# Codex Brief - Domain-Pack Closure Cleanup (PR #97 follow-up) **Audience:** Same agent that landed PR #97 (chain-first capability ledger + 5 domain seeds + ADR-0091 domain-pack contract). **Mission:** The three new English domain seed packs landed with `manifest.json` carrying `"definitional_layer": true`, which opted them into the ADR-0084 definitional-closure verifier - but they were not authored against ADR-0084 closure discipline (atoms must equal `content_tokens(gloss)` exactly; every atom must resolve as a `lemma` somewhere). The verifier is currently red on main solely because of these three packs. Flip the flag on each of the three packs to remove them from the ADR-0084 closure lane. They remain governed by their own `domain_contract_version: 1` contract (ADR-0091), which is a different and intentional layer. **Estimated effort:** Trivial - three one-character JSON edits + checksum refresh + verification. --- ## Background - why this happened PR #97 introduced ADR-0091 (`domain_contract_version`) as a new pack-layer contract for domain seeds. These packs carry axioms, rules, teaching chains, and capability evidence - they are not the closed-under-atoms definitional packs that ADR-0084 governs. ADR-0084's closure verifier requires for every gloss: 1. `definitional_atoms == content_tokens(gloss)` exactly (token equality, after stripping stopwords/prepositions). 2. Every atom in `definitional_atoms` resolves as a `lemma` field in some pack's `lexicon.jsonl`, `glosses.jsonl`, or in `packs/primitives/en_semantic_primitives_v1/primitives.jsonl`. Domain seed packs don't satisfy either rule, by design - they list domain-specific tokens (`mapping`, `input`, `output`, `transition`, `inertia`, ...) that are not lemmas in the lexicon layer, and their glosses are written for human/contract readability, not as atom-graph closure proofs. Both the script `scripts/verify_definitional_closure.py` and the integration test `tests/test_adr_0084_integration_closure.py` filter by `definitional_layer: true`. The integration test additionally hard-codes an `OPTED_IN_PACKS` allowlist that does not include the three domain packs - which is why the test is green even though the script is red. Flipping the manifest flag aligns the script with the test's clearly-intended scope. ## Phase 0 - Baseline ```bash PYTHONPATH=. python3 scripts/verify_definitional_closure.py 2>&1 | head -5 # Expected: 3 packs in unresolved_by_pack and 3 packs in mismatched_atoms_by_pack # (en_mathematics_logic_v1 / en_physics_v1 / en_systems_software_v1) PYTHONPATH=. python3 -m pytest tests/test_adr_0084_integration_closure.py -q # Expected: 30 passed PYTHONPATH=. python3 -m core.cli eval cognition > /tmp/eval_baseline.json # Capture baseline for byte-identity check. ``` ## Phase 1 - Flip the flag For each of these three manifest files, change exactly one line: ``` language_packs/data/en_mathematics_logic_v1/manifest.json language_packs/data/en_physics_v1/manifest.json language_packs/data/en_systems_software_v1/manifest.json ``` Before: ```json "definitional_layer": true, ``` After: ```json "definitional_layer": false, ``` Do not touch any other field. Do not touch `glosses.jsonl`, `lexicon.jsonl`, `axioms.json`, `rules.json`, the chains file, or the `domain_contract_version`. The ADR-0091 domain-pack contract is unchanged. ## Phase 2 - Refresh manifest checksum The `checksum` field on each manifest hashes the bytes of the lexicon file (see `language_packs/loader.py`'s checksum policy). Since we are not touching the lexicon, the lexicon-hash component is unchanged. But some loaders also hash the manifest itself in their own provenance - confirm by running the standard checksum-refresh shell snippet from [ADR-0085-content-style-pass-brief.md](./ADR-0085-content-style-pass-brief.md) Phase 3, applied only to these three packs. If the `glosses_checksum` field exists and the loader does not require it to change when only the manifest flag changes, leave it. If you are unsure, run: ```bash PYTHONPATH=. python3 -m core.cli pack validate en_mathematics_logic_v1 PYTHONPATH=. python3 -m core.cli pack validate en_physics_v1 PYTHONPATH=. python3 -m core.cli pack validate en_systems_software_v1 ``` - and let those tell you whether checksum refresh is needed. If the loader rejects a manifest as stale, refresh `checksum` for that pack only. ## Phase 3 - Verify All five must pass: ```bash # 1. Closure verifier green PYTHONPATH=. python3 scripts/verify_definitional_closure.py # Expected: 0 unresolved, 0 mismatches. # 2. ADR-0084 integration test still green (scope unchanged) PYTHONPATH=. python3 -m pytest tests/test_adr_0084_integration_closure.py -q # Expected: 30 passed. # 3. Domain pack contract test still green PYTHONPATH=. python3 -m pytest tests/ -k domain_contract -q # Expected: same pass count as before the change. # 4. Cognition eval byte-identical PYTHONPATH=. python3 -m core.cli eval cognition > /tmp/eval_post.json diff /tmp/eval_post.json /tmp/eval_baseline.json # Expected: empty diff (closure-layer flag does not affect chat/eval lanes). # 5. Packs lane PYTHONPATH=. python3 -m core.cli test --suite packs -q # Expected: pass. # 6. Smoke lane PYTHONPATH=. python3 -m core.cli test --suite smoke -q # Expected: pass. ``` If `core eval cognition` drifts byte-from-byte from baseline, stop and report - the flag should be inert for runtime, but if it isn't there's an unexpected coupling worth investigating before merge. ## What this brief does not do - Does not modify any pack content (glosses, lexicon, atoms, rules, axioms). - Does not modify the ADR-0091 `domain_contract_version` or any field under it. - Does not modify the closure verifier code or the integration test allowlist. - Does not alter `chat/`, `generate/`, `core/cognition/`, or any other runtime module. If verification surfaces something the manifest-flag flip alone cannot fix, stop and report - do not start patching atoms in the domain packs as a workaround. ## Deliverables 1. Edits on branch `feat/codex/domain-pack-closure-cleanup`. 2. Draft PR titled `fix(packs): flip domain-seed packs out of ADR-0084 closure layer (PR #97 follow-up)` with this report: ``` ## Summary Three domain seed packs from PR #97 (`en_mathematics_logic_v1`, `en_physics_v1`, `en_systems_software_v1`) shipped with `definitional_layer: true` but are governed by ADR-0091 `domain_contract_version: 1` - a different and intentional layer. The ADR-0084 closure verifier was red on main solely because of this mis-labeling. The ADR-0084 integration test was already green because its allowlist excludes these packs. This PR flips the three manifest flags to align the script with the test's intended scope. ## Verification - closure verifier: 0 unresolved, 0 mismatches - ADR-0084 integration test: 30/30 - domain contract test: / - cognition eval: byte-identical to baseline - packs lane: pass - smoke lane: pass ``` 3. Mark Draft. Human reviews before merge. ## Hard rules - Do not touch glosses, lexicons, atoms, rules, axioms, or the chains file. - Do not touch any code. - Do not widen the ADR-0084 integration test's allowlist. - Closure verifier must exit 0 after the flip. - Cognition eval must be byte-identical to baseline.