core/docs/audit/substrate-liveness-registry.md

Substrate Liveness Registry

Scope: substrate-liveness-audit-scope (v2) Status: Active audit — append-only as layers are completed. Discipline: feedback-adr-cross-reference-discipline, feedback-cleanup-as-you-find

Audit progress

Layer	Status	Verdict	Cleanup performed	Last audited
L0 — Algebra primitives	✅ Audited	CLOSED	None — no dead code found	2026-05-24
L1 — Field substrate	✅ Audited	PARTIAL	None — no dead code found	2026-05-24
L2 — Vault	✅ Audited	PARTIAL	None — flagged learning as wiring debt	2026-05-24
L3 — Language packs	✅ Audited	PARTIAL	None — flagged readback as wiring debt	2026-05-24
L4 — Recognition	✅ Audited	PARTIAL	None — flagged connector/storage/integration as wiring debt	2026-05-24
L5 — Cognition pipeline	⏳ Pending	—	—	—
L6 — Chat runtime + surface composition	⏳ Pending	—	—	—
L7 — Teaching loop	⏳ Pending	—	—	—
L8 — Inter-session memory + contemplation	⏳ Pending	—	—	—
L9 — Epistemic state + verdicts	⏳ Pending	—	—	—

L10 / L11 are not audit targets (no design to audit; flagged in scope as gaps the audit will surface need for).

---

L0 — Algebra primitives

Audit date: 2026-05-24 Auditor: primary agent (Claude) Verdict: CLOSED

Scope-hypothesis correction (per audit step 0)

The scope's layering table cited algebra/backend/ (directory). Reality: algebra/backend.py (single 267-line file). Hypothesis drift, not a finding — recorded so the scope's layering map can be amended if it matters elsewhere.

ADRs in scope for L0

Triaged from the broader algebra/versor/CGA keyword grep against docs/decisions/:

ADR	Title	Status	Belongs at L0?
ADR-0001	VocabManifold Versor Invariant	Accepted	Yes — defines the versor_condition < 1e-6 invariant L0 must preserve
ADR-0003	Coordinate System Dissolution	Accepted	Yes — algebraic foundation
ADR-0004	Rotor as Operator, Not Vocabulary Property	Accepted	Yes — defines rotors as L0 primitives
ADR-0009	Compositional Physics	Accepted	Yes — versor composition rules

Other ADRs surfaced by the grep but assigned to higher layers (not audited at L0): ADR-0006 (L1), ADR-0019 (L2), ADR-0010 (L3 identity), ADR-0021/0022/0023/0024/0025 (L5 policy), ADR-0020 (cross-cutting Rust parity, audit when relevant).

Modules in scope for L0

Module	Lines	Live-import sites (outside algebra/, outside tests/)	Test-import sites
algebra/__init__.py	5	(re-export shim)	—
algebra/backend.py	267	21	16
algebra/cga.py	84	16	17
algebra/cl41.py	165	8	10
algebra/holonomy.py	100	2	5
algebra/rotor.py	179	5	8
algebra/versor.py	180	20	19

Every module has at least 2 live-import sites outside algebra/. No dormant modules at L0.

Caller-trace evidence

Sample of live callers (full grep: grep -rn "from algebra\|import algebra" --include="*.py" | grep -v "^algebra/" | grep -v "tests/" — 38 distinct caller files):

• field/propagate.py:23 — versor application during field propagation (L1 → L0)
• ingest/gate.py:33 — versor/energy at injection boundary (L1 → L0)
• language_packs/compiler.py:14 — versor construction during pack compilation (L3 → L0)
• chat/runtime.py — versor operations in the live turn loop (L6 → L0)
• generate/intent_ratifier.py, generate/admissibility.py, generate/proposition.py — versor-gated generation (L5 → L0)
• core/cli.py:446-469 — versor diagnostics surfaced to operator (CLI → L0)

Every live caller traces back to the runtime entry through at least one of: core chat, core eval cognition, or the field/ingest pipeline.

Exercising suite lane

core test --suite algebra — 13 test files, every L0 module covered:

Module	Tests in algebra suite
versor.py	test_versor_closure, test_holonomy, test_energy, test_motor, test_versor_condition_rust_parity, test_versor_apply_rust_parity
rotor.py	test_versor_closure, test_energy
holonomy.py	test_holonomy, test_holonomy_resonance
cga.py	test_holonomy_resonance, test_null_cone, test_vault_recall
cl41.py	test_vault_recall_vectorised
backend.py	test_vault_recall_vectorised, test_vault_recall_rust_parity, test_cga_inner_rust_parity, test_geometric_product_rust_parity, test_versor_condition_rust_parity, test_versor_apply_rust_parity

Verification: python3 -m core.cli test --suite algebra -q → 82 passed, 50 skipped (skipped are Rust-parity tests on a Python- only environment; not a closure gap).

Cross-layer contract check

Pass 1 — mechanical (consumer-exists per exposed symbol):

Exposed symbol	Consumer evidence
versor_apply	field/propagate.py, generate/stream.py, chat/runtime.py (3+ live consumers)
versor_condition	core/cognition/trace.py:34, evals/cognition/runner.py:60 (gated in evals at < 1e-6)
normalize_to_versor	generate/intent_ratifier.py, generate/admissibility.py
cga_inner	vault/store.py, algebra/backend.py (_CGA_INNER_METRIC), evals/lab/vault_epistemic_trace.py
embed_point, is_null, null_project	vault/store.py, language_packs/compiler.py, field/operators.py
using_rust, vault_recall (backend)	vault/store.py, all Rust-parity tests
word_transition_rotor, make_rotor_from_angle	field/operators.py, generate/intent_ratifier.py
holonomy_encode, holonomy_similarity	vault/store.py, evals/lab/
N_COMPONENTS (cl41)	algebra/backend.py, algebra/cga.py

No exposed L0 symbol with zero downstream consumers.

