feat(corpus-seeded-mechanisms): variant findings in MAP, sandbox-eligible, counted in the manifest

Task 2.3 (Req 3.4, 3.5, 3.6, 6.2).

- [variants] enabled / max_mechanisms config; MAP runs variant search
  after the overlay in standard and deep scans only, appends the variant
  findings, rewrites overlay.json with merged ids, and the manifest
  records mechanisms_searched, files_searched, findings and
  merged_into_overlay.
- REGRESS: variant findings join the candidate list after the promotions
  as zero-score hotspots, under the existing safety check and cap.
- Spec notes for group 2 and the design synced (variant_search.py,
  seed.py, derive_shape signature).

Co-Authored-By: Claude Fable 5.1 <[email protected]>
Claude-Session: https://claude.ai/code/session_01T7XD7x5KonMdmGRkp63EQG

.kiro/specs/corpus-seeded-mechanisms/design.md

@@ -93,6 +93,8 @@ src/openultrasast/
 ├── semantic/
 │   ├── mechanisms.py   # Mechanism += origin, review_tier, pairs, shape, guard; append_from_pair; dedupe_by_shape
 │   ├── variants.py     # Shape, GuardKind, derive_shape(vuln_ir, fixed_ir, label, facts) -> Shape|None; match_shapes(file_ir, shapes, facts) -> list[VariantHit]
+│   ├── variant_search.py # search_tree, hits_to_findings, SearchResult (needs store/overlay/findings; variants.py stays free of them)
+│   ├── seed.py         # export_mechanisms(cases, store) -> ExportReport (maintainer command `mechanisms export`)
 │   └── loo.py          # evaluate_loo(cases, *, store_factory) -> LooResult; payload
 ├── findings.py         # origin "variant" via tags/finding_id prefix "variant:" (no schema change)
 ├── cli.py              # MAP: variant search after overlay; manifest counters; `pairs --loo`; `mechanisms export --slice`
@@ -173,8 +175,11 @@ class Shape:
 
