feat(model-grounded-detection): group 1, subtract the noise architecture

99 source modules -> 81. 832 tests -> 646. The whole learning/ package (16
modules, ~4,100 lines) and six semantic/ modules removed, with the three gates
byte-identical to 2026-09-06-gate-baseline.txt at every step.

The sequence is what made it safe: vocabularies ported first (1.1), importers
detached second (1.2-1.3), deletion third (1.4). Every import break during the
deletion was therefore a detachment miss in the importer and was fixed there --
no module was restored to satisfy one. Both misses were the same shape and were
fixed as a class: operations.py and shapes.py each imported trailing_name from
the deleted variants.py, so it moved to semantic/ir.py, its natural home, and
both importers changed in one edit.

Ported before deleting: the closed guard vocabulary (verbatim, nothing else
holds it) into model/specs.py, which derives TaintSpec and DominanceSpec from
the retained ruleset facts rather than copying them. Re-homed: families ->
model/taxonomy, candidates -> model/candidates, endpoint -> model/endpoint,
plus Region, labeled_family and labeled_spans. labeled_family no longer falls
back to the LLM classifier -- an unlabeled pair is honestly unknown.

Four deviations, each recorded in the spec notes with its reason. improve/
evolve.py and validator.py were stripped, not deleted: each mixes the mechanism
lever (gone) with the deterministic rule-status loop `ousast improve` still
runs, which has no LLM in it; a test now asserts the lever's absence by symbol
so it cannot creep back. The learning CLI group became `model candidates`,
because deleting it outright would have orphaned the retained enumerator by
removing its only entry point. thinking moved from [learning] to [models].

A gap named rather than papered over: no retained sink fact routes by CWE to
path, output_encoding, untrusted_destination or prototype -- the same hole the
entailment ceiling diagnosed. The test asserts the seeded set and the gap set
exactly, so task 4.2 must update it when it authors those sinks.

The audit found exactly one genuine orphan: vectorstore.py, a bakeoff harness
with no production caller and no CLI, alive only through its own test. The five
named subsystems each carry an explicit decision. Manifest committed, with a
test asserting the tree still matches it.

Group 2 (the Joern go/no-go) has not started.

Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
Claude-Session: https://claude.ai/code/session_01T7XD7x5KonMdmGRkp63EQG

.kiro/specs/model-grounded-detection/tasks.md

@@ -58,7 +58,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
 
 ## Group 1 — Subtract and audit (gate-protected, no Joern yet)
 
-- [ ] 1.1 Port the security vocabularies out before deleting their modules
+- [x] 1.1 Port the security vocabularies out before deleting their modules
   - Create `src/openultrasast/model/specs.py` and move into it, as data, the knowledge the deleted modules
     carry: `_GUARD_PATTERNS` and the guard-kind vocabulary from `semantic/variants.py`; the sink token tables
     (from `benchmarks/pairs/catalog_gen.py::_SINK_TOKENS` and `semantic/facts.py` SinkFacts) as the seed
@@ -70,7 +70,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
     seed, and that the guard vocabulary is preserved verbatim. `model/specs.py` is read-only data — no LLM and no future optimiser writes it, and a test asserts the module exposes no writer (Req 7.4, the verifier boundary).
   - _Requirements: 1.2, 7.1, 7.2, 7.3, 7.4_
 
-- [ ] 1.2 Re-home the three retained modules
+- [x] 1.2 Re-home the three retained modules
   - Move `learning/families.py` → `model/taxonomy.py`, `learning/candidates.py` → `model/candidates.py`,
     `learning/endpoint.py` → `model/endpoint.py`. Update their imports and every importer. `candidates.py`
     keeps its behaviour exactly (it is the suspicion-band feeder, Req 8.4) — its tests move with it and stay
@@ -80,7 +80,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
   - _Requirements: 4.4, 7.1_
   - _Depends: 1.1_
 
-- [ ] 1.3 Detach the retained paths from the removed code
+- [x] 1.3 Detach the retained paths from the removed code
   - `pairs.py`: remove the hunter-scoring path (`_evaluate_hunter_pair`, `_hunter_outcome`, `_family_metrics`,
     `PairEvalResult.per_family`, `build_pair_signals` split arg, the `k_runs`/`hunter` plumbing) and its
     `learning.*` imports; keep `_evaluate_overlay_pair`/`_evaluate_inventory_pair` and the `context_files`
@@ -95,7 +95,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
   - _Requirements: 1.3, 1.4, 11.2_
   - _Depends: 1.2_
 
-- [ ] 1.4 Remove the noise architecture and the mechanism/evolve loop
+- [x] 1.4 Remove the noise architecture and the mechanism/evolve loop
   - Delete `learning/{rounds,acceptance,proposer,journal,canaries,verifiers,difficulty,scoring,classify,
     detectors,split,publish,slices,predicates,judgments}.py` (everything under `learning/` except the three
     modules re-homed in 1.2, which are already gone from the directory), then remove the now-empty `learning/`
@@ -110,7 +110,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
   - _Requirements: 1.1, 1.2, 1.2b, 1.3, 1.4_
   - _Depends: 1.3_
 
-- [ ] 1.5 Reduce the test suite to surviving behaviour
+- [x] 1.5 Reduce the test suite to surviving behaviour
   - For every deleted module, delete the test files that existed only to pin it (`test_learning_*`,
     `test_mechanism_*`, `test_obligation_*` only where it tested the lever not the checker, `test_pair_*`
     hunter-scoring cases, etc.) in this same change. For every surviving test, confirm it maps to a surviving
@@ -122,7 +122,7 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
   - _Requirements: 2.1, 2.2, 2.3, 2.4, 2.5_
   - _Depends: 1.4_
 
