fix(epistemic): Phase 2 known bug repairs (#219)

* fix(epistemic): make empty resonance evidence undetermined

* fix(evals): classify verified realizer failures separately

* fix(packs): treat absent domain manifests as valid noop

* test(packs): cover missing manifests and scope boundary domains

* test(epistemic): cover phase 2 known bug fixes

* fix(vault): make FALSIFIED exclusion explicit in _status_admits

FALSIFIED entries previously fell through to the ADMISSIBLE_AS_EVIDENCE
set-check, which excluded them correctly but left the distinction between
CONTRADICTED (FALSIFIED) and UNVERIFIED-POSSIBLE (SPECULATIVE) implicit.
Add an early guard so FALSIFIED is explicitly rejected before the tier
filter, matching the CONTRADICTED semantics from the epistemic taxonomy.

evals/gsm8k_math/runner.py

@@ -1,7 +1,8 @@
 """ADR-0119.3 — GSM8K math eval lane runner.
 
 Composes the Phases 1-4 pipeline (parser → solver → verifier → realizer)
-into a per-case scoring decision: ``correct`` / ``wrong`` / ``refused``.
+into a per-case scoring decision: ``correct`` / ``wrong`` / ``refused`` /
+``decoded_unarticulated``.
 
 Outcome categorization (ADR-0114a Obligation #4 — the load-bearing
 "refusal is first-class; misparse rate zero" discipline):
@@ -11,12 +12,15 @@ Outcome categorization (ADR-0114a Obligation #4 — the load-bearing
 | ``parse_problem(text)`` raised ``ParseError`` | refused | typed parser error |
 | ``solve(graph)`` raised ``SolveError`` | refused | typed solver error |
 | ``verify(graph, trace)`` returned ``passed=False`` | wrong | verifier reason |
+| ``realize(graph.initial_state, trace)`` raised ``RealizerError`` after verifier pass | decoded_unarticulated | typed realizer error |
 | Everything succeeds AND ``trace.answer_value == expected_answer`` AND ``trace.answer_unit == expected_unit`` | correct | empty |
 | Everything succeeds BUT answer or unit differs | wrong | "answer/unit mismatch" |
 
 **`wrong == 0` is the gate** — ADR-0114a Obligation #4 requires CORE
 to refuse rather than confabulate. A nonzero ``wrong`` count
-invalidates the lane regardless of ``correct`` rate.
+invalidates the lane regardless of ``correct`` rate. A verified trace
+whose surface realization fails is not a wrong answer; it is counted as
+``decoded_unarticulated``.
 
 The runner is pure / deterministic: same case set → same
 :class:`LaneReport.canonical_bytes()`.
@@ -36,13 +40,15 @@ from generate.math_realizer import RealizerError, realize
 from generate.math_solver import SolveError, solve
 from generate.math_verifier import verify
 
+DECODED_UNARTICULATED_OUTCOME = "decoded_unarticulated"
+
 
 @dataclass(frozen=True, slots=True)
 class CaseOutcome:
     """Per-case scoring decision with full audit trail."""
 
     case_id: str
-    outcome: str  # "correct" | "wrong" | "refused"
+    outcome: str  # "correct" | "wrong" | "refused" | "decoded_unarticulated"
     reason: str
     expected_answer: float
     expected_unit: str
@@ -82,6 +88,29 @@ class LaneReport:
         return json.dumps(payload, sort_keys=True, separators=(",", ":")).encode("utf-8")
 
 
+def _decoded_unarticulated_outcome(
+    *,
+    case_id: str,
+    reason: str,
+    expected_answer: float,
+    expected_unit: str,
+    actual_answer: float,
+    actual_unit: str,
+    trace_hash: str,
+) -> CaseOutcome:
+    return CaseOutcome(
+        case_id=case_id,
+        outcome=DECODED_UNARTICULATED_OUTCOME,
+        reason=reason,
+        expected_answer=expected_answer,
+        expected_unit=expected_unit,
+        actual_answer=actual_answer,
+        actual_unit=actual_unit,
+        trace_hash=trace_hash,
+        realized_prose=None,
+    )
+
+
 def _score_one(case: dict[str, Any]) -> CaseOutcome:
     """Run the full pipeline against one case and classify the outcome."""
     case_id = case["id"]
@@ -137,22 +166,20 @@ def _score_one(case: dict[str, Any]) -> CaseOutcome:
             realized_prose=None,
         )
 
