re-probed after both fixes: the over-broad mounts are gone while a genuine tool-cache prefix carrying npm still binds; planted agents/commands content is caught again; gitnexus/.claude/.cc-writes (the real run-29861768554 failure) stays ignored; and edits to gitnexus/.claude/settings.local.json are still caught. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(eval): gate the node-prefix bind on a working npx, not on an npm directory The guard tested (prefix)/lib/node_modules/npm as a proxy for "this prefix supplies npx". Test the property actually required instead: a working npx sitting beside node in a real bin/ directory. .exists() follows the symlink, so a dangling npx correctly fails the check -- it would not survive the mount either. The "bin" name requirement stays, because it is what keeps the parent.parent derivation honest; an npx sitting directly beside node in a flat directory would make that derivation name the wrong prefix. This matters because the guard can silently disable the fix it guards: if a runner's layout failed the proxy check, the prefix would not be bound and npx would still be missing, reproducing the original failure with no signal. Testing npx directly means the guard can only pass when the bind will actually achieve its purpose. Validated against a real extracted Node distribution (the official nodejs.org tarball layout that actions/setup-node unpacks into the tool cache) staged at a tool-cache-shaped path: bin/node is a real file, bin/npx resolves to ../lib/node_modules/npm/bin/npx-cli.js, and the prefix binds while SANDBOX_NODE is preserved. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-22 08:25:46 +01:00
Gergő Magyar	eb116c8a07	fix(eval): exclude Claude Code's own sandbox-bootstrap noise from the planning-phase check (#2615) ... The first fully successful real workflow_dispatch run on the self-hosted runner (https://github.com/abhigyanpatwari/GitNexus/actions/runs/29843028596) still failed: 17/18 sessions hit error_kind plan-evidence-invalid with "phase changed unauthorized workspace path(s): .claude/.cc-writes, .claude/commands, .env, .env.development, ...". Reproduced directly on the runner (SSM, matching the real sandbox settings exactly, including enableWeakerNestedSandbox): a single trivial "say OK" prompt -- no real task, no real API key even -- is enough to make Claude Code create a synthetic package.json/lockfiles/node_modules, a full set of .env variants, and .claude/agents, .claude/commands, .claude/.cc-writes in the workspace on every single session. None of this is something the model decided to write; it's Claude Code's own internal bootstrap for running inside an already-sandboxed environment, and it happens regardless of task or prompt. enforce_phase_workspace (the planning-phase boundary check: verify the plan session touched only its one plan doc) already excludes .git for exactly this class of reason -- harness/tool noise, not substantive diff. Extends the same exclusion to the empirically-observed bootstrap set. workspace_snapshot has exactly one use (this check, confirmed via every caller), so widening its exclusion list can't hide anything in some other context that actually cares about these paths changing. Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>	2026-07-21 19:19:15 +01:00
Gergő Magyar	bba25b2103	fix(eval): bind resolved node to a fresh sandbox path (corrects #2607) (#2609) ... * fix(eval): bind the resolved node to a fresh sandbox path, not one under /usr #2607 bound the resolved `node` to /usr/local/bin/node, but that path lives inside the /usr tree that _runtime_mount_args already read-only-binds wholesale. The second real workflow_dispatch run on the self-hosted runner (https://github.com/abhigyanpatwari/GitNexus/actions/runs/29840270554) failed immediately in the bubblewrap preflight: "bwrap: Can't create file at /usr/local/bin/node: Read-only file system" -- bwrap can't create a new mount-point file inside a tree it already bound read-only when the real path doesn't already exist there on the host, which is exactly the self-hosted case this bind exists to fix. Introduces SANDBOX_NODE (/opt/claude/node), a fresh path outside every tree _runtime_mount_args binds, following the same pattern SANDBOX_CLAUDE and SANDBOX_PYTHON3 already use. Updates the two real call sites (sanitized_graph.py, runner_sessions.py) to use the constant instead of the hardcoded literal, so the fix can't drift out of sync with itself again, and re-exports it from runner.py alongside the other SANDBOX_* names for the real-bwrap tests that reference it directly. Adds a real-bwrap test (gated behind GITNEXUS_REQUIRE_BWRAP_CANARY, same as the existing ones) that copies a real node binary to a path outside every bound tree and actually launches bwrap against it -- an argv-construction test alone can't catch a bwrap-level "Read-only file system" error, only a real invocation can, and that's exactly the gap that let #2607's version of this fix through review looking correct. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * fix(eval): don't let the new real-bwrap test's node-mock break bwrap's own resolution CI caught this immediately: the new test_real_bubblewrap_runs_node_from_outside_the_bound_trees monkeypatched shutil.which to return None for anything but "node", but prepare_sandbox's own bwrap/claude resolution (_resolve_executable) goes through shutil.which too -- so the test broke bwrap discovery before the sandbox it's supposed to exercise could even be built ("SandboxError: required executable is unavailable: bwrap"). Delegate to the real shutil.which for every other name instead of blanket-returning None. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>	2026-07-21 16:09:45 +01:00
Gergő Magyar	5b906c3189	fix(eval): bind the resolved node binary into the sandbox, not a hardcoded host path (#2607) ... Surfaced by the first real workflow_dispatch run on the self-hosted runner (https://github.com/abhigyanpatwari/GitNexus/actions/runs/29836411744): every session failed with error_kind infra-error, error_detail "bwrap: execvp /usr/local/bin/node: No such file or directory", tripping the outage-streak breaker after 5 consecutive failures. sanitized_graph.py and runner_sessions.py invoke the sandboxed graph CLI at the fixed path /usr/local/bin/node. _runtime_mount_args only binds /usr, /bin, /lib, /lib64 wholesale, so that path resolves correctly when node happens to live under /usr/local/bin on the host -- true on GitHub-hosted runner images, but not on a self-hosted runner, where actions/setup-node installs into its own tool-cache directory instead (outside all four bound trees, so invisible to the sandbox regardless of what PATH says on the host). Fix lives entirely in the mount construction: resolve `node` via shutil.which (correctly picks up wherever actions/setup-node put it, since its tool-cache dir is already on PATH by the time this runs) and bind it read-only to the same fixed sandbox path the two call sites already expect. Neither call site needed to change. Backward compatible with GitHub-hosted runners, where this resolves to the same path and binds a harmless no-op self-mount. Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>	2026-07-21 15:39:56 +01:00
Gergő Magyar	5549403082	fix(eval): self-hosted skill-evolution runner + sandbox Python 3 trust fix (#2600) ... * fix(eval): move skill-evolution to a self-hosted runner and fix the sandbox's Python 3 trust gap GitHub-hosted runners hard-cap job execution at 6 hours, which is too short once a benchmark session actually invokes Skill/MCP tools for real (the --bare fix in #2584 means sessions no longer no-op). Move the job onto a self-hosted runner (5-day cap instead) and document the activation step in the workflow's own checklist. Validating the self-hosted run surfaced a real bug: gitnexus-plan sessions inside the bwrap sandbox failed with "planning must create or modify exactly one plan artifact; observed 0". Root cause: evidence-provenance.mjs's atomic plan-writer only trusts a Python 3 binary owned by root or by the current process. Inside this --unshare-user sandbox only the calling uid is mapped (root isn't), so the real, root-owned /usr/bin/python3 surfaces as the kernel's overflow uid and gets correctly refused as untrusted. Fix: provision a small, self-owned wrapper script (same pattern already used for shell-prefix) that execs the real interpreter, so the sandbox has a Python 3 candidate the existing trust check can actually accept -- without touching that security-sensitive validation logic at all. Also add visibility so this class of failure isn't quiet next time: report.md now shows why each row failed (error_kinds), not just resolved 0/1, and the benchmark now exits non-zero when an incumbent arm -- the currently-shipped skill -- resolves zero across every task, since that reads as a broken harness rather than a normal candidate miss. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * fix(eval): close the broken_incumbent_arms zero-valid-runs gap; document runner exposure tradeoff Addresses the two MEDIUM findings from the gitnexus-review-agent on this PR (https://github.com/abhigyanpatwari/GitNexus/pull/2600#issuecomment-5033363096). broken_incumbent_arms required valid_runs > 0 before flagging an incumbent, so an incumbent that fails every run with an excluded-but-non-systemic error_kind (e.g. evidence-unverified, which the outage-streak breaker explicitly resets on rather than accumulates) never accumulated a single valid run and sailed through silently -- the exact quiet no-promotion outcome this guard exists to catch, and arguably worse than the some-runs-resolved-zero case since here nothing completed at all. aggregate() never marks an excluded/unverifiable row resolved=True, so dropping the valid_runs requirement and checking resolved == 0 alone correctly covers both cases. Added a test for exactly this all-excluded scenario, which none of the existing three did. Updated the workflow's own activation checklist to reflect what's actually true now (the gitnexus-evolution environment's branch policy and the self-hosted runner are both live, codified in infra/gitnexus-evolution/ in a companion PR) and documented the exposure-window tradeoff the review flagged: the runner is stopped between runs but not destroyed/recreated per run, so it isn't fully ephemeral. Stopping already bounds the exposure window to the job's own runtime on one day out of seven; full per-job ephemeral provisioning is a deliberate non-goal for a job that runs at most weekly, revisit if that changes. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * docs(eval): remove public infra/ pointers from the activation checklist PR #2603 (the Terraform codification this checklist pointed to) got closed -- publishing the exact IAM roles, security group rules, and self-hosted runner topology for a real, live AWS account isn't safe to do in a public repo, even with no literal secrets or resource IDs in the diff. The underlying AWS/GitHub setup is unaffected and still documented privately; this just removes the now-dangling references to a directory that won't exist in this repo. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * ci(actionlint): register the gitnexus-evolution self-hosted runner label actionlint rejected `runs-on: [self-hosted, linux, x64, gitnexus-evolution]` in gitnexus-skill-evolution.yml because it can't discover custom runner labels. Register it in .github/actionlint.yaml so the Workflow Lint check passes. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>	2026-07-21 14:40:20 +01:00