Pass 2 — semantic (judgment-required):

ADR-0001's versor_condition < 1e-6 invariant is the primary semantic contract. Verified:

• Measured per turn: L0's versor_condition() is computed and folded into the deterministic trace payload (core/cognition/trace.py:34,70) on every turn.
• Surfaced to operator: displayed by core chat and core info commands (core/cli.py:398,461,469).
• Gated at eval boundary: evals refuse to count a turn as versor_ok if versor_condition >= 1e-6 (evals/cognition/runner.py:60, evals/run_cognition_eval.py:54).
• NOT enforced inline as exception: a turn with vc >= 1e-6 still completes; the violation is visible in trace + eval, not raised as an error. This matches CLAUDE.md's discipline ("Do not weaken this threshold to make tests pass. Fix the operator/construction boundary that violated it.") — violations are surfaced for fix, not catastrophically refused at runtime.

Semantic mismatches flagged for human review: none. The contract is consistently consumed.

Closure criteria scorecard

Criterion	Status	Evidence
1. Design artifact	✅	ADR-0001, ADR-0003, ADR-0004, ADR-0009
2. Code artifact	✅	algebra/{backend,cga,cl41,holonomy,rotor,versor}.py
3. Live caller	✅	38 distinct caller files outside algebra/ and tests/
4. Exercised by suite lane	✅	core test --suite algebra — 82/82 non-skipped pass; every L0 module covered
5. Cross-layer consistency	✅	All exposed symbols consumed; versor_condition invariant measured + traced + gated

Verdict: CLOSED.

Cleanup performed

None. Audit found no dead, redundant, superseded, or orphaned code at L0. Every module has live callers; every exposed symbol is consumed; the suite lane exercises every module; the invariant is preserved end-to-end.

Findings / notes for downstream layers

• L1 (Field substrate) auditor: L0's versor_condition is consumed at L5 (trace) and at the eval boundary, but L1 itself does not appear to enforce the invariant — L1's propagation produces field states that may later violate the invariant, with measurement deferred to L5. Worth verifying that L1's propagation correctness is itself tested independently of L5's downstream measurement.
• L2 (Vault) auditor: vault/store.py is one of the heaviest consumers of L0 (cga_inner, embed_point, is_null, holonomy_encode). L2's closure depends on L0's exact-CGA-recall guarantees; the L2 audit should verify the vault honors the exact-match discipline end-to-end, not just at the algebra layer.
• L6 (Chat runtime) auditor: ADR-0020 (Phase 5 / Rust Parity Sequencing) is cross-cutting; the 50 skipped tests in the algebra suite are Rust-parity tests skipped in a Python-only environment. Audit ADR-0020 wherever Rust integration is live (when it lands) rather than at any single layer.

Audit method footnote

This entry follows the per-layer audit format established here: ADRs in scope → modules in scope → caller traces → suite lane exercise → cross-layer contract (mechanical + semantic) → closure scorecard → cleanup → notes for downstream. Subsequent layers should follow the same format so the registry is uniformly machine- and human-scannable.

---

L1 — Field substrate

Audit date: 2026-05-24 Auditor: Codex Verdict: PARTIAL

Scope-hypothesis correction (per audit step 0)

The scope's layering table cited ADR-0006 as the starting point. Reality: L1 also depends on ADR-0002 / ADR-0012 for injection-gate and single- normalization-site discipline, plus ADR-0024 / ADR-0025 as explicit negative-placement ADRs that keep admissibility out of field/propagate.py. field/operators.py is L1-shaped substrate code for core pulse, but it is not on the current ChatRuntime / CognitiveTurnPipeline path.

ADRs in scope for L1

Triaged from the broader field / propagation / injection / normalization / energy keyword grep against docs/decisions/:

ADR	Title	Status	Belongs at L1?
ADR-0002	Ingest Layer Architecture	Accepted	Yes — original injection-boundary design; superseded by ADR-0012 but still relevant historical design
ADR-0006	The Field Energy Operator (Hamiltonian Companion Field)	Implemented	Yes — defines EnergyClass, EnergyProfile, FieldEnergyOperator, FieldState.energy, and propagation recomputation
ADR-0012	core_ingest Governance Layer	Accepted	Yes — preserves ingest/gate.py as the single normalization site
ADR-0024	Inner-Loop Per-Rotor Admissibility	Accepted	Boundary-only for L1 — explicitly keeps admissibility upstream of propagate_step() and adds no normalization site
ADR-0025	Rotor / Frame Admissibility	Accepted	Boundary-only for L1 — explicitly rejects field/propagate.py as the admissibility home

Other ADRs surfaced by the grep but assigned to other layers (not audited at L1): ADR-0007 (valence layer; orthogonal companion to energy, but not part of this brief's L1 concern set), ADR-0013 (sensorium upstream of the gate), ADR-0014 / ADR-0054 (L2 vault / learning), ADR-0022 / ADR-0023 / ADR-0026 (L5 generation admissibility), ADR-0038 and later surface ADRs (L6/L7 surface and teaching concerns).

Modules in scope for L1

Module	Lines	Live-import sites (outside own package, outside tests/)	Test-import sites
ingest/gate.py	351	4	6
field/propagate.py	72	3	1
field/state.py	122	18 actual imports (raw grep also found one prose false positive)	11
field/operators.py	289	3 (core pulse / benchmark path, not chat runtime)	4
core/physics/energy.py	119	8	1

No module is imported by nothing outside its own package. No unambiguously dead module was found. field/operators.py is live through scripts/run_pulse.py and benchmarks/run_benchmarks.py, but not through the current chat/cognition turn loop.

Caller-trace evidence

Sample of live callers (full greps used the required shape, e.g. grep -rn "from field.propagate\|import field.propagate" --include="*.py" . | grep -v "^./field/" | grep -v "^./tests/"):

• chat/runtime.py:89 and session/context.py:20 — live turn ingest calls ingest.gate.inject() (L6/session → L1).
• generate/stream.py:19,628 — generation walk applies propagate_step() for each emitted token (L5 → L1).
• generate/stream.py:18, core/cognition/pipeline.py:21, core/cognition/result.py:13, chat/runtime.py:80, and session/context.py:15 — live FieldState consumers.
• language_packs/compiler.py:14,72 and ingest/gate.py:33,292 — FieldEnergyOperator computes pack/injection energy.
• vocab/manifold.py:36,74,227, generate/salience.py:44, and packs/common/runtime_rules.py:113,120 — energy profile/class consumers.
• scripts/run_pulse.py:40-41 — ManifoldState, GraphDiffusionOperator, and ConstraintCorrectionOperator are live through the core pulse CLI path, not through core chat.