     def key(self) -> str: ...  # stable, text-free
 
-def derive_shape(vuln: FileIR, fixed: FileIR, *, function: str, sink: str | None, line: int | None, mechanism: str, facts: SemanticFacts) -> Shape | None: ...
-def match_shapes(ir: FileIR, shapes: Sequence[Shape], facts: SemanticFacts) -> list[VariantHit]: ...
+def derive_shape(vuln: FileIR, fixed: FileIR, *, function: str, sink: str | None, line: int | None, mechanism: str, facts: SemanticFacts, vuln_text: str = "", fixed_text: str = "", cwe: str | None = None) -> Shape | None: ...
+    # texts: guard statements are neither calls nor binds in FileIR, so the guard kind is classified from the labeled
+    # function's lines present only on the fixed side (closed set, none of the text enters the shape); cwe: when a label
+    # names no sink and no line, the fact-sink call in the function whose CWE matches is the labeled call.
+def match_shapes(ir: FileIR, shapes: Sequence[Shape], facts: SemanticFacts, *, mechanism_ids: Mapping[str, str]) -> list[VariantHit]: ...
 ```
 
 Invariants: shapes carry no path, line, or literal beyond identifiers; `derive_shape` returns None when the labeled sink call site is not found.

.kiro/specs/corpus-seeded-mechanisms/tasks.md

@@ -15,22 +15,22 @@
   - _Boundary: Store_
   - _Depends: 1.1_
 
-- [ ] 2. Core: export and search
-- [ ] 2.1 Export mechanisms from trusted pairs as a maintainer command
+- [x] 2. Core: export and search
+- [x] 2.1 Export mechanisms from trusted pairs as a maintainer command
   - Only `seeded` and `reviewed`, non-known-limit, parse-ok pairs seed; the command runs offline over the vendored catalog and reports skipped pairs with reasons; extra-absent languages are skipped with a degradation.
   - Observable: `ousast mechanisms export --slice sast` writes corpus rows and reports the skipped `title`/`advisory`/known-limit pairs.
   - _Requirements: 1.1, 1.2, 1.5, 2.5_
   - _Boundary: Export_
   - _Depends: 1.2_
 
-- [ ] 2.2 Search a tree for variants and merge with overlay flows
+- [x] 2.2 Search a tree for variants and merge with overlay flows
   - For each parsed file within the MAP budget, call sites matching a shape's sink name, arity, and source positions (fact source, parameter, container read) produce `variant` findings at `suspicion` with the mechanism id; when the overlay has a flow at the same call site, its record gains `mechanism_id` and no duplicate finding is emitted.
   - Observable: the split-sink Python fixture yields a variant finding merged into the overlay coverage record; a constant-argument call does not match; `quick` emits no variants.
   - _Requirements: 3.1, 3.2, 3.3, 3.6_
   - _Boundary: VariantSearch_
   - _Depends: 2.1_
 
-- [ ] 2.3 Make variant findings sandbox-eligible and count them in the manifest
+- [x] 2.3 Make variant findings sandbox-eligible and count them in the manifest
   - Variant findings enter the candidate set after overlay promotions under the existing safety check and caps; the manifest records mechanisms searched, files searched, findings, and merges.
   - Observable: with the fake sandbox a variant finding runs; the manifest `variants` block is present on standard scans and absent on quick.
   - _Requirements: 3.4, 3.5, 6.2_
@@ -84,5 +84,10 @@
 - Task 1.1 (2026-09-05, RED first: 5 failing tests in `tests/test_variants.py`, `ModuleNotFoundError: openultrasast.semantic.variants`; then green): `semantic/variants.py` with `Shape` (language, sink_name, arity, source_positions, source_kinds, guard, mechanism; `key()`/`to_dict()`/`from_dict()` text-free), closed `GUARD_KINDS`/`SOURCE_KINDS`, `derive_shape(vuln_ir, fixed_ir, *, function, sink, line, mechanism, facts, vuln_text, fixed_text)`. Deviation from the design signature: the two excerpt texts are passed in because guard statements (`if x not in ALLOWED`, `if len(x) > n`) are not call sites or binds in `FileIR`; the guard kind is classified from the lines of the labeled function that exist only on the fixed side, closed set, `none` when unknown; nothing of that text enters the shape. Source kinds trace argument identifiers through binds (fact-source pattern -> `fact_source`; subscript/`.get(`/request container -> `container_read`; parameter -> `parameter`), preferring fact_source, then parameter, then container_read. A constant-only sink call or a missing function/call site yields None.
 - Task 1.2 (2026-09-05, RED first: 3 failing tests in `tests/test_mechanism_export.py` — `Mechanism` lacked `origin`, `append_from_pair` missing; then green): additive `Mechanism.origin/review_tier/pairs/shape/guard` with defaults so sandbox rows load unchanged; `MechanismStore.load()` folds the append-only log by id (latest row wins) so a re-seeded shape carries the extended `pairs`; `append_from_pair` uses a deterministic id `corpus:<sha1(shape.key())[:16]>` so the improve lever can name records across machines; `corpus_mechanisms()` selects searchable rows. Existing `order_promotions` tests unchanged and green.
 - Review round 1 (2026-09-05) APPROVED 1.1 and 1.2 (reviewer re-simulated RED, ran six mutations, verified the import boundary and that sandbox rows load unchanged; isolated suite 493 / 480 green, statics and gates clean). Suggestions carried into group 2: trim `_CONTAINER_READ` to the design's subscript/`.get(` definition so no source vocabulary lives outside facts; intersect line and sink in `_labeled_call`; `append_from_pair` keeps the highest tier and accumulates provenance tags when a shape is re-seeded; sync design §Shape to the implemented signature.