Claude	bb23d2998a	test(eval): update containment-job node-version assertion to 22.18.0 ... test_eval_ci_uses_locked_uv_and_blocking_native_containment_jobs pins the eval-containment-linux job's setup-node version; move it in lockstep with the ci-tests.yml pin bumped to the 22.18 floor. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-21 10:09:35 +00:00
Gergő Magyar	52b06b2642	fix(eval): stop using --bare for arms that need Skill or MCP tools (#2584) ... --bare hard-disables the Skill tool and every mcp__* tool by Claude Code design (confirmed against the pinned 2.1.214 binary; --allowedTools cannot restore what --bare removes). Every workflow_bench arm except baseline_nomcp needs Skill and/or GitNexus MCP tools, so every one of those sessions has been silently unable to invoke gitnexus-plan/work/ review or the CE comparator skills -- the last skill-evolution run (gen 0) scored 0/3 resolution on both arms across every task with error_kind "skill-not-invoked", not because the candidate was bad but because the harness could never invoke either arm's skill at all. Only baseline_nomcp keeps --bare (it explicitly wants zero Skill/MCP access anyway). The rest drop --bare and rely on ANTHROPIC_API_KEY alone; the sandboxed HOME has no OAuth/keychain state to conflict with it, and there's no committed .claude/settings.json in this repo for dropping --bare to newly pick up. Outside --bare the built-in toolset defaults to everything (WebFetch, Task, subagents, ...), and --allowedTools only pre-approves within whatever's available -- it doesn't narrow it. Added --tools for non-bare sessions so the intended tool scope is still enforced instead of silently widening. Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>	2026-07-20 21:26:11 +01:00
Gergo Magyar	c723d420d5	fix(eval): size the buffered-fallback budget for the real graph index ... trusted_gitnexus_runtime_mounts and sanitized_graph both hand the ~290 MiB graph index through TaskAssetSnapshot.materialize(), which reflinks into each arm clone or falls back to a buffered copy under a 16 MiB budget. Neither ext4 (CI runners) nor 9p (this container) support FICLONE, so every real materialization fell to the buffered path and blew the budget instantly (CI run 29750271566). Raises MAX_BUFFERED_FALLBACK_BYTES to 512 MiB - well above the real index size, still a full 4x below MAX_TASK_ASSET_BYTES so a genuinely oversized declaration still fails closed.	2026-07-20 14:42:50 +00:00
Gergo Magyar	cd93b8da23	fix(eval): mount hooks/claude into the benchmark sandbox ... resolve-invocation.ts requires hooks/claude/resolve-analyze-cmd.cjs at module load time, reached whenever the analyze command loads. The sandbox's curated mount list never exposed hooks/, so every benchmark-arm session failed with MODULE_NOT_FOUND (CI run 29742191562). Appends the new mount after the existing six so the function's hardcoded mounts[0]/[1]/[2]/[5] validation reads stay correct. Extends the real-bwrap canary to require analyze.js directly, since --version alone never reaches the lazy import that broke.	2026-07-20 12:53:24 +00:00
Gergő Magyar	497f117075	fix(eval): drop tags from the benchmark's per-arm clone (#2579) ... Every benchmark-arm session failed with "sanitized graph snapshot preparation failed: clone has more than 1024 references; refusing incomplete sanitization" (confirmed via a real workflow_dispatch run, 29738099937, after the prior activation fixes let the proposer succeed end-to-end for the first time). make_worktree() creates each arm's throwaway clone with a plain `git clone`, which inherits every tag and branch from the source. This repo's history has grown to 1144 tags (a v1.6.9-rc.N release-candidate series) out of 1650 total refs, exceeding oracle_assets.MAX_CLONE_REFS=1024 -- a fail-closed guard in sanitize_clone_for_hidden_oracles() that refuses to proceed unless it can enumerate and delete every ref before handing a sanitized snapshot to a benchmark session (so an agent can never discover oracle answers via a ref the sanitization missed). `ref` at every call site (evolve.py, runner.py, sanitized_graph.py) is always a bare SHA or the literal "HEAD", never a branch name, so `--single-branch --branch <ref>` isn't viable (git clone's --branch requires a name). Tags are never used by the checkout fallback or by sanitization's own delete-everything behavior, so dropping them via --no-tags removes the 1144-ref majority without touching branch-fetch behavior or the existing ref/origin-ref checkout fallback, and without weakening MAX_CLONE_REFS itself. Verified against the real repository (not just the test fixture): cloning /workspace (1650 refs, 1144 tags) via the fixed make_worktree() now produces a clone with 237 total refs and 0 tags. Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-20 13:25:16 +01:00
Abhigyan Patwari	6b1c4d4540	fix(eval): surface stdout tail on session failure, not just stderr (#2577) ... The proposer's second real-run failure (after the ENV_SCRUB permission fix landed) exited 1 with subtype "success" and an EMPTY stderr_tail -- opaque: the downloaded CI artifact showed num_turns:1, cost_usd:0, tokens:0, duration_s:0.1, meaning the session terminated before any real model turn completed (consistent with an early, pre-flight-style failure), but nothing in the persisted record said why. The actual JSON event stream (permission_denials, tool_use/tool_result, is_error) lives in stdout, which run_managed already captures as proc.stdout_tail -- it just never made it into the session's error_detail. Add it there, bounded and truncated the same way stderr_tail already is. It flows through evolve.py's existing whole-record redaction before being written to disk / the uploaded artifact, so this closes the diagnostic gap without a new blind CI dispatch: the next failure of this shape is readable directly from the artifact. Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-20 12:06:02 +01:00
Abhigyan Patwari	f832239462	fix(eval): pre-approve proposer tools under Claude Code 2.1.214 ENV_SCRUB hardening (#2576) ... The first real skill-evolution run got past task binding, then the proposer session exited 1 with "Permission mode forced to default — CLAUDE_CODE_SUBPROCESS_ENV_SCRUB is set (allowed_non_write_users hardening)". On 2.1.214 the permission resolver unconditionally forces permission mode to "default" whenever CLAUDE_CODE_SUBPROCESS_ENV_SCRUB is set — `--permission-mode dontAsk`, settings `permissions.defaultMode`, and `autoAllowBashIfSandboxed` are all ignored for the mode decision. The proposer runs headless `-p --bare` where Bash is its only writable tool (it writes the candidate overlay); under forced "default" Bash was no longer auto-approved, so the session blocked. We cannot set ENV_SCRUB=0 (it scrubs the Anthropic auth token from the sandboxed proposer's Bash subprocesses). Instead, align with the forced mode: pre-approve the proposer's exact tool surface via settings `permissions.allow` (["Read","Grep","Glob","Bash"]) — under "default" a tool runs without a prompt iff it matches an allow rule — and stop requesting a non-default mode so no warning fires. ENV_SCRUB and the full sandbox filesystem/network lockdown are unchanged. The real-binary containment canary is updated to the new invocation (no --permission-mode) so the CI job is the authoritative empirical gate, and a fast unit assertion pins the new permissions.allow / absent defaultMode. Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-20 11:25:49 +01:00
Gergő Magyar	becac9a5d3	feat(eval): run the skill-evolution loop online (#2571) ... * feat(eval): run the skill-evolution loop online Add a scheduled + dispatch-gated workflow that runs the offline propose -> benchmark -> gate loop (workflow_bench.evolve) in CI with the pinned Claude canary runtime and bubblewrap containment, uploads the benchmark evidence as an artifact, and on a gate-passed promotion opens a human-reviewed PR via the release App token. The applied overlay is bounded to the canonical skill tree and its shipped mirrors; any escape fails the run instead of reaching a PR. The scheduled lane ships disabled behind GITNEXUS_EVOLUTION_ENABLED and requires the new GITNEXUS_BENCH_AUTH_TOKEN secret (benchmark sessions bill real API usage), mirroring the review agent's staged rollout. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): restructure promotion-PR script so no lint suppression is needed Replace the inline single-quoted credential helper with a GIT_ASKPASS file written via a quoted heredoc (the App token still reaches git only through step env at push time), and assemble the PR body from quoted heredocs plus double-quoted printf instead of a backtick-laden single-quoted template. Every run script in the workflow now passes shellcheck with zero findings and zero disables; the body and askpass rendering are smoke-tested. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): apply gate-passing overlays in the evolution loop The loop invoked workflow_bench.evolve without --apply, so apply_promoted_overlay (its only working-tree writer, gated by `if args.apply:`) never ran. git status stayed clean, promoted=false was emitted every run, and the App-token/PR-open steps were unreachable dead code — a gate-passing run went green as "No promotion this run". validate_promotion_for_apply already runs before the apply gate, so adding --apply lets a passing candidate reach the tree without weakening the deterministic gate; the boundary check then confirms it stayed in the skill trees. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): provision ~/GitNexus so the benchmark repo resolves on CI Every scenario in tasks.scenarios.yaml addresses the target repo as ~/GitNexus; runner_tasks.py resolves it with expanduser().resolve() then `git -C <repo> rev-parse`, which raises when the path is missing. On a hosted runner the checkout lands in $GITHUB_WORKSPACE and nothing created ~/GitNexus, so the first real run failed at task-binding. Symlink ~/GitNexus -> $GITHUB_WORKSPACE before the loop. The checkout uses fetch-depth: 0 (full history for the parentless clone), and the benchmark only clones the repo copy-on-write and mounts deps read-only, so the checkout is never mutated. GITNEXUS_BENCH_ORACLE_ROOT stays unset — it defaults to the in-repo oracles dir and is staged by the harness. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): harden promotion summary output and PR branch recovery Three fixes to the promotion-detection and PR-open steps: - GITHUB_OUTPUT summary used a fixed `PROMOTION_EOF` heredoc delimiter; a value containing that marker on its own line could close the block early and inject output keys. Use a per-run random delimiter, matching the pattern already in tree-sitter-upgrade-readiness.yml. - The summary concatenated every generation's promotion.json (including rejected ones), so the PR body could show a losing generation's decisions. The loop returns on the first promotion, so emit only the highest-numbered gen-N/bench/promotion.json — the decision that fired. - The promotion branch name omitted the run attempt. GITHUB_RUN_ID is stable across re-runs, so a re-run after push-succeeds/PR-create-fails could never push. Include ${GITHUB_RUN_ATTEMPT} (the artifact name already does). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): least-privilege the promotion App token and gate on an Environment The Mint-App-Token step passed only app-id + private-key, so the minted token inherited every permission the Release App installation holds (including Workflows: write) — far more than "push a branch, open a PR". Switch to `client-id` (as publish.yml does) and request only permission-contents: write + permission-pull-requests: write. Bind the job to a protected Environment (gitnexus-evolution) so promotion runs can be gated server-side. workflow_dispatch runs the workflow and in-tree evolve.py from the *dispatched ref*, so a code-side ref guard is removable by the dispatched branch itself; an Environment deployment-branch rule (main only) is the boundary that holds. The admin steps to create it and scope the secrets are documented in the activation checklist. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(ci): correct upload-artifact pin comment and add shell strict-mode - The upload-artifact SHA 043fb46d… is v7.0.1 (labeled so in the sibling workflows that pin it); the comment mislabeled it # v6.0.0. Correct the comment; the pin is unchanged. - Add `set -euo pipefail` to the two build steps that lacked it, matching every other run block in the file (GitHub's default shell already sets -eo pipefail; this adds -u and consistency). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * docs(ci): complete the skill-evolution activation checklist - Add RELEASE_APP_ID / RELEASE_APP_PRIVATE_KEY to the required-secrets checklist (the Mint step hard-fails without them on a promotion) and the App-install-scope verification. - Document the protected Environment admin step and why it is the real boundary for the workflow_dispatch ref-secret exposure. - Note that workflow_dispatch runs the billing loop regardless of GITNEXUS_EVOLUTION_ENABLED. - Justify the weekly cron against the README's ~90-day guidance and note the 355-minute timeout ceiling. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * fix(eval): redact API tokens from diagnostic fields before artifact upload results.jsonl (runner.py) and proposer-session.json (evolve.py) serialize session records whose error_detail can carry a stderr_tail that echoed the API key. Transcripts are redacted before persistence, but these two sinks were not, and both land in the 14-day evolution artifact. Run each record's serialized JSON through the existing redact_text with the run's auth token before writing. Scoped to these diagnostic sinks only: the promoted overlay and proposal.md are left untouched (the overlay is the applied artifact and must stay byte-identical for apply and the shipped-skills-sync guard). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * test(ci): add a contract test for the skill-evolution workflow No test exercised this workflow's path, which is why both P1 blockers (missing --apply, unresolvable ~/GitNexus task repo) reached production. Parse the workflow YAML and assert the structural contract: --apply is passed, the task repo is provisioned, the promotion branch carries the run attempt, the App token is permission-scoped and the job is Environment- gated, the output summary uses a random delimiter and a single generation, the artifact pin is labelled correctly, and every multi-line shell step sets strict mode. Follows the review-agent-workflow.test.ts precedent. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ * feat(ci): run the proposer on its own (stronger) model One `model` input drove both the benchmark arms and the proposer/diagnosis session. Split them: `model` stays the benchmark arms (match the model your skill users run, so a promotion is valid for them and the tasks aren't ceiling-saturated), and a new `proposer_model` input runs the proposer — the harder meta-reasoning task that writes the candidate skill, and only one session per generation, so a stronger model is cheap here. evolve.py already supports --proposer-model; the workflow just didn't expose it. Defaults: arms = claude-sonnet-5, proposer = claude-opus-4-8 (both overridable via workflow_dispatch). The weekly cadence bounds the added spend. Contract test asserts the split stays wired. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-20 05:37:07 +01:00
Gergő Magyar	8b5057f325	feat(skills): GitNexus Engineering Tool Kits (#2566) ... * feat(skills): add ce-plan — GitNexus+PDG implementation-planning skill Adds .claude/skills/ce-plan: a planning-only skill that builds implementation-ready plans from GitNexus graph navigation (query/context/ impact/trace), bounded statement-level PDG slices (pdg_query, impact mode:pdg, explain), and targeted source verification, with a context ledger to prevent repeated reads and a machine-readable implementation context pack (stable contract for a future ce-implement). Whitelisted in .gitignore and registered in AGENTS.md and CLAUDE.md outside the auto-managed gitnexus block. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills): apply ce-plan validation findings (tool contract, consistency, conventions) Tool contract: impact mode:'pdg' shape now includes the schema-required direction param; CDG branch sense documented as the result 'label' field (reason is cypher/raw-edge only); explain caveats corrected to its real false-negative classes (cross-function TAINT_PATH is modeled). Consistency: PDG slice homed in working memory (ledger keeps one-liners); depth knob defined and category-overrides-baseline ordering stated; call_depth (consumed by nothing) and content-hash bookkeeping dropped; Never section folded into Hard rules; Phase 3 deduplicated to a pointer; allowed-repeat escalations defined; budget/discard accounting clarified; verification-commands gathering added to Phase 4; open_questions added to the context pack. From scenario runs: plans now pin the verified-at HEAD commit and index freshness in a header, tag claims [verified]/[graph]/[inferred]/[assumed], quote load-bearing tool output, prefer pre-hook-carrying npm scripts, and support an out:<path> destination override; output path defined as the Phase 1 target repo root. Conventions: AGENTS.md 1.9.0 / CLAUDE.md 1.4.0 changelog rows + metadata bumps; future ce-implement qualified as future. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): rename ce-plan → gitnexus-plan; add cross-CLI (Codex) entrypoints Renames the skill dir, frontmatter, output filename convention, plan H1 (GitNexus Engineering Plan), the future executor handle (gitnexus-implement), the .gitignore whitelist entry, and all AGENTS.md/CLAUDE.md references. Follows the pr-swarm-review cross-CLI pattern: SKILL.md is the canonical CLI-neutral spec, AGENTS.md § Engineering planning is the Codex/any-agent entrypoint, and the README documents the optional user-level ~/.codex/prompts/gitnexus-plan.md slash command plus an invocation matrix. Skill prose de-branded from Claude Code (agent-neutral verification layer). Also fixes two post-review README contradictions: the anti-reread claim now names the ledger's allowed escalations, and 'read-only by contract' is now 'planning-only' (the skill writes exactly one repo file — the plan); the scope-creep rule and template §12 now agree on where deferred follow-ups land. Drops the stale plugin-collision limitation. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(skills): document Codex user-level install path for gitnexus-plan Codex discovers SKILL.md skills from ~/.agents/skills (same path the other gitnexus-* skills install to); README now documents the cp install plus the optional ~/.codex/prompts slash-command file, with the prompt body preferring the repo copy and falling back to the user-level install. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): gitnexus-plan freshness gate + active PDG-layer refresh Freshness is now a Phase 1 gate, not advisory: under the default freshness:strict, a stale index is refreshed once per planning session via node .gitnexus/run.cjs analyze --index-only (appending --pdg when the task will reach the PDG phase), then the context resource is re-read. A missing PDG layer likewise triggers the one permitted --index-only --pdg refresh and re-probe instead of a passive recommendation. freshness:accept (or a failed/impractical refresh) preserves the old behavior: plan on the stale graph, source-weighted, labelled in the plan header. --index-only is the load-bearing flag choice — it suppresses all file generation, so the planning-only contract holds (only the .gitnexus store changes). Ledger gains an index_refresh record; plan header states fresh / refreshed / refresh-skipped-with-reason. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): gitnexus-plan runner build check before freshness refresh When the target repo builds the analyzer from its own source (bin → dist/ mapping, as gitnexus/ does), the Phase 1 freshness gate now verifies dist/ is current before running the analyze refresh — rebuilding via the package's build script when any analyzer source file is newer than the built entrypoint — and prefers that freshly built CLI. Otherwise a stale dist re-indexes with outdated extraction logic and the 'fresh' index lies. Rebuilds are recorded in the ledger's index_refresh; the PDG-phase refresh inherits the same check. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): add gitnexus-work executor and gitnexus-lfg pipeline gitnexus-work executes a gitnexus-plan as verified atomic commits: consumes the §11 implementation_context pack, drift-checks the plan's evidence pin against HEAD, re-verifies assumptions before relying on them, runs impact before every symbol edit and detect_changes before every commit (repo mandates), builds tests from the plan's scenarios, and routes structural drift back to gitnexus-plan Deepen mode instead of coding around it. gitnexus-lfg is a thin orchestrator: gitnexus-plan → blocking user gate (deepen / proceed / stop, deepen loops allowed) → gitnexus-work → review via the existing gitnexus-pr-review skill (open PR, else branch diff vs default). One bounded fix cycle for review findings; never pushes or opens a PR on its own. gitnexus-plan gains a Deepen mode (re-run freshness gate, escalate to depth:deep, re-verify graph/inferred/assumed claims toward verified, rewrite the same file); its 'future gitnexus-implement' placeholder is retired in favor of gitnexus-work. Registered via .gitignore whitelists, AGENTS.md 1.10.0 (section renamed to Engineering planning & execution), CLAUDE.md 1.5.0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills): apply cross-skill review findings to the gitnexus skill family Two P1s: gitnexus-plan Deepen mode now re-anchors before re-pinning (diffs the old evidence pin over every [verified]-claim file and re-reads or downgrades before the header moves — moving the pin without this laundered stale claims as verified); the index-refresh budget is stated once in Phase 1 (one --index-only refresh plus at most one Phase 3 --pdg upgrade per session, Deepen = its own session) with ledger and pdg-slice deferring to it. Contract fixes: gitnexus-work's drift check now covers every file the pack cites (not just files_to_modify) and parses the full pack incl. primary/related symbols and acceptance_criteria (walked in Phase 4 alongside §13); a pre-completed check skips §7 steps already landed and Deepen gains a reconcile-execution-state step, closing the mid-execution route-back loop; pack assumptions must name what to check and how. lfg: Lane 4 passes the merge-base to detect_changes compare (two-dot diff misattributes upstream commits when default advanced), branch-diff is the stated normal case, oversized review findings route to the plan gate instead of overflowing direct mode, the one-fix-cycle cap is explicit on re-run, and headless runs end at the plan gate with the plan as deliverable. work: blank mode narrowed to *gitnexus-plan*.md with a re-execution guard, direct-mode discipline spelled out, branch meaningfulness defined against the plan slug, and the plan document is committed as the branch's docs commit (review diff includes it). Planning-only contract now names the dist/ rebuild as the second permitted state change; Phase 5.1 names the four claim tags; stale AGENTS.md anchors fixed. Known latent issue left untouched: gitnexus/gitnexus-pr-review pairs a three-dot example with a two-dot detect_changes compare — that skill is also shipped by the plugin, so fixing it here would drift the copies; lfg compensates by passing the merge-base. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): ship the engineering skill family with the gitnexus package npm i -g gitnexus users now get gitnexus-plan / gitnexus-work / gitnexus-lfg: the three skills are added to gitnexus/skills/ in directory form (SKILL.md + references/), which installSkillsTo already enumerates dynamically and copies recursively to every editor target (~/.agents/skills for Codex, Cursor, OpenCode, Qoder, ...) on gitnexus setup — uninstall enumerates the same root, so removal stays clean. The Claude Code plugin channel (gitnexus-claude-plugin/skills/) carries the same copies plus the standard per-skill mcp.json. Global-install support in the skill text: gitnexus-plan Phase 1 now resolves the analyzer runner explicitly — node .gitnexus/run.cjs analyze when the project has a runner, else gitnexus analyze (installed CLI), else npx gitnexus analyze — and all analyze mentions route through it, satisfying the skills-steering policy (#1939/#1945) which sweeps the plugin copies. New drift guard test/unit/shipped-skills-sync.test.ts asserts the npm and plugin copies stay byte-identical to the canonical .claude/skills/ family (plugin = canonical + mcp.json), same discipline as run.cjs ↔ resolve-invocation.ts. skills-steering + shipped-skills-sync: 11/11 green. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): workflow_bench — measure the skill workflow's token savings Benchmarks gitnexus-plan → gitnexus-work against a baseline agent (--disallowedTools Skill) on identical tasks, in fresh detached worktrees, using real headless Claude Code sessions; every number comes from the CLI's --output-format json usage report (field names validated against a live 2.1.207 session). Reports per-arm medians (input/cache/output tokens, cost, wall time, turns), a savings row, and resolve status from a per-task verify command — savings on failed tasks are flagged, not celebrated. Per-task setup hook prepares fresh worktrees (deps); --permission-mode bypassPermissions (default) lets sessions run unattended in the throwaway trees. Free-model support: --base-url/--auth-token/--model route headless sessions through any Anthropic-compatible endpoint; free-model.litellm.yaml is a ready litellm-proxy template for OpenRouter :free variants or local Ollama, so benchmarking burns no paid tokens (README documents rate limits and the small-model skill-following caveat). Harness validated end-to-end with a stub CLI (worktree lifecycle, both arms, plan→work chaining, verify, aggregation, report) and 4 pytest units for the pure aggregation/savings/report helpers. AGENTS.md 1.11.0. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record first workflow_bench calibration run Trivial-task calibration (add -V alias): both arms resolved; workflow arm ~4.3x baseline cost — the documented overhead-dominated regime, recorded so the regime boundary is empirical rather than asserted. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): workflow_bench scenario matrix — arm variants, task classes, churn Ground-base measurement across scenarios: tasks.scenarios.yaml spans four labeled classes (trivial → investigation-bug → investigation-feature → cross-module) with deterministic verifies (prescribed test files). New arms: workflow_direct (gitnexus-work direct mode — the middle option that locates the routing boundary lfg's gate and work's triage encode) and baseline_nomcp (no skills AND no graph tools — separates workflow-discipline value from GitNexus-tool value; off by default). Records now carry task class and diff churn (files/+ins/−del vs the starting commit) as an over-engineering proxy; the report renders a class column and per-arm savings rows vs baseline. 5 pytest units + stub-CLI e2e of the full three-arm matrix. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record workflow_bench ground base; fix churn measurement bias Ground base (3 classes x 3 arms, n=1/cell): every arm resolved every task — pass/fail quality saturates at this difficulty, making the comparison pure cost. Full plan→work never amortized its ~$9-11 fixed cost on tasks a baseline finishes in ≤35 turns (−211% to −333% cost); workflow_direct sits near baseline (−15% to −55%, once faster wall) with more test coverage. Routing implication recorded: direct mode/plain agent below this scale, full workflow for cross-module / multi-session / plan-as-deliverable work. The cross-module cell and multi-run variance are the next measurements. Churn fix: git add --intent-to-add -A before diffing (arms that never commit no longer undercount new files) and :(exclude)docs/plans (the committed plan doc no longer inflates workflow churn); this run's churn numbers predate the fix and are omitted from the recorded table. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * perf(skills): cost-optimize the workflow from measured ground base Every optimization targets a measured fixed-cost component (eval/workflow_bench ground base: workflow arm −211% to −333% vs baseline, all tasks resolved): - Plan form is category-priced: compact form (core sections w/ § anchors preserved, ≤80 lines excl. pack, mini-pack subset of the context pack) for narrow/default categories; the full 13 sections only for deep work (refactor/security/performance/concurrency/architecture). A compact plan outgrowing its cap reclassifies to full rather than overflowing. - Freshness gate is category-priced: compact categories default to accept (source-weighted, refresh only when a graph claim becomes load-bearing); strict stays the default for full-plan categories — the rebuild+re-index was the largest single fixed cost. - Turn economy: per-category tool-call budgets (~10 to ~45; architecture uncapped); budget exhaustion routes open questions to §12 instead of more digging. - gitnexus-work fast path: HEAD == evidence pin → skip all citation re-reading (the pin's entire point); mini-pack fields tolerated. - lfg Lane 1 boundary triage: tasks below the measured ~35-turn boundary get offered gitnexus-work direct mode before the plan lane is spent. Copies re-synced (npm skills/, plugin, ~/.agents); steering + sync guards green. Re-measurement of the workflow arm follows to verify the numbers actually improve. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): record optimization re-measurement — inv-bug workflow cell −20% cost Same task, same conditions, post-830a0459 skills: $14.56→$11.70 (−20%), 83→72 turns, cache_read −24%; verified in-transcript that the compact form, turn budget, and skipped rebuild/re-index all fired. Wall +15% from a work- session test-debugging tail (n=1 variance). Regime unchanged (~3.5x baseline on this class) — routing rule stands. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): per-arm clone isolation — worktree ref-namespace leak contaminated an arm The cross-module workflow_direct cell reported an impossible 28-turn solve with churn byte-identical to the workflow arm: git worktree add shares the repo's ref namespace, so the workflow arm's slug branch (created by gitnexus-work Phase 2) survived worktree removal and the direct arm found and adopted the completed work. Arms now get isolated git clone --shared copies (object store via alternates, refs clone-local — agent branches and stashes die with the clone; origin/<ref> fallback for non-default refs). Leaked branch deleted; baseline arm verified clean (0 branch references in its transcript); cell marked invalidated pending re-run. Records the valid cross-module cells: workflow $18.32 vs baseline $18.03 (premium −1.6%, vs −211%..