The live chat/cognition trace is:

core chat / ChatRuntime → SessionContext.commit_ingest() → ingest.gate.inject() → FieldState → generate.stream.generate() → field.propagate.propagate_step() → GenerationResult.final_state → CognitiveTurnPipeline trace/result.

Exercising suite lane

Two documented suite lanes are relevant:

Suite lane	What it exercises	Verification
core test --suite smoke	Live chat/pipeline reach path plus architectural normalization doctrine (tests/test_architectural_invariants.py)	python3 -m core.cli test --suite smoke -q → 67 passed
core test --suite algebra	ADR-0006 energy operator and propagate_step() energy recomputation independent of L5 trace measurement (tests/test_energy.py)	python3 -m core.cli test --suite algebra -q → 82 passed, 50 skipped

Additional evidence for the pulse-only field-operator path: python3 -m core.cli test --suite pulse -q → 24 passed.

Cross-layer contract check

Pass 1 — mechanical (consumer-exists per exposed symbol):

Exposed symbol	Consumer evidence
inject	chat/runtime.py, session/context.py, core/cli.py, evals/lab/rotor_manifold_explorer.py
propagate_step	generate/stream.py; lab probes in evals/lab/
FieldState.F	generate/stream.py, session/context.py, chat/runtime.py, core/cognition/trace.py via result path
FieldState.node / FieldState.step	generate/stream.py, generate/salience.py, session/context.py, tests in smoke/cognition lanes
FieldState.holonomy / energy / valence	carried by session/context.py and generate/stream.py; energy also consumed by generate/salience.py through vocab energy and by runtime surface helpers
EnergyClass / EnergyProfile.energy_class	ingest/gate.py, packs/common/runtime_rules.py, core_ingest/compiler.py, core/physics/learning.py
EnergyClass.vault_candidate	core/physics/learning.py (L2 follow-up; internal physics import, not a live L1 turn-loop consumer)
FieldEnergyOperator.compute	ingest/gate.py, language_packs/compiler.py, field/propagate.py
aspect_weight	Internal to FieldEnergyOperator.compute; direct tests only
FieldState.advance	Tests only (tests/test_energy.py)
ManifoldState.with_fields / ManifoldState.advance	Tests only (tests/test_manifold_state.py)
GraphDiffusionOperator / ConstraintCorrectionOperator	scripts/run_pulse.py, benchmarks/run_benchmarks.py, pulse/proof tests

Mechanical gaps: FieldState.advance, ManifoldState.with_fields, and ManifoldState.advance have no non-test consumer. They are small helpers on public dataclasses, so they were not deleted as unambiguous dead code.

Pass 2 — semantic (judgment-required):

ADR-0012's single-normalization-site contract is mostly honored:

• ingest/gate.py is the only production call site for normalize_to_versor() in the L1 live path (ingest/gate.py:237,342).
• field/propagate.py has no normalization, unitization, projection, repair, monitor, or versor_condition() check. It calls only versor_apply() and recomputes energy (field/propagate.py:47-71).
• tests/test_architectural_invariants.py mechanically guards normalize_to_versor() call sites and forbids unitize_versor() in field/, generate/, and vault/ except the existing generate/stream.py final-state closure exception.

ADR-0006 energy propagation is independently tested:

• tests/test_energy.py covers all energy classes, aspect weights, anchor-adjacent escalation, requires_architect_review, FieldState energy storage, and propagate_step() recomputation.
• This directly answers the L0 note: L1 propagation correctness is not tested only through L5's downstream versor_condition trace/eval measurement.

Cross-layer consistency gaps:

• Gate threshold mismatch: ingest/gate.py documents versor_condition(F) < 1e-6 at the gate contract (ingest/gate.py:22-24) but raises only when cond > 1e-5 (ingest/gate.py:344-345). tests/test_architectural_invariants.py also pins the weaker < 1e-5 post-condition (tests/test_architectural_invariants.py:339-367). This conflicts mechanically with the project/L0 hard invariant versor_condition(F) < 1e-6.
• ADR-0006 threshold drift: ADR-0006 specifies E2 begins at raw 0.38, while code classifies E2 at raw >= 0.37 (core/physics/energy.py:104-105). Tests exercise the code behavior, not the exact ADR table boundary.

Semantic mismatches flagged for human review:

• field/operators.py contains a private _unitize_f32() and uses it in graph diffusion / correction (field/operators.py:69-118,190,272). This is not field/propagate.py, and it is reached through core pulse rather than the live chat/cognition turn loop. It is nevertheless field-substrate code that re-projects blended fields, so the operator should decide whether it is an allowed construction boundary, a pulse-only legacy path, or a normalization-site violation.
• session/context.py performs final-turn hemisphere correction and anchor pull with unitize_versor() (session/context.py:207-246). This is outside L1 and was not verdicted here, but it is a forward note for the L6 runtime auditor because it changes live session field state after generation.

Closure criteria scorecard

Criterion	Status	Evidence
1. Design artifact	✅	ADR-0002, ADR-0006, ADR-0012; ADR-0024/0025 for negative placement at the propagation seam
2. Code artifact	✅	ingest/gate.py, field/propagate.py, field/state.py, core/physics/energy.py; pulse-only field/operators.py
3. Live caller	✅	Chat runtime/session/generation callers for gate/state/propagate/energy; pulse callers for graph operators
4. Exercised by suite lane	✅	smoke walks live turn path; algebra independently tests ADR-0006 propagation; pulse covers graph operators
5. Cross-layer consistency	⚠️	Gate/test threshold is < 1e-5 while project/L0 invariant is < 1e-6; ADR-0006 E2 boundary drifts by 0.01; several dataclass helpers are test-only

Verdict: PARTIAL.

Cleanup performed

None. Audit found no module that was unambiguously dead, redundant, superseded, or orphaned. Test-only helper methods and pulse-only field operators are ambiguous rather than safe deletion candidates.

Findings / notes for downstream layers

• L2 (Vault) auditor: ADR-0006 says vault recall re-activates a region to E2 transiently and lets it cool. L1 verifies the energy operator exists and is used at injection/propagation, but did not trace a live vault-recall path that updates energy on recall. Audit this in L2.
• L5 (Cognition/generation) auditor: generate/stream.py has an explicit final-state unitize_versor() closure exception. L1 did not verdict it because it belongs to generation, but it is adjacent to the normalization-site discipline.
• L6 (Chat runtime) auditor: session/context.py performs live post-generation field orientation and anchor pull, including unitize_versor(). Verify whether that runtime correction boundary is documented and suite-protected.
• Future scope cleanup: Decide whether field/operators.py is still a first-class pulse substrate, a benchmark-only substrate, or legacy code. It is live through core pulse, so this audit did not delete it.

