Fix bare-Potato material identity and preserve mapping-refresh provenance

docs/MIM_REVIEWED_RELEASE.md

@@ -12,10 +12,11 @@ old September 21 release. Its `candidate_only` mode controls candidate generatio
 not permission to publish or silently replace production mappings. Paired
 production promotion remains the separate reviewed step below.
 
-The [2026-09-27 invalid-CAS mapping review](reviews/mim-invalid-cas-20260927/PROMOTION.md)
-records the latest proposed paired staging change and its remaining gates.
+The [2026-09-29 Potato scope record](reviews/mediadive-potato-scope-20260929/PROMOTION.md)
+records the latest isolated paired staging change and its remaining gates.
 Paired-change tests, CI, production integration and fresh KG validation remain
-separate required gates. The [earlier native-category record](reviews/mim-native-category-20260927/PROMOTION.md)
+separate required gates. The [2026-09-27 invalid-CAS mapping review](reviews/mim-invalid-cas-20260927/PROMOTION.md),
+[earlier native-category record](reviews/mim-native-category-20260927/PROMOTION.md)
 and [2026-09-25 acceptance record](reviews/mim-admission-20260925/PROMOTION.md)
 are preserved as historical evidence, not reassigned to the new candidate. The
 first hydration candidate exposed three further legacy scope defects (#1169)
@@ -194,7 +195,12 @@ The legacy full consolidator now refuses to run while the release pin is present
 including with `--dry-run` or `--allow-stale-vendored`: its additive seed and raw
 companion paths would undo the migration. Its narrowly scoped
 `--identity-policy-only --output ...` operation remains available; it does not
-constitute a MIM refresh.
+constitute a MIM refresh. That bounded operation names its actual writer,
+`scripts/consolidate_chemical_mappings.py`, and its code SHA-256 in the tool/version
+metadata. It preserves the description's meaning and adds one current identity
+policy fingerprint. Original reconstruction provenance is retained through the
+reviewed baseline hash and prior record, not a mismatched old tool/new version.
+Unrelated metadata and retained mapping rows remain unchanged.
 
 The earlier input-schema repair added explicit empty `verified_date` cells to
 two canonical chemical rows. That formatting-only repair did not install the
@@ -205,17 +211,19 @@ receipts to hide input or code drift.
 ## Promotion, transforms, and merge
 
 Candidate generation does not publish files or run production transforms. Once
-the final delta and consumer behavior are accepted, promote **both** the reviewed
-unified candidate and the byte-exact supported MIM table to their canonical
-mapping paths in one reviewed change:
+the final delta and consumer behavior are accepted, verify and promote the
+reviewed unified candidate and the byte-exact supported MIM table **together** at
+their canonical mapping paths in one reviewed change:
 
 - `mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz`
 - `mappings/ingredient_mappings.sssom.tsv`
 
 The supported file must match the committed pin's supported-product hash; the
 unified file must match the final accepted candidate hash. Do not install the
 upstream source SSSOM, the withheld product, a floating sibling checkout, or
-only one member of the pair. `mode=candidate_only` remains the CLI's publication
+an unverified counterpart. If the supported table already has the pinned bytes,
+retain it unchanged; paired review does not require a meaningless rewrite or a
+new MIM release pin. `mode=candidate_only` remains the CLI's publication
 boundary: paired installation is an explicit reviewed repository operation,
 not permission for future automatic refreshes.
 

