Correct assay attribution and qualify cofactor and host graphs (batch 33)

[realmarcin]

Scope

Three graph-only corrections: Diclofenac MC, Dolichospermum FBCC-A233 and Drosophila five-species microbiota. Two reviews completed; Drosophila remains needs_research for species-resolved expansion. Corpus: 141 reviewed / 312 pending / 7 needs_research across 460 records in both roots.

Closes #1402. Closes #1403. Closes #1404. Non-graph #765/#1406/#1407 and graph research #1408 remain open. #1405 was withdrawn and publicly corrected, not fixed: it incorrectly claimed a non-graph metabolite entry existed.

Changes And Review

Seven nodes retained; one arrow retained as PARTIAL and one redundant outcome-to-panel arrow removed. No new structure. Correct MC-specific metabolite attribution using exact assay Results, distinguish relative community profiles from degraders, and preserve the prior workflow-arrow removal.

Remove unsupported cross-feeding from computational cofactor predictions and over-specific canonical cobalamin annotations. Three recovered genomes are not a complete culture census. Update existing knowledge-gap discussions and use canonical participants without taxonomy changes.

Represent joint host outcomes without untested exchange or mutualism. Qualify abundance-mediated host effects, preserve species dependence and host-genotype context. Species-resolved expansion remains pending under #1408; one-community Edison dry run only, no job/charge.

Verification

368 passed in 260.55s (0:04:20); eight new tests. Schema, strict, ontology, independent snippet and history gates passed. All three reference-validator commands exit 0 but perform zero checks: no-op, not evidence validation. Textual MATCH is not scientific support.

Zero structural errors and all 31 baseline warnings unchanged. Participant registry 176 to 178 adds only Diclofenac MC and Drosophila; measured connectivity survey unchanged. No algorithms or numeric bounds changed.

Three guarded writes, append-only histories, llm-assisted events and regenerated pages. All non-graph raw blocks, 457 other records and 920 caches preserved. Repeat rendering deterministic and exact descriptions checked across 456 pages. Actual post-commit docs-current passed with a clean tree. No browser screenshots claimed.

Decision ledger, validation report and self-adversarial findings are committed under reports/causal_graph_review, dated 20261006, batch33. Primary access is bounded per source, including targeted 2015 PDF reading rather than a complete-body claim; no figures visually inspected or supplement files read. No article body/PDF committed. This is self-adversarial review, not independent approval.

Dependency

Draft depends on #1401; do not merge into the topic parent. Require protected exact-head main checks and queue after parents merge. Move dependents before deleting branches. Full-corpus completion is not claimed.

[realmarcin]

Source-based self-adversarial review at exact head 5a3e1c3; not independent approval.

Addressed existing graph defects #1402/#1403/#1404 after source review and actual diff inspection. Seven nodes retained, one qualified arrow retained, one redundant arrow removed. Assay-specific attribution, genomic potential and host mediation are distinguished. Species-resolved expansion remains pending.

368 passed in 260.55s (0:04:20); eight new tests. Focused schema/strict/terms/snippet/history checks, deterministic rendering, exact descriptions across 456 pages and actual post-commit docs-current passed. Reference validator performed zero checks despite exit 0; no-op is not evidence validation. Zero structural errors and 31 unchanged warnings. Two participant registry additions, measured survey unchanged; no algorithms or numeric bounds changed. All non-graph raw blocks, 457 other records and 920 caches preserved.

Metadata #765/#1406/#1407 and research #1408 remain OPEN. Drosophila is needs_research, not a completed graph review. Incorrect-premise #1405 withdrawn with public correction, not claimed fixed. Edison dry run only, no job/charge. No article body/PDF committed; no visual figure or supplement inspection claimed. Protected main merge and full-corpus completion are not asserted. Committed decisions/validation/self-review records retain source limitations.

[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 31 warning across 12 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial review refreshed at exact head 441f6302d39d11b6d18da88316330f382e22d8ce
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 3507e2c7f50508eb0b7488a2ba166d9dc974c167
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 7441e72281fd39aa59b8982ba8b1574b2a6e67a2
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Reference-counter correction (#1469)

The earlier statement that linkml-reference-validator 0.1.7's Total checks: 0 means zero executed checks or a no-op is incorrect and withdrawn. The installed CLI prints the number of validation issues, not checks performed. Existing positive/negative and field-discovery canaries pass; EvidenceItem snippets are genuinely checked. SupportingReference coverage remains incomplete under #476. Text matching is not scientific support or independent source provenance.

The source-backed correction and historical candidate inventory are committed in #1470 at 22b5b12c2386a949d1ec4ddb1f79ee288085bd1c, under reports/causal_graph_review/README.md and reference-validator-correction-20261006-batch42.json. Earlier raw command output, source review, biological decisions and tested bytes are preserved; this notice does not claim a rerun of this PR's validation or change its biological findings. The older CLI counter is not a coverage metric.

The new Fucoidan batch separately retains 14 baseline reference-CLI failures and 15 baseline snippet-audit mismatches for supplement-sidecar excerpts. Those are not failures attributed to this older PR. This correction is self-review, not independent approval or merge authorization beyond the existing protected workflow.

[realmarcin]

Self-adversarial review refreshed at exact head 4d900a71b0ea561d09023593be8a182e62ecc181
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head d572bc7f326fc8e5c2555b70e960491c76926931
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 94c2336dc3029df217c0a4b5a05e65bc1feafad8
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head d3db0fefd93d84ec986d9049c5e52dae70e0ccbd
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head f6543e9dbf71882c6af611f1d45ecaf8067ce456
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 133c6e0eb3b41b0618c132d3f4a86133710c598c
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 195a0a3110933c063bc571b6b347e87e18f110b4
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3e87a74227fe28617c521c39c3f6d4c5d9c8d7b2.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial integration review at exact head e44c5c01bf4083d852b9cc7d21eb7f7528144ae0. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 195a0a3110933c063bc571b6b347e87e18f110b4, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head bd2719978772a93d630ce1165708afe132cbe123
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 6ff0aa6728e7f1a274a4ccbda5dbe3a4c90c2c97.
The batch-owned binary patch is byte-identical
(SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial governance integration review at exact head 2b8f2b06fda327ab4085d4e57f55fa4a56eb7a71. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head bd2719978772a93d630ce1165708afe132cbe123, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at 3c9c9ad9c824a664c405248d623c484cc797c6cf.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 7cd073cfd5f440feaf71c4987c9163fd57eabf945361ffdadbddf891b8518dbb.
Tree d5860fc0cbaff1bc665a39b887e8bc68b27f471f matches the independently computed clean merge.
Compared with historical tree 9d1a2e4d78799e61a1910ed2fca3acfc0e0dfb2e, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head bcebf2bc2da40062d3cf777cf1a2a9d508adee43 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.