---

L2 — Vault

Audit date: 2026-05-24 Auditor: primary agent (Gemini) Verdict: PARTIAL

Scope-hypothesis correction (per audit step 0)

None. The scope's layering table correctly maps Layer L2 concerns (exact CGA recall, indexing, batching, promotion gate) to vault/store.py and core/physics/learning.py.

ADRs in scope for L2

Triaged from Keyword grep (vault / recall / crystallization / promotion / settled / coherence-residual) against docs/decisions/:

ADR	Title	Status	Belongs at L2?
ADR-0014	train/ Learning Loop	Accepted (Stub)	Yes — specifies learning constraints and the Supervised Seeding Epoch (which owns VaultPromotionPolicy)
ADR-0019	Exact Vault Recall Acceleration	Accepted	Yes — defines Stages 1-3 of vectorised scan, norm-bucketing, and layered store
ADR-0054	Vault Recall: Matrix-Cache Indexing + Batched API; Holdout Split Wired	Accepted	Yes — defines VaultStore matrix cache, batched recall API, and --split holdout

Other ADRs/Scope files surfaced and assigned to adjacent layers:

• ADR-0006: Implemented. Belongs at L1, but specifies L2 integration points (vault recall transiently raising region to E2).
• ADR-0045: Accepted. Belongs at L6/Evals, but provides needle-in-a-haystack verification of exact recall.
• ADR-0055: Accepted. Belongs at L8, but catalogs Tier 1 (VaultStore) as session memory.

Modules in scope for L2

Module	Lines	Live-import sites (outside vault/, outside tests/)	Test-import sites
vault/__init__.py	10	(re-export shim)	—
vault/store.py	301	1 (session/context.py)	7
vault/decompose.py	224	1 (chat/runtime.py)	1
core/physics/learning.py	33	0 (re-exported in core/physics/__init__.py but not imported downstream)	0

core/physics/learning.py (VaultPromotionPolicy / PromotionDecision) is confirmed dormant with 0 live callers outside its own package and 0 test callers. Per the L2-specific cleanup instruction, it is retained as future-wiring debt instead of being deleted.

Caller-trace evidence

Sample of live callers (grep: grep -rn "from vault\|import vault" --include="*.py" | grep -v "^vault/" | grep -v "tests/"):

• session/context.py:25 — imports VaultStore for ephemeral session-level storage, storing input/output states and performing exact recall.
• chat/runtime.py:94 — imports default_decomposer and default_gate to perform check gates before planning.
• generate/stream.py:169 — invokes vault.recall during generation walk telemetry.
• vault/decompose.py:124, 179 — invokes vault.recall during fallback grade-split decomposition and domain gate checks.

Every live caller traces back to the runtime entry through core chat, core trace, core eval, or the session/dialogue pipeline.

Exercising suite lane

• core test --suite algebra — Exercises tests/test_vault_recall.py, tests/test_vault_recall_vectorised.py, and tests/test_vault_recall_rust_parity.py.
• core test --suite full — Exercises tests/test_vault_store.py and tests/test_vault_recall_indexing_batch.py.

Verification:

• python3 -m core.cli test --suite algebra -q → 82 passed, 50 skipped
• python3 -m pytest tests/test_vault_*.py -q → 42 passed, 4 skipped

Cross-layer contract check

Pass 1 — mechanical (consumer-exists per exposed symbol):

Exposed symbol	Consumer evidence
VaultStore	session/context.py:25
VaultStore.store	session/context.py:149, 289, 300
VaultStore.recall	session/context.py:347, chat/runtime.py:1643, generate/stream.py:169, vault/decompose.py:124, 179
VaultStore.recall_batch	None (exposed for batched querying, e.g. for offline evaluation or future batching)
VaultStore.reproject	session/context.py:125
FieldDecomposer, default_decomposer	chat/runtime.py:94, 1649
UnknownDomainGate, default_gate	chat/runtime.py:94, 1645
VaultPromotionPolicy	None (dormant)

No exposed L2 symbol other than the batched API (recall_batch) and the dormant VaultPromotionPolicy lacks consumption. Note that recall_batch is fully tested and verified in tests/test_vault_recall_indexing_batch.py but not called in the main production path (which uses single-query recall at runtime).

Pass 2 — semantic:

We verified three load-bearing invariants:

1. Exact-CGA-recall: Checked vault/store.py and algebra/backend.py's vault_recall and vault_recall_batch. There are no ANN, HNSW, cosine similarity, or other approximations on the recall path. It strictly uses vectorised exact scans via diagonal CGA inner-product metric, satisfying CLAUDE.md and ADR-0019/0054.
2. Promotion-path liveness: Confirmed that VaultPromotionPolicy (core/physics/learning.py) has 0 live/test callers. Flagged clearly as wiring debt. Verdict is PARTIAL.
3. Re-thaw path: Traced vault.recall callers to check if recall transiently raises the energy profile of a region to E2 (per ADR-0006 §"Integration Points"). Checked vault/store.py and its callers (session/context.py, chat/runtime.py). Verified that recall does not update or re-raise the energy class/profile of recalled entries. Flagged as specified-not-verified-live.

Semantic mismatches flagged for human review

• Re-thaw path integration: The spec in ADR-0006 for vault recall to "transiently raise region to E2, then let it cool again" is not currently implemented. The system operates on exact recall returning data structures without modifying their companion field energy values or re-injecting them into the propagating field state. Flagged for review on whether this integration is needed or if the design has moved on.
• Batched recall usage: VaultStore.recall_batch is implemented and verified but has no caller in the main runtime path. Review if it should be wired to support batch processing of turn sequences.