-- [ ] 1.6 The module audit manifest
+- [x] 1.6 The module audit manifest
   - Add `model/audit.py` that classifies every `src/**/*.py` as `load_bearing` (reachable from a gate, the
     scan CLI, or a surviving requirement), `standalone_capability` (its own CLI/users — e.g. `mcp.py`,
     `skills.py`), or `orphaned` (no importer, no entry, no requirement). Remove the orphans. Give
@@ -250,3 +250,66 @@ queries in group 4). The gates, `redaction.py`, `pairs.py` overlay/inventory pat
   mistake this whole spec was written to stop.
 - `(P)` parallelism is deliberately absent: the subtraction is sequential by dependency, and the Joern spike
   gates everything after it. Do not fan out.
+
+## Implementation Notes — group 1 (2026-09-08)
+
+Landed as one change. Gate baseline captured before the first edit and re-checked after every step; the three
+gates are **byte-identical to `2026-09-06-gate-baseline.txt`** at the end, as Req 1.4 and 11.2 require.
+
+**What the subtraction cost and bought.** 99 source modules -> 81; 832 tests -> 646 (642 passing, 4 skipped);
+the whole `learning/` package (16 modules, ~4,100 lines) plus six `semantic/` modules removed. mypy clean over
+82 files, ruff clean, core `dependencies = []` untouched.
+
+**Sequence that made it safe.** Vocabularies ported first (1.1), importers detached second (1.2-1.3), deletion
+third (1.4). Every import break during 1.4 was therefore a detachment miss in the importer, fixed there — no
+module was ever restored to satisfy one. Two such misses appeared, both handled as a class rather than an
+instance: `semantic/obligations/{operations,shapes}.py` both imported `trailing_name` from the deleted
+`variants.py`, so the helper was re-homed to `semantic/ir.py` (its natural place — it is a pure helper over
+`CallSite.name`) and both importers updated in the same edit.
+
+**Deviations from the design, each recorded with its reason.**
+
+1. *`improve/evolve.py` and `improve/validator.py` were stripped, not deleted.* The design's Removed list named
+   them whole, but each is a mix: the mechanism lever (removed) and the deterministic rule-status improve loop
+   that `ousast improve` still runs from benchmark evidence. That loop has no LLM in it, predates the noise
+   architecture, and is not what this feature supersedes; deleting the files would have taken a retained
+   capability with them. `test_subtraction_complete` now asserts the lever's absence **by symbol**, so it
+   cannot creep back.
+2. *The `learning` CLI group became `model candidates`.* Deleting the group outright would have orphaned
+   `model/candidates.py` — the retained suspicion-band enumerator — by removing its only entry point, and
+   Req 3 would then have flagged it for deletion. The offline ceiling report survives as `ousast model
+   candidates`.
+3. *`thinking` moved from `[learning]` to `[models]`.* It is a model setting, and `LearningConfig` was removed;
+   its coverage moved to `test_model_endpoint` rather than being dropped.
+4. *Three helpers were re-homed rather than lost:* `Region` (promoted from `_Region`, since the detector module
+   that owned the type is gone), `labeled_family` and `labeled_spans` (from the deleted `rounds`/`scoring`).
+   `labeled_family` no longer falls back to the LLM classifier — an unlabeled pair is honestly `unknown`, the
+   same discipline the evidence ladder applies to a claim the model cannot arbitrate.
+
+**A measured gap, named rather than papered over (Req 9.2).** Task 1.1's observable asked that every family
+have a `TaintSpec` or `DominanceSpec` seed. It cannot today: the retained sink facts have **no sink whose CWE
+routes to `path`, `output_encoding`, `untrusted_destination` or `prototype`** — the same hole the entailment
+ceiling diagnosed ("closed literal sink table: misses per-family sinks"). Rather than weaken the test, it now
+asserts the seeded set *and* the gap set exactly, so neither can change silently, and task 4.2 must update it
+when it authors those sinks.
+
+**Test reduction (Req 2), by cluster.** 34 files deleted whole: 21 `test_learning_*` (rounds, acceptance,
+scoring, classify, detectors, proposer, journal, canaries, verifiers, publish, split, cli, scan, pairs_path,
+cutoff, reliability, aggregation, classifier_report, pairs_evidence, round evidence x2, thinking), 4
+`test_mechanism_*`, `test_variants`, `test_variant_search`, `test_loo`, `test_obligation_export`,
+`test_mechanism_reports`, `test_fixture_difficulty`. Partial trims where a file mixed retained and removed
+behaviour: `test_semantic_pipeline` (3 mechanism tests of 12), `test_degradation_matrix` (3 rows for removed
+capabilities), `test_pair_corpus` (the hunter scorer), `test_obligation_check` (the `known_fix` assertion,
+which depended on the deleted store — the id contract, suspicion rung and tags it also covered are kept),
+`test_index` (the bakeoff test). Two files re-homed with their subject: `test_learning_families` ->
+`test_model_taxonomy`, `test_learning_endpoint` -> `test_model_endpoint`.
+
+**The audit (Req 3) found exactly one genuine orphan:** `vectorstore.py`, a store bakeoff harness with no
+production caller and no CLI entry, alive only through its own test — removed with it. The five named
+subsystems each carry a decision: `mcp`, `skills`, `fusion`, `harness_ext`, `hunter_harness` are all
+`standalone_capability` (own entry point or protocol), joined by `stage_processors` and `slot_contract`, which
+the zero-dependency guard in `test_gate` pins. Manifest committed at
+`benchmarks/measurements/2026-09-08-module-audit.json`; a test asserts the tree still matches it.
+
+Group 2 (the Joern go/no-go) has not started. `semantic/engines.py` already exposes `joern_available`, which
+the `CpgBackend` capability probe in task 2.1 should build on rather than duplicate.