docs/reviews/mediadive-potato-scope-1236.md

@@ -0,0 +1,60 @@
+# Bare Potato is not an evidenced extract identity (#1236)
+
+The [official EINECS inventory](https://www.mhsr.sk/uploads/files/Zwx10C5G.pdf)
+(PDF page 21, checked 2026-09-29) pairs CAS 93348-51-7 and EC 297-194-4 with
+`zemiak, Solanum tuberosum aegrotans, extrakt`. Its described scope is extractives
+and physically modified derivatives. Preserve the `aegrotans` qualifier; this
+is not a declaration that every potato extract or starting tuber is identical.
+
+The historical nine MediaDive ingredient-1606 observations are retained in
+`tests/resources/mediadive/potato_scope.json`, including their exact original
+recipe JSON and immutable historical witness/archive hashes. Five say peeled
+and cut, one says fresh/washed/peeled/sliced, and three say only Potato. The six
+explicit starting-material descriptions do not establish the extract identity;
+the three unqualified observations lack the specificity to choose it. Neither
+group proves that every eventual prepared extract is chemically different.
+All nine observations, including amounts and optional concentration fields,
+remain valuable source data and must survive withholding this grounding.
+
+The source recipe JSON contains no CAS property. The imported unified lexical
+claim and both legacy MicroMediaParam rows are separate evidence layers. The
+fixture preserves the complete unified row and identifies the legacy rows;
+the producer audit must preserve full original mapping rows/input identities,
+not invent a CAS assertion inside the unchanged raw recipe record. MediaDive's
+[ingredient page](https://bacmedia.dsmz.de/ingredients/1606) also cautions that
+identifiers are largely automatically matched. Its
+[recipe 3653](https://bacmedia.dsmz.de/solutions/3653) boils and strains the starting
+material, which does not establish ingredient-to-extract identity by itself.
+
+The finite policy therefore withholds **bare Potato → cas:93348-51-7** through
+the existing shared name/target guard. It does not ban the CAS identifier,
+reject arbitrary strings containing potato, select a replacement identity, or
+approve other extract names. Explicit authority labels and direct registry
+queries remain eligible for separately supplied evidence. Potato flour,
+starch, and other named preparations remain distinct; none is an inferred
+replacement for these records.
+
+The same guard covers the unified reader, strict/hydrate fallback parsing,
+embedded CAS-RN aliases, and nested solution-name lookup. With no independent
+exact target, MediaDive retains its existing source-local ingredient identity;
+no pure compound, botanical taxon, or flour identity is invented. Rebuilding
+from a stale synonym or legacy file must not resurrect the held claim.
+Candidate quarantine and producer-bound audit retain imported claims separately
+from active graph identity. Audit reasons distinguish
+`unsupported_material_form_identity` from `insufficient_material_specificity`.
+
+The policy change alone does not replace mapping artifacts. The separate
+[2026-09-29 staging record](mediadive-potato-scope-20260929/PROMOTION.md)
+records the reviewed identity-only unified candidate staged in an isolated
+worktree; the pinned supported MIM product and release pin remain byte-identical.
+Production integration, full replay and release acceptance are separate gates.
+Candidate generation and reviewed paired promotion follow
+`docs/MIM_REVIEWED_RELEASE.md`; changing a shared policy can stale consumers and
+requires fresh producer/merge admission. The historical nine-record fixture is
+not an expected count or release acceptance for a future rebuilt graph.
+
+The primary inventory was read directly, but the fixture is a small cited
+transcription, not a retained complete PDF or CAS Registry response. Failed
+Common Chemistry/PubChem retrievals supplied no evidence of registry absence.
+See [#1236](https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/1236), linked
+to the broader [#286](https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/286).