Closure criteria scorecard

Criterion	Status	Evidence
1. Design artifact	✅	ADR-0014, ADR-0019, ADR-0054
2. Code artifact	✅	vault/store.py, vault/decompose.py, core/physics/learning.py
3. Live caller	⚠️ PARTIAL	session/context.py and chat/runtime.py consume store/decompose; but core/physics/learning.py has no live caller
4. Exercised by suite lane	✅	algebra suite lane exercises recall; full lane exercises store/indexing
5. Cross-layer consistency	⚠️ PARTIAL	Exchanged symbols match expectations, but VaultPromotionPolicy is dormant and the re-thaw path is not wired

Verdict: PARTIAL (due to dormant promotion policy and unwired re-thaw path).

Cleanup performed

None. Checked vault/ files (store.py, decompose.py). Both modules have live callers and tests. core/physics/learning.py is dormant but retained as future-wiring debt per L2-specific cleanup rules.

Findings / notes for downstream layers

• L3 (Language packs) auditor: Lexicons and identity packs specify aspect-class weights (e.g. yiqtol, qatal) which feed into field energy calculation (ADR-0006). Since the L2 vault recall does not currently implement the re-thaw path (raising energy back to E2), downstream language readback rules receive vaulted E0 crystalline concepts rather than transiently warmed E2 concepts. The L3 audit should look at whether language readback rules actually handle E0 vs E2 correctly at the surface.
• L8 (Inter-session memory + contemplation) auditor: ADR-0055 details Tier 1 session vault (vault/store.py) and its relation to Tier 3/4 memory. Contemplation and memory discovery will need to query the session vault. Ensure that the lack of re-thaw path and the dormant VaultPromotionPolicy do not block Tier 1 to Tier 3/4 promotion/crystallization logic when those layers are audited.

---

L3 — Language packs

Audit date: 2026-05-24 Auditor: primary agent (Gemini) Verdict: PARTIAL

Scope-hypothesis correction (per audit step 0)

The scope's layering table cited packs/ directories and ADRs ADR-0027..0047, ADR-0070..0073. Reality: L3 primary concerns also extend to ADR-0005 (language pack contract), ADR-0015 (linguistic manifolds & holonomy resonance), ADR-0091 / ADR-0093 (domain pack contract & implementation), ADR-0102 / ADR-0103 (Hebrew/Greek textual reasoning and fluency), and proposed-only/substrate-only ADR-0084 (definitional layer) and ADR-0087 (rhetorical style axis).

ADRs in scope for L3

Triaged from Keyword grep against docs/decisions/:

ADR	Title	Status	Belongs at L3?
ADR-0005	Language Pack Contract	Accepted	Yes — defines language_packs/ format, schemas, and loader contract
ADR-0015	Language Packs as Compiled Linguistic Manifolds	Accepted	Yes — compiled linguistic manifolds and holonomy resonance
ADR-0027	Identity Packs — Load-Bearing, Swappable, Ratified	Accepted	Yes — defines swappable, ratified identity packs
ADR-0028	Identity Surface Wiring	Accepted	Boundary-only — L3 compiles/loads identity packs; realizer/composition is L6
ADR-0029	Safety Packs — Always-Loaded, Never-Replaceable Boundaries	Accepted	Yes — always-loaded safety boundaries
ADR-0030	Depth-Language Hedge Wiring	Accepted	Boundary-only — L3 compiles safety/hedging lemmas; realizer is L6
ADR-0033	Ethics Packs — Swappable Domain Commitments	Accepted	Yes — swappable ethics domain commitments
ADR-0043	Phase-2 pack measurements: claims -> numbers	Accepted	Yes — compiles claims to numbers/weights
ADR-0044	Medical / clinical ethics pack	Accepted	Yes — worked-example domain pack
ADR-0051	Trust-Boundary Hardening Pass	Accepted	Yes — defines PackMutationProposal validation and compiler trust rules
ADR-0068	Register pack class	Accepted	Yes — specifies RegisterPack class and cataloging
ADR-0070	Second ratified register pack: terse_v1	Accepted	Yes — register pack definition
ADR-0073	Anchor lens: substrate-driven substantive variation	Accepted	Yes — anchor lens pack layout and structure
ADR-0073a	Anchor lens content phase	Accepted	Yes — anchor lens content
ADR-0073b	Anchor lens class + loader	Accepted	Yes — loader class for anchor lens
ADR-0073c	First non-trivial lenses + composer wiring	Accepted	Boundary-only — L3 compiles anchor lenses; composer is L6
ADR-0073d	Anchor-lens telemetry, CLI, and tour demo	Accepted	Boundary-only — CLI/telemetry is L6
ADR-0084	Definitional Layer for Lexicon Packs	Proposed	Yes — optional definitional block for glosses and primitives
ADR-0087	Rhetorical Style as Selection Axis	Proposed	Yes — rhetorical style pack loader and catalog
ADR-0091	Domain Pack Contract v1	Accepted	Yes — domain pack schema
ADR-0093	Domain Pack Contract v1 Implementation	Accepted	Yes — compiler validation for domain packs
ADR-0102	Hebrew-Greek Textual-Reasoning Reasoning-Capable Ratification	Accepted	Yes — multi-pack ratification for Greek/Hebrew
ADR-0103	Fluency Lane Attachment for ADR-0102	Accepted	Boundary-only — L3 compiles Greek/Hebrew fluency lanes; runner/gate is L6