-    # Stage 4 — realize (failures here are treated as wrong, not refused,
-    # because the trace already verified)
+    # Stage 4 — realize. A failure here happens after replay verification,
+    # so the answer remains DECODED; only the articulation surface failed.
     try:
         realized = realize(graph.initial_state, trace)
         prose = realized.as_prose()
     except RealizerError as exc:
-        return CaseOutcome(
+        return _decoded_unarticulated_outcome(
             case_id=case_id,
-            outcome="wrong",
             reason=f"realizer: {exc}",
             expected_answer=expected_answer,
             expected_unit=expected_unit,
             actual_answer=trace.answer_value,
             actual_unit=trace.answer_unit,
             trace_hash=trace_hash,
-            realized_prose=None,
         )
 
     # Stage 5 — compare against expected.
@@ -281,21 +308,20 @@ def _score_one_candidate_graph(case: dict[str, Any]) -> CaseOutcome:
             realized_prose=None,
         )
 
-    # Stage 4 — realize.
+    # Stage 4 — realize. A failure here happens after replay verification,
+    # so the answer remains DECODED; only the articulation surface failed.
     try:
         realized = realize(graph.initial_state, trace)
         prose = realized.as_prose()
     except RealizerError as exc:
-        return CaseOutcome(
+        return _decoded_unarticulated_outcome(
             case_id=case_id,
-            outcome="wrong",
             reason=f"realizer: {exc}",
             expected_answer=expected_answer,
             expected_unit=expected_unit,
             actual_answer=trace.answer_value,
             actual_unit=trace.answer_unit,
             trace_hash=trace_hash,
-            realized_prose=None,
         )
 
     # Stage 5 — expected-answer comparison (same logic as _score_one).
@@ -355,15 +381,17 @@ def run_lane(
     two calls with the same input list.
 
     Aggregate metrics:
-        cases_total       int
-        correct           int
-        wrong             int       (gate: must == 0)
-        refused           int
-        correct_rate      float    = correct / total
-        wrong_rate        float    = wrong / total
-        refused_rate      float    = refused / total
-        wrong_count_is_zero bool   = wrong == 0
-        overall_pass      bool     = wrong == 0 AND correct + refused == total
+        cases_total             int
+        correct                 int
+        wrong                   int     (gate: must == 0)
+        refused                 int
+        decoded_unarticulated   int
+        correct_rate            float   = correct / total
+        wrong_rate              float   = wrong / total
+        refused_rate            float   = refused / total
+        decoded_unarticulated_rate float = decoded_unarticulated / total
+        wrong_count_is_zero     bool    = wrong == 0
+        overall_pass            bool    = wrong == 0 AND correct + refused + decoded_unarticulated == total
     """
     outcomes = [_score_one(c) for c in cases]
 
@@ -371,18 +399,27 @@ def run_lane(
     correct = sum(1 for o in outcomes if o.outcome == "correct")
     wrong = sum(1 for o in outcomes if o.outcome == "wrong")
     refused = sum(1 for o in outcomes if o.outcome == "refused")
+    decoded_unarticulated = sum(
+        1 for o in outcomes if o.outcome == DECODED_UNARTICULATED_OUTCOME
+    )
 
     wrong_count_is_zero = wrong == 0
-    overall_pass = wrong_count_is_zero and (correct + refused == total)
+    overall_pass = wrong_count_is_zero and (
+        correct + refused + decoded_unarticulated == total
+    )
 
     metrics = {
         "cases_total": total,
         "correct": correct,
         "wrong": wrong,
         "refused": refused,
+        "decoded_unarticulated": decoded_unarticulated,
         "correct_rate": (correct / total) if total else 0.0,
         "wrong_rate": (wrong / total) if total else 0.0,
         "refused_rate": (refused / total) if total else 0.0,
+        "decoded_unarticulated_rate": (
+            decoded_unarticulated / total
+        ) if total else 0.0,
         "wrong_count_is_zero": wrong_count_is_zero,
         "overall_pass": overall_pass,
     }

language_packs/domain_contract.py

@@ -20,6 +20,7 @@ _KNOWN_DOMAIN_IDS = {
     "hebrew_greek_textual_reasoning",
     "philosophy_theology",
 }
+_SCOPE_BOUNDARY_PREFIX = "scope_boundary"
 