+- Task 2.1 (2026-09-05, RED first: 4 failing tests in `tests/test_mechanism_seed.py` — `ModuleNotFoundError: semantic.seed` x3, `argparse` rejected `mechanisms`; then green): `semantic/seed.py` `export_mechanisms(cases, store)` seeds only `seeded|reviewed`, non-known-limit, parsing pairs with cached excerpts, skips with reasons (`tier:<t>`, `known_limit:<why>`, `parse_failed`, `variants_language_unsupported` + degradation, `pointer_pair_not_cached`, `no_labeled_sink_call_site`) and keeps catalog order; CLI `ousast mechanisms export --slice S [--store P] [--json]`, default store `.openultrasast/calibration/mechanisms.jsonl` (the path the scan reads; the store module's `DEFAULT_MECHANISM_LOG` differs and is left alone). Discovery: vibe-py labels carry a function and a mechanism but no sink or line, so `derive_shape` gained a facts-driven fallback (the fact-sink call inside the labeled function, CWE-matching and non-constant first) and now intersects line and sink when both exist (round-1 suggestion); `_CONTAINER_READ` trimmed to subscript/`.get(`; `append_from_pair` keeps the highest tier and accumulates provenance tags. Measured export (offline, scratchpad stores): vibe-py 35 pairs -> 16 seeded, 10 records (7 pairs share `execute/1 parameter`; the 19 skips are absence-class labels — IDOR, open redirect, missing guard — with no sink call to shape); local 3 -> 0 (fixtures label no sink call site); sast 11 and vfc-js 17 -> 0, all `tier:advisory` as Req 1.2 requires. Guards are mostly `none` because Real-Vuln fixed twins are separate trap functions, not patched code.
+- Task 2.2 (2026-09-05, RED first: 3 failing tests in `tests/test_variant_search.py`, `ImportError: match_shapes|VariantHit|search_tree`; then green): `variants.match_shapes(ir, shapes, facts, mechanism_ids=)` matches trailing callee name + arity and requires every shape source position to carry a source of any kind (a shape learned from `request.args` fires on a parameter); constants and arity mismatches never match. New module `semantic/variant_search.py` (design deviation: the file plan put `search_tree`/`hits_to_findings` in `variants.py`, but they need the store, the overlay records and `StaticFinding`, which `variants.py` must not import): `search_tree(root, targets, store, facts, max_mechanisms)` -> `SearchResult(hits, mechanisms_searched, files_searched, degradations)`; `hits_to_findings` merges a hit into an overlay promote/coverage record at the same path and line (`mechanism_id` set, no duplicate) and otherwise emits `variant:<id>:<path>:<line>` at `suspicion` with tags `variant`, `mechanism:<id>` and the pair provenance in the rationale. `OverlayRecord.mechanism_id` added (additive).
+- Task 2.3 (2026-09-05, RED first: 3 of 4 tests in `tests/test_variant_scan.py` failing — no variant finding, no overlay merge, variant not offered to the sandbox; the quick-mode test passed trivially and guards the invariant; then green): `[variants] enabled=true, max_mechanisms=500` config; MAP runs `_search_variants` after the overlay (standard/deep only; skipped when facts fail to load), appends variant findings, rewrites overlay.json with merged ids, and the manifest carries `variants = {mechanisms_searched, files_searched, findings, merged_into_overlay}`; in REGRESS variant findings join the candidate list after the promotions with a zero-score hotspot each, under the same safety check and cap. Verified with the fake sandbox: a variant of a project-specific sink with no inventory rule is offered. Suite 504 passed / 4 skipped, extra-free 491 / 17, statics clean, three gates PASS.
+- Task 3.1 (2026-09-05, RED first: 3 failing tests in `tests/test_loo.py` — `ModuleNotFoundError: semantic.loo` x2, `pairs --loo` unknown flag; the two API tests went green on the first implementation): `semantic/loo.py` `evaluate_loo(cases)` holds every scorable pair out once (known_limit and uncached pointer pairs skipped with a reason), seeds a temporary store from the *other* `seeded|reviewed` pairs (advisory/title pairs are scored as targets, never teach), materializes both sides, runs `search_tree`, and scores: detected when a hit lies inside the labeled function and names the labeled mechanism or sink; silent when the fixed side yields no hit; `found_by` lists the record id and the pairs that taught it; metrics (pairs, detected, silent, recall, silence, Youden, teaching) per slice, profile and mechanism; `to_dict()` is the `loo.json` artifact. Shape derivation is duplicated from `seed.py` (`_lessons`) pending a shared helper once group 2 is accepted. First measurement, vibe-py vendored (35 pairs, 1.0 s): 11 detected (recall 0.314), 21 silent (0.600), Youden -0.086, 16 teaching pairs; per mechanism source_reaches_sink 27 pairs 9 detected / 19 silent, missing_auth_guard 4 / 2 / 2, permissive_default 3 / 0 / 0, path_join_user_input 1 / 0 / 0. The 14 leaks are the coarse `execute/1 parameter` shape firing on Real-Vuln's false-positive trap twins: the honest over-match rate the `mechanisms` lever (group 4) retracts on.
+- Review round 2 (2026-09-05) APPROVED 2.1, 2.2, 2.3 (reviewer re-simulated all three REDs, killed 11 of 12 mutants, ran the export offline in a network namespace and reproduced the counts, confirmed gates byte-identical to HEAD; judged the zero-score-hotspot candidate path a closer fit to Req 3.4 than the forced path). Suggestions carried into round 3: a test that a hit on a `demote`/no-flow overlay record is not merged (the surviving mutant); `search_tree` skips a malformed store row with `variants_store_row_invalid` instead of aborting the scan; design §VariantSearch/§Modified Files synced (`SearchResult`, `regress/candidate.py` untouched); `_load_variants` uses `_int_value`; the exporter passes line and sink together; `no_labeled_function` skip reason; one shared `hotspot_from_finding` helper.
 - Seeding reads `PairCase.review_tier` from `pair-corpus-honesty` task 8.1; until it lands, sast and vibe-py rows default to `advisory`/`seeded` per that design and only vibe-py seeds.
 - Guard classification is heuristic and closed; `none` is allowed and reported, never used to demote.