Modules in scope for L3

Module	Lines	Live-import sites (outside own package, outside tests/)	Test-import sites	Status
language_packs	74	31	53	Live
language_packs.__main__	157	0	0	Live (CLI entrypoint)
language_packs.compiler	620	7	31	Live
language_packs.definitions	312	0	4	Dormant (ADR-0084 proposed)
language_packs.domain_contract	217	3	1	Live
language_packs.en_seeder	276	1	0	Live (Scripts/run_pulse)
language_packs.evidence	64	0	1	Dormant (ADR-0015 test only)
language_packs.loader	387	5	3	Live
language_packs.numerics_loader	459	3	3	Live
language_packs.schema	202	6	4	Live
packs.anchor_lens	25	3	4	Live
packs.anchor_lens.loader	422	3	2	Live
packs.common.runtime_rules	122	8	0	Live
packs.common.validator	133	4	0	Live
packs.el.lift_rules	14	0	0	Live (Dynamic)
packs.el.readback_rules	9	0	0	Live (Dynamic)
packs.el.validators	19	0	0	Live (Dynamic)
packs.en.lift_rules	14	0	0	Live (Dynamic)
packs.en.readback_rules	9	0	0	Live (Dynamic)
packs.en.validators	19	0	0	Live (Dynamic)
packs.ethics	38	3	13	Live
packs.ethics.check	408	2	8	Live
packs.ethics.loader	409	1	5	Live
packs.grc.lift_rules	14	0	0	Live (Dynamic)
packs.grc.readback_rules	9	0	0	Live (Dynamic)
packs.grc.validators	19	0	0	Live (Dynamic)
packs.he.lift_rules	14	0	0	Live (Dynamic)
packs.he.readback_rules	9	0	0	Live (Dynamic)
packs.he.validators	19	0	0	Live (Dynamic)
packs.identity	14	3	4	Live
packs.identity.loader	494	3	4	Live
packs.primitives	33	0	3	Dormant (ADR-0084 proposed)
packs.primitives.loader	285	0	2	Dormant (ADR-0084 proposed)
packs.register	24	11	7	Live
packs.register.loader	608	11	7	Live
packs.rhetorical_style	36	0	3	Dormant (ADR-0087 proposed)
packs.rhetorical_style.loader	425	0	2	Dormant (ADR-0087 proposed)
packs.safety	39	3	13	Live
packs.safety.check	332	2	9	Live
packs.safety.loader	259	1	4	Live

Note: Individual language-pack rule files (packs/<lang>/lift_rules.py, readback_rules.py, validators.py) are loaded dynamically by packs/common/validator.py and core/cli.py via importlib.util (registered under local dynamic paths), hence having 0 static Python import sites.

Caller-trace evidence

Exposed symbols of the layer are cleanly resolved through static imports across multiple layers:

• language_packs.compiler.load_pack is called by chat/runtime.py to mount the live vocabulary.
• language_packs.compiler.load_mounted_packs is used in tests/test_oov_grounding_cache.py and tests/test_dialogue.py.
• language_packs.loader.lookup_unit is consumed by the math parsers generate/math_parser.py:120 and generate/math_candidate_parser.py:660.
• language_packs.loader.lookup_cardinal / parse_compound_cardinal are consumed in generate/math_roundtrip.py:377,400.
• packs.common.validator.validate_pack_dir is called by every pack-specific validation entrypoint (packs/<lang>/validators.py).

Exercising suite lane

• core test --suite packs — Exercises pack loading, compilation, and ratification checks:

  python3 -m core.cli test --suite packs -q
  

  Verification: 13 passed, 0 skipped.
• core test --suite smoke — Exercises the end-to-end turn loop pipeline mounting default packs:

  python3 -m core.cli test --suite smoke -q
  

  Verification: 67 passed, 0 skipped.
• verify_lane_shas.py — Exercises all 7 pinned lanes:

  python3 scripts/verify_lane_shas.py
  

  Verification: lanes: 7/7 match pinned SHAs.

Cross-layer contract check

Pass 1 — mechanical (consumer-exists per exposed symbol):

Exposed symbol	Consumer evidence
compile_entries_to_manifold	tests/test_epistemic_phase3_state_tagging.py:84, tests/test_holonomy_resonance.py:93
load_pack	chat/runtime.py, scripts/run_pulse.py:78, tests/test_proof_properties.py:24
load_mounted_packs	chat/runtime.py, tests/test_dialogue.py:11, tests/test_oov_grounding_cache.py:10
lookup_unit	generate/math_parser.py:121, generate/math_candidate_parser.py:661
lookup_cardinal	generate/math_roundtrip.py:377,402
validate_pack_dir	packs/he/validators.py:7, packs/grc/validators.py:7, packs/el/validators.py:7, packs/en/validators.py:7

Pass 2 — semantic (three load-bearing invariants checked):

1. Pack manifest checksums match bytes on disk: Verified in language_packs/compiler.py and language_packs/__main__.py that manifest checksums are computed using hashlib.sha256(Path(...).read_bytes()).hexdigest(). This ensures byte-level disk hashing instead of serialization of Python strings, fully respecting CLAUDE.md guidelines.
2. Pack mutation is proposal-only: Grep scans confirm that no production runtime code path in language_packs/ or packs/ writes to or mutates on-disk ratified packs. Changes are strictly proposed via PackMutationProposal / TeachingChainProposal and applied via offline reviewed CLI commands (e.g. core teaching review --accept).
3. E0 vs E2 readback handling: Checked readback_from_intent in packs/common/runtime_rules.py. While it receives field_state.energy and places its value into the SurfaceRealization metadata dataclass, it silently treats E0 identically to active E1/E2/E3 regions, returning the raw requested surface without modulating tense, framing, or hedging. This is a semantic inconsistency with ADR-0006/0007.

Semantic mismatches flagged for human review

• Dormant Readback rules: The local readback logic (packs/<lang>/readback_rules.py) is completely unwired and has 0 callers outside validation checks (packs/common/validator.py). Surface generation is performed by generate/realizer.py instead of the local pack readback functions.
• E0/E2 Readback modulation mismatch: Readback rules do not implement the energy-based tense or hedging modulations specified in ADR-0006/0007. E0 (recalled vault crystal) is formatted the same as E2/E3 (warmed/active field regions) at the pack level.

Closure criteria scorecard

Criterion	Status	Evidence
1. Design artifact	✅	ADR-0005, ADR-0015, ADR-0027, ADR-0029, ADR-0033, ADR-0051, ADR-0068, ADR-0070, ADR-0073, ADR-0091, ADR-0093, ADR-0102
2. Code artifact	✅	language_packs/ (compiler, loader, schema), packs/ (common rules, check loaders, register loader)
3. Live caller	⚠️ PARTIAL	Live turn loop mounts packs and resolves vocabulary, but local pack readback rules are dormant and unwired
4. Exercised by suite lane	✅	packs exercises compilation/ratification; smoke exercises turn pipeline e2e
5. Cross-layer consistency	⚠️ PARTIAL	Local readback rules silently treat E0/E2/E3 identically, conflicting with ADR-0006/0007 modulation rules

Verdict: PARTIAL (due to dormant readback rules and unwired E0 vs E2 surface modulation).

Cleanup performed

None. Audit found no unambiguously dead code. All dormant modules are either CLI entrypoints, proposed-only substrates (ADR-0084 definitions, ADR-0087 rhetorical styles), or dynamically loaded pack boundary scripts (lift, readback, validators).