−333% on smaller classes) — fixed costs amortize at this scale, with a less destructive diff and a plan artifact as bonus; resolve rate still tied. Churn fingerprinting is what caught the contamination — noted in the README as an integrity check. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(eval): complete cross-module cell — direct mode wins 47% cost / 56% wall Clean clone-isolated re-run: workflow_direct resolved the hardest class at $9.53/52 turns/15m vs $18.03/98/34m baseline and $18.32/107/37m full workflow. The measured story across all four classes: the execution discipline (gitnexus-work) is the consistent sweet spot and delivers real token savings on hard tasks; the planning pass buys its artifact, not same-session savings. Resolve rate tied everywhere (n=1/cell caveat). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): add trajectory-gated skill evolution (#2431) - Pair prompt candidates with incumbent workflow arms - Gate promotions on pinned-model quality and efficiency - Expire router evidence and document its lifecycle * fix(eval): allow pr-review skill candidates * feat(skills): rename and generalize GitNexus review * feat(eval): external-comparator and review arms for workflow_bench - ce_workflow / ce_workflow_direct: compound-engineering ce-plan/ce-work arms prompted with the same structure as the gitnexus arms - review / ce_review: gitnexus-review vs ce-code-review on an identical diff applied by the task's setup - plan handoff is snapshot-based: committed example plans in docs/plans/ tie on clone mtimes and broke the name-glob pick (executed a stale plan) - verify output tail is recorded per run and the final working-tree patch is kept, so failed rows are diagnosable after the clone is destroyed Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(skills,eval): address #2431 review — data-safe rename migration, fail-closed bench evidence - setup: never delete a legacy renamed skill dir — the installer cannot prove ownership (users customize or hand-write skills under these names); warn with the path instead, and the test now asserts survival - workflow_bench: fail closed when a session's --output-format json report is empty, malformed, or missing usage fields — an exit-0 shell with no parseable usage no longer counts as measured evidence (5 parametrized regression tests) - workflow_bench: document the trust model prominently (task setup/verify are shell-executed, sessions run bypassPermissions with the parent env, candidate overlays are prompt injection surface) in README + docstring - free-model.litellm.yaml: master_key from LITELLM_MASTER_KEY env instead of a static token; loopback-binding warning - ci: run the eval workflow_bench pytest suite on ubuntu (pytest+pyyaml only — no full eval stack) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): demand observed foreground verification in headless work-arm prompts In a headless -p session there is no later turn: a work arm backgrounded its slow test run, scheduled wakeups that can never fire, and reported done while two of its tests failed. All four work-arm prompts (both skill families, symmetric) now require verification output to be observed inside the session. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): ask plan depth up front instead of offering deepen afterwards gitnexus-plan Phase 0 now asks one blocking question in interactive sessions — quick / standard / deep, mapped onto the existing depth/form/ freshness knobs — when the invocation carries no explicit depth signal. Explicit knobs and headless runs skip the question (category posture unchanged, so benchmarks and automation behave as before). gitnexus-lfg's plan gate slims to proceed/stop: depth was already the user's up-front choice, so deepening is no longer offered by default — an explicit deepen request at the gate and executor route-backs still run Deepen mode, which remains the mechanism for strengthening an existing plan document. All shipped copies resynced (npm skills/, Claude plugin); AGENTS.md 1.13.0 and CLAUDE.md 1.7.0 pointers updated, including the analyzer's regenerated index-stats block at this branch's head. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): taint pass, expert lenses, and post-work index refresh gitnexus-review gains a PDG-backed taint-and-dependence pass (explain + pdg_query, --pdg folded into the stale refresh on trust-boundary diffs) and an Expert lenses section: domain reviewers derived from the graph's clusters plus four cross-cutting lenses (architectural fit, language conformance per the repo's own contract, Definition of Done, simplicity), dispatched once after the evidence-gathering steps and scaled to the diff. gitnexus-work Phase 4 now refreshes the knowledge graph after the DoD walk via the resolved-runner ladder with analyze --index-only, so the lfg review lane and later sessions query the finished work without dirtying the tree. lfg's threshold-governance paragraph moves to its README; eval citations are tagged as measured in the GitNexus repo. All shipped copies re-synced. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(cli): remove legacy gitnexus-pr-review on uninstall; cover the rename migration uninstall's removal set now includes LEGACY_SKILL_DIR_NAMES derived from RENAMED_SKILL_DIRS, so a pre-rename install is cleaned up instead of orphaned. The rename warning gains behavioral coverage (fires with a legacy dir present, silent without), and shipped-skills-sync asserts legacy names stay absent from every shipped tree. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(eval): metric provenance, error-kind rows, skill-invocation verification, gate noise floor The promotion gate defaults to cost_usd (the only metric that includes subagent spend); token metrics carry an explicit main-loop-only warning in the report and promotion.json. Rows are classified by error_kind (session-error / verify-failed / infra-error), excluded from efficiency medians, and the gate requires equal valid-run counts. Each session's transcript is scanned for the expected Skill invocation and fails closed on a verified miss; a one-run resolution edge no longer promotes (noise floor). Per-run timeouts and setup failures record an infra-error row instead of aborting the sweep. Overlays touching skills no candidate arm exercises are rejected up front. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: fix skill routing paths, version headers, and skill rosters Routing tables point at the tracked direct skill paths (matching the post-#2434 generator output), AGENTS.md/CLAUDE.md headers match their latest changelog rows, the 1.12.0 row describes what the migration actually does, package/cursor READMEs list the full shipped skill roster, and the swarm READMEs describe /gitnexus-review's expert lenses instead of calling it single-agent. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * ci: drift-guard workflow for skill copies; pin eval pip deps; track docs/plans ci.yml ignores '**.md', so an md-only skill edit would merge without the shipped-skills-sync test running — skill-sync.yml triggers exactly on the guarded trees. The eval job's pip install is version-pinned, and docs/plans/ is unignored so gitnexus-plan output can be committed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(ci): keep the runner-invocation literal in gitnexus-review; add concurrency block to skill-sync skills-steering requires skills with a stale-index hint to carry the exact 'node .gitnexus/run.cjs analyze' form — restore it with the fallback ladder as a parenthetical instead of replacing it. skill-sync.yml gains the top-level concurrency block the workflow-convention check enforces. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(skills): token-economy guidance for expert lenses Merge lenses that ground in the same material into one reviewer, and use cheaper model/effort tiers for mechanical lenses where the harness offers them, reserving the strongest engine for adversarial judgment. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test(eval): isolate transcript home on Windows Ensure workflow_bench transcript tests set USERPROFILE alongside HOME so Path.home() resolves to the temporary test home on Windows. * docs(skills): fold PR #2522 execution learnings into review/work/plan Eight incident-backed hardenings from running the full skill cycle (review -> plan -> work, 28-finding fix series) on PR #2522: gitnexus-review: - Expert lenses execute the code under review on candidate failing shapes (empirical probe outranks source reading — every HIGH the language lenses found came from a probe, not a read). - Step 7 re-runs the exact CI check for refreshed baselines/fingerprints (a stale committed artifact is invisible in the diff; caught a red benchmarks arm). - Step 8 treats version/invalidation constants as review surface (INCREMENTAL_SCHEMA_VERSION class recurred verbatim from #2494). gitnexus-work: - Step 4 proves regression tests discriminate against the pre-fix tree. - Step 5 rebuilds executed build output before every verification run (parse workers load dist/; a correct fix 'failed' until rebuilt). - Step 6 makes stage -> detect_changes -> commit one unbroken sequence. gitnexus-plan: - Phase 0 seeded-evidence mode: plan FROM a completed review's verified findings instead of re-running the graph ladder. - Template §7: fingerprint/golden-guarded output rebaselines once, at the series tip. All distribution copies resynced; shipped-skills-sync + skills-steering 24/24 locally. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(eval): close the skill-evolution loop with an automated proposer driver workflow_bench.evolve adds the three arrows the README described as manual: a proposer session that turns loser trajectories (results.jsonl rows, transcripts, patches, the learning queue) into ONE bounded candidate overlay, a driver that iterates propose -> paired benchmark -> deterministic gate up to --generations, and an --apply step that copies a promoted overlay onto the canonical skills and shipped mirrors as a working-tree diff. The trust boundary is unchanged: overlays re-validate through candidate_overlay_files before any benchmark or apply consumes them, and committing, CI, and the PR merge stay human. learnings.jsonl is gitignored: it is machine-local evidence, like the session transcripts it complements. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs(skills): route live-task friction into the evolution learning queue Each family skill gains a short 'Skill feedback' section: on friction with the skill's own instructions, append one JSON line to eval/workflow_bench/learnings.jsonl (GitNexus repo only) — never self-edit the skill from a live task. The proposer in workflow_bench.evolve consumes the queue as hints; a learning reaches a shipped skill only by beating the incumbent on the paired benchmark. All shipped mirrors re-copied byte- identical. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * ci(tests): run the evolve helper tests in the eval pytest job test_evolve.py needs only pytest+pyyaml, same as the harness tests the job already runs — without this line the new module had no CI coverage. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(ci): comment-triggered GitNexus review agent for PRs '@gitnexus review' from a maintainer (OWNER/MEMBER/COLLABORATOR; the action re-validates write access) runs the repo's gitnexus-review skill headlessly against the PR and posts the review as a sticky comment — remote triggering with no local setup. Read-only by construction: contents: read token, Write/Edit and web tools disallowed, Bash allowlisted to git reads and the gitnexus CLI; analyze parses PR code with tree-sitter, never executes it. Requires the ANTHROPIC_API_KEY repository secret; activates once the file is on the default branch. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * feat(ci): dispatch lane + existing OAuth secret for the review agent Align with claude.yml: same action pin and the CLAUDE_CODE_OAUTH_TOKEN secret the repo already carries — no new secret to configure. Add a workflow_dispatch lane (PR number input) so the agent can be triggered from the Actions UI and tested before the issue_comment trigger reaches the default branch. Allowlist gh pr view/diff and gh api, which the review skill uses to pin PR SHAs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(ci): close a fork-PR RCE vector in the review agent's tool allowlist A live headless run of the exact workflow session against PR #2431 (66 turns, full gitnexus-review pass) surfaced a real HIGH-severity confused deputy: .gitnexus/ is gitignored, not blocked — a fork PR can commit its own .gitnexus/run.cjs, issue_comment checks out PR-head content, and the skill's runner ladder tries 'node .gitnexus/run.cjs analyze' first. That would execute fork-controlled JS inside a job holding CLAUDE_CODE_OAUTH_TOKEN and a write-scoped GITHUB_TOKEN — the opposite of the 'PR code is read, never executed' claim in the workflow's own header. Fix: drop the run.cjs allowlist entry so analyze always resolves through npx gitnexus (npm registry, not the checked-out tree); the skill's documented fallback mode covers the resulting graceful degradation. Also drop 'gh api' (not read-only — accepts -X POST/PATCH/DELETE) and downgrade pull-requests: write to read (comment posting only needs issues: write; the prompt already forbids formal review submission). Same session flagged a latent evolve.py bug: select_evidence's cost sort used dict.get's missing-key default, which doesn't cover an explicit JSON null in a foreign --seed-results row and crashes proposer setup with TypeError. Guarded with 'or 0.0' and added a regression test. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix: harden PR review and evolution trust boundaries * ci: follow workflow concurrency convention * fix(eval): make terminating error paths explicit * fix: unblock hardened review runtime checks * test: make containment canaries deterministic * test: expose Claude canary tool failures * fix: adapt clean shell environment for Claude * fix(eval): accept the runner's transcript source key in evidence preflight The proposer evidence preflight required transcript-artifact metadata to be exactly {path, sha256, bytes}, but the runner stamps a fourth provenance key (source=parent-captured-stream-json). Any --seed-results or generation>=2 run therefore aborted with SandboxError before proposing or promoting. Pin the producer literal as PARENT_EVENT_STREAM_SOURCE and validate it in the metadata check, and round-trip real producer output through sum_sessions into the preflight so the schema can't drift again. * fix(eval): treat an unmeasured session cost as unavailable, not $0 well_formed validated only the nested usage block, so an otherwise-successful session missing total_cost_usd was recorded as cost_usd=0.0 — and cost_usd is the default promotion metric (lower wins), so a cost-less session scored as free and could win promotion it never earned. Extract cost via measured_cost() (None on absent/garbage, a measured 0.0 preserved), propagate None through sum_sessions/aggregate/savings/report, and have the gate refuse to rank on a metric that was not measured on every run in both arms. * fix(eval): warn when ranking on the main-loop-only num_turns metric num_turns comes from the CLI's top-level usage (main-loop session only), like output_tokens, but selecting it emitted no metric_warning — so a subagent-heavy candidate could look artificially efficient. Add num_turns to MAIN_LOOP_ONLY_METRICS and broaden the warning to cover turns. * fix(eval): fail closed when an overlay adds a file with no committed base An overlay adding a new .md under gitnexus-{plan,work} passes the structural overlay checks but has no committed base for committed_destination_base_digests to bind against, so it raised an uncaught ValueError that crashed the evolve driver (and runner --candidate-overlay) mid-run. Catch it at both call sites: evolve reports NOT PROMOTED and exits, runner routes it through parser.error. * feat(eval): circuit-break the runner sweep on a systemic outage A sustained upstream outage used to pay out every remaining --timeout window one session at a time. Track consecutive session/infra/cleanup failures via a pure systemic_outage_streak helper; after --outage-streak (default 5) in a row, stop the sweep, still write report.md/promotion.json from partial evidence, and exit non-zero so evolve.py halts instead of proposing from truncated evidence. A task's own resolved=False never trips the breaker. * fix(cli): report a dirty working tree as stale in gitnexus status status --json (and the human output) computed up-to-date from commit + runner identity + completeness only, so a repo with uncommitted source changes at a matching HEAD was reported up-to-date while analyze would still re-index it. A graph-backed agent gating on that JSON could skip re-analysis on a stale graph. Extract analyze's dirty-tree check into a shared isWorkingTreeDirty() in storage/git and fold it into the status freshness decision. * fix(ci): use single-slash deny globs in the review agent's disallowedTools github.workspace already expands to an absolute path, so Read(/${{ github.workspace }}/**) and Read(//proc/**),(//sys/**),(//dev/**) produced double-slash patterns that a normalizing matcher may not match — silently no-opping the deny layer. Not exploitable (the allowlist is the primary control and never grants those paths), but the globs should be well-formed. Update the pinned test strings. * ci: install gitnexus-shared with npm ci from the committed lockfile The gitnexus-shared build floated its deps via npm install in three workflows (skill-sync, ci-tests, and — most importantly — the release publish.yml) while every other install step uses npm ci. The lockfile is committed and in sync, so switch all three to npm ci for reproducible, locked installs. * test(cli): make the shipped-skills drift guard reject symlinks listFilesRecursive walked with readdirSync and snapshotDir read with readFileSync, both of which follow symlinks — so a mirror file symlinked to the canonical tree passed the byte-compare (and a symlinked mirror dir would be followed too). Reject a symlinked root via lstat and any symlinked entry via Dirent.isSymbolicLink, with negative tests (skipped on Windows). * test(eval): guard the candidate-skill vs mirror-root coverage invariant MIRROR_SKILL_ROOTS omits the Cursor tree, safe only because no candidate skill is cursor-shipped. Pin that invariant: every CANDIDATE_SKILLS entry must exist under canonical + every mirror root and must not ship to Cursor, so adding a cursor-shipped skill to the candidate set (the PR #2488 asymmetric-sync class) fails loudly instead of syncing three of four trees. * docs(ci): describe the review agent's staged post-merge rollout The DoD asked for a dry-run or triggered run before merge, but an issue_comment (or newly added workflow_dispatch) workflow only ever executes the default-branch copy, so it cannot be exercised from the PR that introduces it. Reword the DoD and the activation checklist to a staged rollout: merge registered-but-disabled, validate same-repo and fork execution post-merge, then enable the variable. * fix: pin plugin skill mcp.json to the release version via #2445 tooling The ten plugin skill mcp.json launched `npx -y gitnexus@latest mcp` on every skill connect — non-reproducible and a supply-chain surface, and (unlike the persisted setup config) never pinned. Extend sync-plugin-manifests.mjs with an mcp surface kind that stamps the gitnexus@<version> launch arg, pin all ten to 1.6.9 now, and keep them byte-identical so the drift guard stays green. The release lifecycle + publish.yml --check now re-stamp them like the four manifest surfaces; only READMEs stay on @latest as docs. * test(eval): prove the proposer's built-in file tools are confined The real-Claude canary only exercised Bash + MCP, so it proved process/MCP containment but not that the proposer's built-in file tools stay inside their mounts. Add a canary over the exact PROPOSER_ALLOWED_TOOLS surface and the same read-only /evidence mount as run_proposer (allowlist extracted to a shared constant so it can't drift): Read reaches /evidence, a Write into the read-only evidence mount is denied, and a Write lands in the output tree. * fix(eval): apply the candidate overlay after task setup for fair arms The candidate overlay was applied before the task's untrusted setup ran, so setup could observe candidate prose and the incumbent/candidate arms started from different pre-overlay state. Reorder within the sandbox: capture the base (pre-overlay) skill digest, run setup against the base skills, verify setup did not tamper them, then apply the overlay and capture the post-overlay digest the model must preserve. apply_candidate_overlay stages path-specific overlay files, so setup's uncommitted changes stay out of the baseline and churn is unchanged. Graph freshness for the review arm is handled by the status dirty-tree fix plus the review skill's stale-triggered re-index, not by reordering the cached per-task-sha graph materialization (which is mechanically blocked). * test(eval): end-to-end containment proof of the autonomous proposer Drives the real run_proposer through bubblewrap with a deterministic scripted model (no paid API): it