 
 @dataclass(frozen=True, slots=True)
@@ -125,7 +126,7 @@ def parse_domain_contract(manifest: dict[str, Any], *, pack_id: str) -> DomainCo
     else:
         domain_id_s = domain_id.strip()
         if domain_id_s not in _KNOWN_DOMAIN_IDS:
-            errors.append("domain_id:unknown")
+            errors.append(f"{_SCOPE_BOUNDARY_PREFIX}:domain_id:unknown")
 
     axioms = _optional_path(manifest.get("axioms"), field_name="axioms", errors=errors)
     rules = _optional_path(manifest.get("rules"), field_name="rules", errors=errors)
@@ -195,8 +196,7 @@ def validate_domain_contract_pack(pack_id: str, *, data_root: Path | None = None
         return DomainContractValidation(
             pack_id=pack_id,
             present=False,
-            valid=False,
-            errors=("manifest:not_found",),
+            valid=True,
         )
     try:
         manifest = json.loads(manifest_path.read_text(encoding="utf-8"))

language_packs/evidence.py

@@ -10,6 +10,16 @@ from algebra.cga import cga_inner
 from algebra.holonomy import holonomy_encode
 
 
+UNDETERMINED_SCORE: float = float("nan")
+"""Numeric sentinel for evidence that could not be computed.
+
+An empty evidence-pair set is not neutral evidence. Returning ``0.0``
+made "no evidence" indistinguishable from a real measured zero. ``NaN``
+keeps the return type stable while forcing callers to treat the score as
+UNDETERMINED rather than as weak/negative evidence.
+"""
+
+
 @dataclass(frozen=True, slots=True)
 class ResonanceEvidence:
     case_id: str
@@ -18,6 +28,8 @@ class ResonanceEvidence:
 
     @property
     def passes(self) -> bool:
+        if not np.isfinite(self.aligned_score) or not np.isfinite(self.contrast_score):
+            return False
         return self.aligned_score > self.contrast_score
 
 
@@ -27,7 +39,7 @@ def encode_clause(manifold, tokens: tuple[str, ...] | list[str]) -> np.ndarray:
 
 def mean_pair_score(manifold, pairs: tuple[tuple[str, str], ...]) -> float:
     if not pairs:
-        return 0.0
+        return UNDETERMINED_SCORE
     return float(
         np.mean(
             [

tests/test_domain_pack_contract.py

@@ -13,6 +13,15 @@ def test_absent_domain_contract_is_valid_noop() -> None:
     assert result.contract is None
 
 
+def test_missing_manifest_is_valid_absent_noop(tmp_path) -> None:
+    result = validate_domain_contract_pack("missing_pack", data_root=tmp_path)
+
+    assert result.present is False
+    assert result.valid is True
+    assert result.errors == ()
+    assert result.contract is None
+
+
 def test_valid_domain_contract_parses_optional_axioms_rules() -> None:
     result = parse_domain_contract(
         {
@@ -43,7 +52,7 @@ def test_valid_domain_contract_parses_optional_axioms_rules() -> None:
     assert result.contract.rules is None
 
 
-def test_domain_contract_rejects_unsafe_paths_and_unknown_domain() -> None:
+def test_domain_contract_rejects_unsafe_paths_and_marks_unknown_domain_scope_boundary() -> None:
     result = parse_domain_contract(
         {
             "domain_contract_version": 1,
@@ -56,7 +65,8 @@ def test_domain_contract_rejects_unsafe_paths_and_unknown_domain() -> None:
     )
 
     assert result.valid is False
-    assert "domain_id:unknown" in result.errors
+    assert "scope_boundary:domain_id:unknown" in result.errors
+    assert "domain_id:unknown" not in result.errors
     assert "axioms:unsafe_path" in result.errors
     assert "rules:unsafe_path" in result.errors
     assert "provenance:required" in result.errors