Findings / notes for downstream layers

• L4 (Recognition) auditor: L3 domain/lexicon schemas provide the foundational vocabulary. Ensure recognition anti-unification uses the compiled domain namespaces from the VocabManifold.
• L5 (Cognition pipeline) / L6 (Chat runtime) auditor: Note that the local readback rules within packs are dormant. Downstream surface generation utilizes generate/realizer.py. If future work activates local pack-driven readback or requires energy-modulated surface forms, the readback rules must be wired in and updated to differentiate E0 (vault recall) vs E2 (transiently warmed) states.

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L4 — Recognition

Audit date: 2026-05-24 Auditor: Codex Verdict: PARTIAL

Scope-hypothesis correction (per audit step 0)

The scope's layering table cited ADR-0143 and ADR-0144 as starting points. Reality: L4 also has a boundary dependency on ADR-0142, because the recognition outcome and carrier emit the ADR-0142 epistemic-state vocabulary. Dispatch trace has no standalone ADR; it is an ADR-0142 implementation-debt closure that landed in chat/dispatch_trace.py and chat/runtime.py.

ADRs in scope for L4

Triaged from recognition / anti-unification / epistemic / proposition graph / feature-bundle / dispatch-trace keyword grep against docs/decisions/:

ADR	Title	Status	Belongs at L4?
ADR-0142	Epistemic State Taxonomy — First-Class Vocabulary	Accepted	Boundary-only — defines states that recognition may emit and names dispatch trace as provenance debt
ADR-0143	Teaching-Derived Structural Recognition via Multi-Resolution Anti-Unification	Accepted	Yes — defines RecognitionOutcome, DerivedRecognizer, derive_recognizer(), recognize(), refusal layers, and byte-identity guarantees
ADR-0144	PropositionGraph — Epistemic Carrier and Recognition Integration Gate	Accepted	Yes — defines EpistemicGraph, connector, pipeline recognizer parameter, and opt-in recognition-grounded graph

Related scope docs in this layer, not ADRs: teaching-derived-recognition-scope.md, proposition-graph-scope.md, recognizer-storage-scope.md, and epistemic-state-taxonomy-scope.md.

Other ADRs surfaced by the grep but assigned to other layers: ADR-0021 (general epistemic grade policy / teaching safety), ADR-0115 / ADR-0126 / ADR-0132..0136 (math candidate/proposition graph corridor), ADR-0127 / ADR-0128 (pack-typed units/numerics recognition for math parser), and ADR-0131.G.3 / ADR-0131.G.3.1 (literal-recognition axes). These are not the teaching-derived L4 recognition mechanism audited here.

Modules in scope for L4

Module	Lines	Live-import sites (outside own package, outside tests/)	Test-import sites	Status
recognition.__init__	11	0	0	Re-export shim; no external direct consumers
recognition.anti_unifier	628	1 (core/cognition/pipeline.py)	3	Mechanism coded; live only when a recognizer is explicitly supplied
recognition.outcome	367	0 outside recognition/; 3 package-internal live consumers	3	Contract coded; live through anti_unifier / carrier / connector
recognition.carrier	128	2 (core/cognition/pipeline.py, core/cognition/result.py)	1	Carrier coded; live result field exists
recognition.connector	66	1 (core/cognition/pipeline.py)	1	Connector coded; live only under opt-in flag and supplied recognizer
chat.dispatch_trace	13	1 outside chat/ (core/cognition/result.py), plus chat/runtime.py live consumer	1	Live in ChatRuntime and surfaced through CognitiveTurnResult

No unambiguously dead code was found. recognition/connector.py is exactly the connector-style module the recognizer-storage scope warns about: it is coded and imported by the pipeline, but its meaningful path requires a supplied DerivedRecognizer and recognition_grounded_graph=True. Flagged, not deleted.

Caller-trace evidence

• core/cognition/pipeline.py:38-40 imports DerivedRecognizer, recognize, EpistemicGraph, EpistemicNode, and epistemic_node_to_graph_node.
• core/cognition/pipeline.py:117-127 accepts recognizer: DerivedRecognizer | None = None and stores it on self._recognizer.
• core/cognition/pipeline.py:152-169 tokenizes once and calls recognize(self._recognizer, raw_tokens) only when a recognizer was attached. Admitted outcomes become a per-turn EpistemicGraph.
• core/cognition/pipeline.py:201-211 invokes the connector only when self.runtime.config.recognition_grounded_graph is true and an epistemic_graph exists.
• core/cognition/result.py:105-115 exposes epistemic_graph and dispatch_trace on CognitiveTurnResult.
• core/config.py:245-250 defines recognition_grounded_graph: bool = False.
• chat/runtime.py:46,840-1134,1656-1686,1901-1986 builds dispatch attempts and selected-source traces; chat/runtime.py:415 exposes the trace on ChatResponse.
• All non-test CognitiveTurnPipeline(...) constructions found in scripts/, benchmarks/, and evals/ omit the recognizer argument. core chat constructs ChatRuntime, not a CognitiveTurnPipeline with a recognizer.

The recognizer branch is therefore present in the cognitive spine but has no normal runtime constructor that supplies a derived recognizer. The mechanism is coded; integration into normal operation is absent.

Exercising suite lane

• core test --suite smoke exercises the default cognitive pipeline and verifies pre-existing behavior with recognizer=None.

  python3 -m core.cli test --suite smoke -q
  

  Verification: 67 passed.
• Direct L4 tests exercise the recognition mechanism, carrier, connector, and dispatch trace:

  python3 -m pytest tests/test_epistemic_carrier.py tests/test_recognition_phase1.py tests/test_recognition_phase2.py tests/test_dispatch_trace.py -q
  

  Verification: 28 passed.
• scripts/verify_lane_shas.py still matches all pinned evidence lanes:

  python3 scripts/verify_lane_shas.py
  

  Verification: lanes: 7/7 match pinned SHAs.

Lane gap: the direct L4 tests are not named in any curated core test --suite {smoke|cognition|teaching|packs|runtime|algebra} alias except the broad full alias. smoke covers the default recognizer=None path, but no documented curated lane exercises CognitiveTurnPipeline(..., recognizer=...).