reads the read-only evidence bundle and writes a candidate gitnexus-plan skill edit plus a rationale into the sandbox output tree; run_proposer enforces the trust boundary and copies only the validated overlay + proposal out. This exercises the autonomous-proposal stage of the self-evolution loop end-to-end in the eval/containment CI job (the gate and apply stages are covered by test_workflow_bench_evolution and test_promotion_apply). Env-gated on GITNEXUS_REQUIRE_CLAUDE_CANARY, so it runs only where the pinned Claude binary and user namespaces are available. * fix(eval): let the proposer author its overlay via Bash Running the end-to-end proposer canary in the containment CI job surfaced a real bug: run_proposer starts the session with --bare, which hard-disables the Write/Edit tools ("Write exists but is not enabled in this context"), yet allowlisted Edit/Write and omitted Bash. The proposer therefore had no working way to write its candidate overlay — the self-evolution loop could never produce a candidate. The sandbox settings already pre-authorize Bash (autoAllowBashIfSandboxed) and confine writes to workspace/tmp/home, so switch PROPOSER_ALLOWED_TOOLS to Read/Grep/Glob/Bash and tell the proposer to author files with Bash. The end-to-end test now drives the real run_proposer through bubblewrap and asserts a validated overlay + proposal are produced (this also replaces the earlier file-tool canary, whose Write/Edit premise was moot). * test(eval): author the proposer overlay with newline-free Bash content The nested shell-sandbox prefix mangles embedded newlines, so the multi-line overlay content never landed. Use single-line content for the deterministic proposer canary. * test(eval): drop the unverifiable end-to-end proposer canary The scripted proposer overlay never materialized in the containment job across runs, and the model tool-result content is not visible in CI logs, so the test cannot be finalized without an environment where the sandbox can actually run. Keep the verified production fix (Bash-authoring in run_proposer); the proposer sandbox/containment stays covered by the existing Bash+MCP and process-tree canaries. * test(cli): drop run-analyze.ts from the windowsHide spawn-family list U7 moved run-analyze.ts's only child_process call (the git status --porcelain dirty check) into storage/git.ts (already covered by this test, with windowsHide). run-analyze.ts no longer imports a spawn-family function, so the windowsHide-regression test's 'must have >=1 spawn call' invariant failed for it. Remove it from SRC_FILES. --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: Zander Raycraft <zanderjraycraft@gmail.com> Co-authored-by: Azizur Rahman <azizur100389@gmail.com>	2026-07-19 15:07:24 +01:00
Gergő Magyar	0005574dce	docs: restructure root README, fact-check all READMEs (#2360) ... * docs(readme): restructure for readability, fix stale facts Reorganize the README so the visible page reads as a short narrative (Quick Start -> Two Ways -> Why -> What Your Agent Gets -> Editor Setup -> CLI -> How It Works -> Docker -> Enterprise) and move deep operational detail into 13 collapsible <details> sections: env vars, .gitnexusrc, Cosign/Kubernetes verification, manual MCP configs, install troubleshooting, and extended tool examples. Accuracy fixes verified against gitnexus/src: - MCP tools: 17 (15 per-repo + 2 group), not 16/11+5; drop group_contracts/group_query/group_status (CLI + resources now, not tools); add check, trace, explain, pdg_query, route_map, tool_map, shape_check, api_impact rows from src/mcp/tools.ts - Agent skills: 6 installed (adds Guide + CLI), not 4 - Wiki default model: minimax/minimax-m2.5, not gpt-4o-mini - Resources: add gitnexus://setup and gitnexus://group/{name}/... - CLI: document group impact, doctor, and the direct terminal query commands (query/context/impact/trace/cypher/detect-changes/check); note the optional branch param on per-repo tools (#2106) Structural cleanups: dedupe the two Codex config blocks, move Community Integrations out of the MCP setup flow, move Star History to the bottom. No content deleted - verbose material is collapsed, not cut. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: fact-check and fix the remaining READMEs Reviewed all 9 tracked non-root READMEs against the source; fixed the four with stale facts, left the already-accurate ones untouched (pr-swarm-review, .claude reviewer-swarm adapter, and the three bench/ methodology docs). gitnexus/README.md (npm package page): - MCP tools table: 17 tools (15 per-repo + 2 group), was 7 rows - Resources: add gitnexus://setup and gitnexus://group/{name}/... - Skills: 6 bundled (adds Guide + CLI) plus --skills generated ones - Languages: add Dart (14 total) to the list and feature matrix - Wiki default model: minimax/minimax-m2.5, not gpt-4o-mini - Requirements: Node >= 22 (package.json engines), not >= 18 - Claude Code hooks: PreToolUse + PostToolUse - CLI: add --skills/--skip-skills/--skip-git/--workers, doctor, trace, check, group impact - Optional grammars note: include Proto, mention GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 gitnexus-cursor-integration/README.md: - 17 MCP tools, was 16; skills list: all 9 bundled skills, was 5 eval/README.md: - Model list matches configs/models/: Claude Haiku 4.5 (was '3.5 Haiku'), adds MiniMax M2.5 and DeepSeek - Node.js 22+ for GitNexus, was 18+ .devcontainer/README.md: - Add a table of contents (364 lines, ~15 sections, no navigation) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * chore: empty commit to retrigger CI Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-03 08:46:59 +01:00
dependabot[bot]	aee73aadaa	chore(deps): bump aiohttp in /eval in the uv group across 1 directory (#2224) ... --- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.1 dependency-type: indirect dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2026-06-18 06:00:01 +01:00
dependabot[bot]	1bb5b31745	chore(deps): bump aiohttp in /eval in the uv group across 1 directory (#2008) ... --- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2026-06-04 07:02:09 +01:00
Shane Thurston Wijaya	4d2ed0e525	fix(eval-server): localhost now doesn't normalize into IPv4 instead lets OS decide which to bind (#1722) ... * fix(eval-server): localhost now doesn't normalize into IPv4 instead lets OS decide which to bind * fix(eval-server): EADDRNOTAVAIL now treats as potential IPv6 * test(eval-server): new integration test for --host localhost * docs(eval-server): updated eval/README.md based on latest update * fix(eval-server): clarify EADDRNOTAVAIL diagnostic, guard server.address(), and soften localhost docs	2026-05-20 16:14:13 +01:00
dependabot[bot]	92ad0f5491	chore(deps): bump idna in /eval in the uv group across 1 directory (#1713)	2026-05-20 05:38:26 +01:00
Shane Thurston Wijaya	33f18ceaa2	feat(eval-server): added --host for user configured host IP instead of system hardcoded IP (127.0.0.1) (#1667) ... * feat(eval-server): added --host for user configured host IP instead of system hardcoded IP (127.0.0.1) * fix(eval-server): localhost value in --host now returns 127.0.0.1 instead of the raw input to fix wrong address, handled error for ipv6 disabled containers * feat(eval-server): add --host flag with validation and error handling Co-Authored-By: Val Vladescu <val.vladescu@thirdbridge.com> * fix(eval-server): bracketed IPv6 addresses to remove ambiguity * docs(eval-server): document --host flag, READY signal format, and parser migration note * fix(eval-server): use actual bound port in READY signal; strengthen --host e2e tests Co-Authored-By: Val Vladescu <val.vladescu@thirdbridge.com> * feat(eval): wire eval-server --host through gitnexus_docker.py * docs(eval): added guidance for docker user * docs(eval): revise the imprecise documentation * fix(e2e): updated original stdout for new format	2026-05-18 16:00:42 +01:00
dependabot[bot]	a9d72e2dbf	chore(deps): bump urllib3 in /eval in the uv group across 1 directory (#1512) ... Bumps the uv group with 1 update in the /eval directory: [urllib3](https://github.com/urllib3/urllib3). Updates `urllib3` from 2.6.3 to 2.7.0 - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.6.3...2.7.0) --- updated-dependencies: - dependency-name: urllib3 dependency-version: 2.7.0 dependency-type: indirect dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-05-13 13:31:07 +01:00
dependabot[bot]	ed4dad2129	chore(deps): bump python-dotenv (#1320) ... Bumps the uv group with 1 update in the /eval directory: [python-dotenv](https://github.com/theskumar/python-dotenv). Updates `python-dotenv` from 1.0.1 to 1.2.2 - [Release notes](https://github.com/theskumar/python-dotenv/releases) - [Changelog](https://github.com/theskumar/python-dotenv/blob/main/CHANGELOG.md) - [Commits](https://github.com/theskumar/python-dotenv/compare/v1.0.1...v1.2.2) --- updated-dependencies: - dependency-name: python-dotenv dependency-version: 1.2.2 dependency-type: direct:production dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2026-05-04 14:55:28 +01:00
dependabot[bot]	e92328d474	chore(deps): bump the uv group across 1 directory with 4 updates (#1315) ... --- updated-dependencies: - dependency-name: litellm dependency-version: 1.83.7 dependency-type: direct:production dependency-group: uv - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:production dependency-group: uv - dependency-name: aiohttp dependency-version: 3.13.5 dependency-type: indirect dependency-group: uv - dependency-name: requests dependency-version: 2.33.0 dependency-type: indirect dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2026-05-04 10:36:54 +01:00
Brandy Good	2a799ae369	fix: start MCP bridge correctly when using npx (#1114) ... * fix: start MCP bridge correctly when using npx * test: add MCPBridge command discovery and spawn tests; fix stdin isolation --------- Co-authored-by: genoshide <genoshide@users.noreply.github.com>	2026-04-27 18:19:02 +01:00
Subham Kundu	d90d1ba96f	fix(eval): exclude litellm 1.82.7 and 1.82.8 due to compatibility issues (#580)	2026-03-29 05:23:37 +01:00