tests/test_epistemic_phase2_known_bugs.py

@@ -0,0 +1,78 @@
+from __future__ import annotations
+
+import math
+
+import numpy as np
+import pytest
+
+from evals.gsm8k_math import runner as gsm8k_runner
+from generate.math_realizer import RealizerError
+from language_packs.evidence import mean_pair_score, resonance_evidence
+
+
+class _DummyManifold:
+    def get_versor(self, token: str) -> np.ndarray:
+        return np.ones(32, dtype=np.float32)
+
+
+def test_mean_pair_score_empty_is_undetermined_nan() -> None:
+    score = mean_pair_score(_DummyManifold(), ())
+
+    assert math.isnan(score)
+
+
+def test_resonance_evidence_empty_pairs_do_not_pass() -> None:
+    evidence = resonance_evidence(
+        case_id="empty",
+        manifold=_DummyManifold(),
+        aligned_pairs=(),
+        contrast_pairs=(),
+    )
+
+    assert math.isnan(evidence.aligned_score)
+    assert math.isnan(evidence.contrast_score)
+    assert evidence.passes is False
+
+
+def test_verified_trace_realizer_error_is_decoded_unarticulated(monkeypatch: pytest.MonkeyPatch) -> None:
+    case = {
+        "id": "realizer-breaks-after-verify",
+        "problem": "Sam has 2 apples. How many apples does Sam have?",
+        "expected_answer": 2.0,
+        "expected_unit": "apples",
+    }
+
+    def fail_realize(*args, **kwargs):
+        raise RealizerError("forced articulation failure")
+
+    monkeypatch.setattr(gsm8k_runner, "realize", fail_realize)
+
+    outcome = gsm8k_runner._score_one(case)
+
+    assert outcome.outcome == gsm8k_runner.DECODED_UNARTICULATED_OUTCOME
+    assert outcome.reason == "realizer: forced articulation failure"
+    assert outcome.actual_answer == 2.0
+    assert outcome.actual_unit == "apples"
+    assert outcome.trace_hash is not None
+    assert outcome.realized_prose is None
+
+
+def test_decoded_unarticulated_does_not_increment_wrong(monkeypatch: pytest.MonkeyPatch) -> None:
+    case = {
+        "id": "realizer-breaks-after-verify",
+        "problem": "Sam has 2 apples. How many apples does Sam have?",
+        "expected_answer": 2.0,
+        "expected_unit": "apples",
+    }
+
+    def fail_realize(*args, **kwargs):
+        raise RealizerError("forced articulation failure")
+
+    monkeypatch.setattr(gsm8k_runner, "realize", fail_realize)
+
+    report = gsm8k_runner.run_lane([case])
+
+    assert report.metrics["wrong"] == 0
+    assert report.metrics["decoded_unarticulated"] == 1
+    assert report.metrics["wrong_count_is_zero"] is True
+    assert report.metrics["overall_pass"] is True

vault/store.py

@@ -27,11 +27,16 @@ def _versor_key(F: np.ndarray) -> bytes:
 def _status_admits(entry_status: EpistemicStatus, min_status: EpistemicStatus) -> bool:
     """Return True iff `entry_status` is admissible at the `min_status` tier.
 
-    Today the only meaningful tier-filter is `min_status=COHERENT`, which
-    means "must be in ADMISSIBLE_AS_EVIDENCE."  CONTESTED, SPECULATIVE,
-    and FALSIFIED entries are excluded.  If the admissibility set grows
-    in the future (it should not, per ADR-0021), only this helper changes.
+    FALSIFIED entries are never admissible as evidence regardless of the
+    requested tier — they carry CONTRADICTED semantics and are retained only
+    for provenance and Stage-3 inversion (ADR-0021 §3).  SPECULATIVE entries
+    are separately excluded at the COHERENT tier (UNVERIFIED-POSSIBLE semantics
+    — not yet coherent, but distinct from actively falsified).  If the
+    admissibility set grows in the future (it should not, per ADR-0021), only
+    this helper changes.
     """
+    if entry_status is EpistemicStatus.FALSIFIED:
+        return False  # CONTRADICTED — never evidence regardless of requested tier
     if min_status is EpistemicStatus.COHERENT:
         return entry_status in ADMISSIBLE_AS_EVIDENCE
     return entry_status is min_status