Cross-layer contract check

Pass 1 — mechanical (consumer-exists per exposed symbol):

Exposed symbol / field	Consumer evidence
derive_recognizer()	Direct tests only (tests/test_recognition_phase1.py, tests/test_recognition_phase2.py, tests/test_epistemic_carrier.py); no live constructor derives a recognizer
DerivedRecognizer	Type-consumed by core/cognition/pipeline.py:121; no non-test caller passes an instance
recognize()	core/cognition/pipeline.py:160, but only when _recognizer is not None; direct tests call it heavily
RecognitionOutcome / FeatureBundle / typed refusals	Consumed by recognition.anti_unifier, recognition.carrier, recognition.connector, and direct tests
EpistemicGraph	Produced by core/cognition/pipeline.py:166-169, stored on CognitiveTurnResult.epistemic_graph; no downstream live consumer reads it yet
EpistemicNode.with_transition()	Direct tests only; no verifier/vault transition caller yet (ADR-0144 explicitly defers verifier/vault transitions)
epistemic_node_to_graph_node()	core/cognition/pipeline.py:207-210 under opt-in flag; direct connector tests
RuntimeConfig.recognition_grounded_graph	Read by core/cognition/pipeline.py:206; default false
DispatchTrace / DispatchAttempt	Built in chat/runtime.py, surfaced on ChatResponse.dispatch_trace and CognitiveTurnResult.dispatch_trace, asserted by tests/test_dispatch_trace.py

Mechanical closure gaps:

• No non-test caller derives, stores, loads, or passes a DerivedRecognizer into CognitiveTurnPipeline.
• The ADR-0144 refusal path is incomplete in the pipeline: refused recognition produces no carrier, but _rec_outcome.refusal_reason is not copied into CognitiveTurnResult.refusal_reason; that field is populated from ChatResponse.refusal_reason instead.
• EpistemicGraph is exposed on the turn result but has no live downstream consumer beyond tests.

Pass 2 — semantic (three L4 invariants checked):

1. Recognizer integration into live turn loop: Confirmed partial. The pipeline accepts a recognizer and can call it, but every normal constructor found in scripts, benchmarks, evals, and tests outside L4-specific direct fixtures omits recognizer=.... No main/runtime path constructs or persists one. L4 is therefore at most PARTIAL.
2. Anti-unifier determinism: Mostly satisfied by construction and tests. DerivedRecognizer.to_json() sorts keys with compact JSON; FeatureBundle.from_mapping() sorts features; allowed verb phrases are sorted before serialization and matching; ignored prefix tokens are sorted. teaching_set_id is SHA-256 of json.dumps(sorted(token_sequences), ensure_ascii=False, separators=(",", ":")), so example order does not affect the id. Caveat: the hash covers token sequences only, not the full feature bundles. Same tokens with different taught feature values would share a teaching_set_id; this is a semantic identity mismatch against the phrase "same teaching examples" if "example" includes labels/bundles.
3. Vocabulary source: Recognition does not consume L3's compiled VocabManifold, domain namespaces, or pack-resident lexicon. Grep across recognition/ found no VocabManifold, language_packs, load_pack, compiled, lexicon, or vocab references except a prose comment in outcome.py. derive_recognizer() operates on raw token sequences plus taught FeatureBundle evidence.

Semantic mismatches flagged for human review

• Teaching-set hash scope: ADR-0143 says teaching_set_id is a hash of the teaching set. The implementation hashes only sorted token sequences, not the feature bundles. If two reviewed teaching sets share tokens but differ in feature labels, values, or evidence, they collide at the recognizer identity layer even though the derived recognizer may differ.
• L3 vocabulary bypass: Per L3's forward note, L4 does not use the compiled vocabulary/domain namespaces from VocabManifold. This may be acceptable for the token-level spike, but it means L4 recognition is not yet grounded in L3's pack-resident domain schema.
• Recognition refusal observability: ADR-0144 describes typed recognition refusal materialization on the turn result. The current pipeline discards _rec_outcome.refusal_reason on refused recognition and leaves CognitiveTurnResult.refusal_reason to the generation/chat path.

Closure criteria scorecard

Criterion	Status	Evidence
1. Design artifact	✅	ADR-0142 boundary vocabulary, ADR-0143, ADR-0144
2. Code artifact	✅	recognition/{anti_unifier,outcome,carrier,connector}.py, chat/dispatch_trace.py, pipeline/result/config fields
3. Live caller	⚠️ PARTIAL	Pipeline imports and conditionally calls recognizer, but no normal runtime constructor supplies one; dispatch trace is live
4. Exercised by suite lane	⚠️ PARTIAL	smoke exercises default no-recognizer path; direct L4 tests pass but are not in a curated lane except full
5. Cross-layer consistency	⚠️ PARTIAL	Carrier/result fields exist; recognizer storage/loading absent; refusal reason not propagated; L3 vocabulary not consumed

Verdict: PARTIAL (mechanism and carrier are coded; dispatch trace is live; derived recognizer storage/construction and normal turn-loop integration are absent).

Cleanup performed

None. No unambiguously dead, redundant, superseded, or orphaned code was found. Connector-style modules are flagged as wiring debt rather than deleted because the recognizer-storage scope explicitly leaves these awaiting integration/storage ADRs.

Findings / notes for downstream layers

• L5 (Cognition pipeline) auditor: The pipeline has a recognition branch, but it is cold unless a caller supplies DerivedRecognizer. Verify whether L5's current verdict should treat this as an optional observability branch or an unclosed live cognitive step. Also check the recognition-refusal drop: _rec_outcome.refusal_reason is not folded into the turn result.
• L6 (Chat runtime) auditor: Dispatch trace is live in ChatRuntime and surfaced through ChatResponse / CognitiveTurnResult, but it is observability only and not folded into trace hash. Confirm whether L6 contracts require trace-hash participation or only operator-visible provenance.
• L7 (Teaching loop) auditor: Recognition refusals are intended to be teaching signals, but the live pipeline currently discards typed recognizer refusals. If teaching-derived recognition is to feed review, L7 needs a concrete consumer or the L4/L7 boundary remains open.
• Recognizer-storage ADR: This audit confirms the storage scope's core finding: DerivedRecognizer is serializable and accepted by the pipeline, but nothing in main constructs, persists, loads, shares, or reactivates one across sessions.

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