Gergő Magyar	bf09eab95b	feat: configure prettier with pre-commit hook (#563) ... * feat: configure prettier with pre-commit hook integration Add prettier, lint-staged, and prettier-plugin-tailwindcss at the repo root with husky pre-commit hook integration. Moves husky from gitnexus/ to root package.json for reliable hook installation. - Root package.json with prepare/format/format:check scripts - .prettierrc with endOfLine:lf and tailwindStylesheet for TW v4 - .prettierignore excluding fixtures, vendor, generated, *.d.ts, *.md - .gitattributes enforcing LF line endings for Windows consistency - Pre-commit hook uses direct node_modules/.bin/ paths (no npx) * style: apply prettier formatting to entire codebase One-time bulk format. No logic changes. Use .git-blame-ignore-revs to skip this commit in git blame. * chore: add .git-blame-ignore-revs for prettier format commit * perf: pre-commit hook runs only tests related to staged files Use vitest --related to scope test execution to tests that import the changed files, instead of running the full suite on every commit. * perf: remove vitest from pre-commit hook, keep in CI only Pre-commit now runs lint-staged + tsc only. Tests run in CI (ci-tests.yml) where they belong — keeps commits fast. * ci: add prettier format check to quality workflow PRs will now fail if code isn't formatted with prettier.	2026-03-28 14:58:04 +00:00
John R. Eakin	c68d7975e6	docs: agent development framework, GitHub templates, eval refactor (#479) ... * ci: E2E workflow, web typecheck job, pre-commit hook, test suite CI: - ci.yml consolidated to reference ci-tests.yml - ci-quality.yml: add typecheck-web job for gitnexus-web/ - ci-e2e.yml: E2E workflow with dorny/paths-filter (web changes only) - ci-report.yml: remove dead integration-reports references - CI gate allows skipped E2E status - .gitignore: playwright artifacts, eval test artifacts Pre-commit hook: - .githooks/pre-commit: typecheck + unit tests for both packages - Activated via git config core.hooksPath in prepare script Test infrastructure: - Vitest + React Testing Library: 58 unit tests (graph, server-connection, mermaid, settings, constants, utils, paths) - Playwright E2E: 5 tests + manual recording harness - vitest.config from vitest/config, engines.node >= 20 - Playwright artifacts retain-on-failure - wait-on in devDependencies - vitest/coverage-v8 aligned with vitest 4.x Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * chore: update gitnexus-web package-lock.json Reflects devDependency additions (vitest, playwright, wait-on, @testing-library, etc.) from package.json changes in this PR. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(e2e): add missing process-list-loaded testid, increase CI timeouts - Add data-testid="process-list-loaded" to ProcessesPanel (E2E tests were waiting for an element that didn't exist) - Increase server connect timeouts from 5s to 10s for slower CI Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(ci): run gitnexus-web unit tests in CI, remove unused variable - Add gitnexus-web npm ci + vitest run to ci-tests.yml so web unit tests are gated by the CI status check (were only running locally) - Remove unused IS_PLAYWRIGHT_AUTOMATION variable from E2E spec Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(e2e): add process-row testid, wait for networkidle on page load - Add data-testid="process-row" to ProcessItem component (E2E tests referenced it but it didn't exist in the source) - Use waitUntil: 'networkidle' on page.goto to ensure Vite dev server is fully ready before interacting (fixes first-test timeout in CI) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(e2e): add process-view-button and process-highlight-button testids E2E tests referenced these data-testid attributes but they didn't exist in ProcessItem. All 6 E2E testids now have matching source elements: status-ready, process-list-loaded, process-row, process-view-button, process-highlight-button, server-url-input. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(e2e): remove networkidle — Vite HMR WebSocket prevents it from resolving networkidle waits for zero network activity for 500ms, but Vite's HMR WebSocket stays open permanently, causing page.goto to timeout at 60s on all tests after the first. The explicit toBeVisible waits on UI elements are sufficient and deterministic. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(e2e): wait for Server button visibility, add CI retry, all 5 tests pass locally Root cause: test 1 clicked the Server button before React hydrated, so the tab content never rendered and the input wasn't found. Fixes: - Wait for Server button toBeVisible before clicking - Increase input wait to 15s - Remove networkidle (Vite HMR WebSocket prevents it from resolving) - Add retries: 1 in CI for transient cold-start flakiness Verified locally: all 5 E2E tests pass, 198 unit tests pass, typecheck clean. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(ci): tolerate LadybugDB native crash during analyze step gitnexus analyze can crash with "double free or corruption" (known issue #273) during the LadybugDB native addon shutdown. The index is usually written successfully before the crash. The workflow now: 1. Allows analyze to exit non-zero with a warning 2. Verifies .gitnexus index was actually created 3. Only fails if no index exists (real failure) All tests verified locally: 198 unit, 5 E2E pass, typecheck clean. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(ci): fix shell quoting in analyze step, simplify to || true The previous echo string had special characters that broke bash quoting in GitHub Actions. Simplified to: analyze || true, then check if .gitnexus exists. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: add agent development framework, GitHub templates, eval refactor Agent framework (layered docs for AI-assisted contributions): - AGENTS.md: canonical instructions, impact analysis, MCP tools - CLAUDE.md: Claude Code-specific deltas and hooks - GUARDRAILS.md: safety boundaries, non-negotiables, escalation - ARCHITECTURE.md: monorepo layout, data flow map - TESTING.md: test structure, commands, categories - RUNBOOK.md: copy-paste operations for dev/CI/MCP - llms.txt: minimal LLM context pointer Editor integration: - .cursor/index.mdc + rules/100-monorepo.mdc GitHub templates: - PR template with areas-touched checkboxes - Bug report + feature request issue forms Eval harness: - Refactored mcp_bridge, tool_registry, constants - Error sanitization utilities - Property-based tests via Hypothesis Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix(eval): use format_exception instead of format_exc in sanitize_exception format_exc() returns the currently handled exception traceback, which may be unrelated if called outside an active except block. Using format_exception(type(exc), exc, exc.__traceback__) reliably captures the passed exception's traceback. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: update CONTRIBUTING.md and TESTING.md for current CI/hook setup - CONTRIBUTING.md: add gitnexus-web typecheck command, pre-commit hook checklist item - TESTING.md: add gitnexus-web typecheck command, pre-commit hook section (husky), update CI integration to list actual workflow files (ci-quality, ci-tests, ci-e2e) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: update testing docs to reflect CI/E2E changes from PR #486 - AGENTS.md: update test counts (CLI ~2000 unit, ~1850 integration), add gitnexus-web testing section (198 unit, 5 E2E with commands) - RUNBOOK.md: fix Node requirement to >=20, fix E2E local repro command - TESTING.md: E2E uses data-testid selectors + real servers, not mocks - .cursor/rules/100-monorepo.mdc: add web test/E2E commands Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: address context engineering review — deduplicate tokens, expand Cursor rules - Remove ~100-line gitnexus:start block from CLAUDE.md (was duplicated from AGENTS.md) - Fix gitnexus:start block inlined inside AGENTS.md Reference Docs bullet (doubled) - Replace CLAUDE.md scope table with pointer to AGENTS.md (single source of truth) - Expand .cursor/index.mdc with 5 non-negotiable safety rules for always-on context - Add .cursor/rules/200-eval.mdc with Python/eval commands (glob-scoped to eval/**) - Improve llms.txt with priority annotations and descriptions - Bump version headers to 1.2.0, last-reviewed to 2026-03-24 Saves ~1,400 tokens/session with zero information loss. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>	2026-03-25 06:48:41 +00:00
Zander Raycraft	f2edbb4f82	CI sticky note test	2026-03-19 18:26:56 -05:00
Candido Sales Gomes	5a5850832c	refactor: migrate from KuzuDB to LadybugDB v0.15 (#275) ... * refactor: migrate from KuzuDB to LadybugDB v0.15 KuzuDB was archived (Apple acquisition, Oct 2025). LadybugDB is the community fork with full API compatibility. - Package swap: kuzu → @ladybugdb/core, kuzu-wasm → @ladybugdb/wasm-core - Rename all internal paths: kuzu → lbug (adapters, schema, storage) - Storage path: .gitnexus/kuzu → .gitnexus/lbug (with auto-cleanup) - Add explicit VECTOR extension loading (required in v0.15) - Update CI workflow, documentation, and all tests - 1151 unit + 27 integration tests passing Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: address code review findings (P1-P3) P1: Fix WASM adapter to use getAll() API, wire cleanupOldKuzuFiles into analyze command, add symlink path traversal protection. P2: Cache VECTOR extension load state, batch augmentation engine queries (20→4), fix web getCopyQuery for multi-language tables, fix stale KuzuDB references, correct brainstorm package names. P3: Complete lbug-wasm.d.ts type declarations, batch semantic search per-label, update stale BM25 comment. * chore: remove outdated KuzuDB migration brainstorming document * fix: load FTS extension in MCP pool adapter on init The read-only pool adapter never loaded the FTS extension, so all QUERY_FTS_INDEX calls failed silently. This broke search-pool and augmentation integration tests, and caused empty results in the web UI server mode. * feat: implement shared Database caching and connection reference counting * feat: enhance KuzuDB migration handling and status reporting * fix: mock cleanupOldKuzuFiles in local backend callTool tests * fix: update mock for cleanupOldKuzuFiles and adjust imports in callTool tests --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-15 15:53:01 +00:00
Jason	c2bd8667a3	feat(models): add DeepSeek model configurations ... Add configurations for DeepSeek-V3 and DeepSeek-Chat models via OpenRouter integration. - DeepSeek-V3: Reasoning model (input: /usr/bin/bash.27, output: .10) - DeepSeek-Chat: Chat model (input: /usr/bin/bash.14, output: /usr/bin/bash.28) Fixes #215	2026-03-08 15:50:25 +08:00
abhigyanpatwari	470a3377b3	fix(eval): import paths, patch extraction, model configs ... - Fix imports from eval.agents/eval.environments to relative (agents/environments) - Add hatch wheel config for correct package discovery - Extract git diff patch from container for SWE-bench submission - Use sys.executable instead of hardcoded "python" for venv compat - Upgrade claude-haiku config to 4.5 - Add minimax-m2.1 model config Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-02-25 17:11:00 +05:30
abhigyanpatwari	6ce715b62c	repowiki CLI command implemented	2026-02-17 02:25:07 +05:30