docs/reviews/mediadive-potato-scope-20260929/PROMOTION.md

@@ -0,0 +1,103 @@
+# Bare-Potato identity-only candidate: isolated staging, 2026-09-29
+
+Status: the independently reviewed candidate is staged in the isolated
+`fix/mediadive-potato-scope-1236` worktree only. It has **not** replaced the
+production checkout's unified artifact. Full MediaDive replay, final whole-suite
+gates, CI, production integration, fresh transforms/merge, and KG release review
+remain pending at this checkpoint. This record does not certify a release.
+
+The [scientific scope review](../mediadive-potato-scope-1236.md) and
+[#1236](https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/1236) hold only
+bare Potato → `cas:93348-51-7`, preserving source observations and imported
+grounding claims separately. No replacement chemical, registry identity or
+botanical identity is inferred. The
+[metadata correction #1237](https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/1237)
+makes the identity-only refresh identify its actual writer and preserve the
+semantic description without corrupting YAML scalar values.
+
+## Exact artifacts and origin
+
+| Role | SHA-256 |
+| --- | --- |
+| Original unified baseline | `f1545663016b3871d2176ccbdc76caffdefa472838b716956e8d722aaa2caff9` |
+| Accepted isolated unified candidate, 13,374,364 bytes | `09c44642ab13b234e89ce113f7510aa9efb56969e4b539cb7843b43dcb425ba7` |
+| Unchanged supported MIM table | `6b52b30e018b369aa322d41dfd4e81fcfae0e895e34d7fe48900abf5835815fb` |
+| Unchanged reviewed-release pin | `f082c05656a0910c85176eec7b41deeb77c27967aecb80393fddc262819b6d97` |
+| Current identity-only writer, `scripts/consolidate_chemical_mappings.py` | `257fe4d8bf16f92eb78d5e375065e030ea56d7c1174d859fecd2baa80ac18c27` |
+| Identity-policy fingerprint | `61786a46effa48de9901f77713b172db16a7d6797f35711d5c15c01b0e0ea926` |
+| Complete finite candidate review result | `447aff5399cea0dc06c947d67e25f9354ac1c9b98fbb1add204dfa3756c07232` |
+| Retained removed full-row TSV, 321 bytes | `07503b97da62d9ef0d5024e167bc55a79a6bea1a6bcb96202b2be658632391b0` |
+
+The original reconstruction writer was
+`scripts/mim_conservative_refresh.py`, SHA-256
+`58ec62b9b01a28f4f3b6b47ff319a11396617d4a07ada409acc2742bcb77ae6a`.
+That historical provenance remains bound to the original baseline and the
+[previous review](../mim-invalid-cas-20260927/PROMOTION.md); it is not presented
+as the writer of the new identity-only bytes.
+
+The upstream origin remains immutable MIM commit
+`1848b0fe521bc2462f165912fcf92d09ad9a8cec`, with reviewed manifest
+`9bb29d5605d93dea351be9624d99c5d8ada57d4b9831b22764957b784bd685af`.
+This is not a new upstream MIM export or tag. Both mapping products were checked
+as a pair; the already correct supported table and pin were not rewritten.
+
+## Verified finite delta
+
+The complete streaming comparison found exactly one removed 13-column lexical
+row: `kgm.name:potato` / `Potato` / `skos:closeMatch` /
+`cas:93348-51-7`, source `mediadive_compounds`, comment `synonym`, mapping date
+`2026-09-04`. Its exact original fields remain in
+`tests/resources/mediadive/potato_scope.json` (fixture SHA-256
+`b4755925efe8cde9871569b047e28c185ac56e2cba6295fca20fef2901062723`)
+and the removed-row evidence above. All retained mapping row bytes and order
+were identical. No new mappings or replacement targets were introduced.
+
+The candidate has 591,949 rows, 120,183 distinct targets, 336,050 exact matches
+and 255,899 close matches. Only three metadata fields changed:
+`mapping_tool`, `mapping_tool_version`, and `mapping_set_description`. The
+description retains the original conservative-MIM manifest statement and adds
+exactly one identity-policy fingerprint. All unrelated metadata bytes/order,
+assertion dates, historical unified version and legacy direction contract are
+unchanged. Supported MIM remains 1,747 exact mappings covering 1,696 names.
+
+A second identity-only refresh removed/relabelled zero rows and produced the
+same compressed candidate SHA-256, not merely equivalent parsed rows. Fresh
+runtime lookups returned no target for `Potato`, `potato`, `(Potato)` and
+`Pot.ato`; they preserved `CrKSO42 x 12 H2O` → `cas:7788-99-0`, `KH2PO3` →
+`cas:13977-65-6`, `TAPSO` → `cas:68399-81-5`, `TitaniumIII chloride` →
+`cas:7705-07-9`, and `Potato flour` → `FOODON:03302378`. Explicit extract and
+direct-CAS query eligibility does not invent a mapping absent from these inputs.
+
+The immutable local review directory is
+`data/issue1224-quarantine-20260929.xjuS9H/identity-candidate-1236-fixed.rxU4PT/review-complete-01/`.
+It contains the hash-bound `result.json`, before/after input guards,
+`removed-claim.tsv` / `removed-claim.json`, and exact `second-cycle.sssom.tsv.gz`.
+The earlier interrupted candidate remains diagnostic only and is not this
+accepted artifact. These candidate checks do not replace producer execution
+receipts or a full baseline/replay comparison.
+
+## Remaining gates
+
+The targeted native mapping-pair and legacy predicate-semantics modules passed
+**19 tests** against the staged candidate:
+
+```bash
+python -m pytest -q tests/test_sssom_asymmetric_direction.py tests/test_sssom_predicate_semantics.py
+```
+
+The changed test module also passed Ruff, and `git diff --check` passed. These
+are targeted checks, not full-suite or CI completion. The existing invalid-CAS,
+native-category, supported-pair and historical-fixture controls remain intact;
+the same full stream also checks absence of the exact held Potato row.
+
+The producer audit
+must retain actual complete strict/hydrate/embedded claims, source recipes and
+their hashes; the historical nine-record fixture is not an assumed current
+cohort. Whole-source replay must conserve all fields and occurrence multiplicity
+except the reviewed grounding delta, with explicit node review. Shared policy
+changes require current freshness assessment, potentially all 15 canonical
+producers, followed by fresh merge admission and KG model/path/release reviews.
+
+Green candidate checks or future green code CI alone do not complete these
+production and scientific gates. No freshness receipt may be restamped to make
+older outputs appear current.