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	⏳ Pending	—	—	—
L2 — Vault	✅ Audited	PARTIAL	None — flagged learning as wiring debt	2026-05-24
L3 — Language packs	⏳ Pending	—	—	—
L4 — Recognition	⏳ Pending	—	—	—
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).

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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.

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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.

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