Bound SynCom35, Deepwater and enamel graph claims to primary evidence (batch 29)

[realmarcin]

Scope

Three whole-record graph reviews: SynCom35, Deepwater Horizon and the enamel caries model. Corpus: 132 reviewed / 324 pending / 4 needs_research across all 460 records in both roots.

Closes #1375. Closes #1376. Closes #1377. Separate non-graph follow-ups #1378, #1379 and #1380 remain open.

Repairs And Adversarial Review

SynCom35 retains four positive immune/colonization observations. Whole-community suppression is not attributed exclusively to MF79, its secretion-system requirement is strain-specific, and the smaller-community and retentate experiments remain distinct. WRKY-specific detail was checked in the primary body; the cached abstract snippet is explicitly partial. Remove three unsupported nodes asserting metabolic complementarity, nutrient exchange and control competition. Keep both existing arrows with bounded experimental scope, not reciprocal fitness or a resolved effector.

Deepwater retains cold biodegradation, Colwellia-dominated flocs and positive SIP/genome evidence. Consolidate the duplicate oxygen-conserving node and remove its restatement arrow. Two retained arrows are explicitly hypotheses, distinguishing laboratory from field, surface-PAH from deep-alkane enrichments, room-temperature SIP from cold plume conditions, and coordinated metabolism from incomplete genomes or unknown enzymes. Canonical taxa and the withheld Colwellia grounding are preserved.

The enamel model retains its three positive observations without unsupported facilitation, cross-feeding or competition signs. Remove two assay-context arrows. The four taxa are the starting roster, not universal persistence; calcium does not change every count and mineral effects are endpoint-specific. Proposed pH/EPS mechanisms and an internally inconsistent source comparison are not promoted to demonstrated facts.

Verification

342 passed in 165.07s (0:02:45); six new focused tests. Schema, strict, terms, references, independent snippet audit and history checks passed. Raw reference diagnostics and actual snippet counts are retained separately. Fourteen original nodes become ten; seven arrows become four. Every original node and arrow has a decision, and exact names/targets/anchors are checked.

Zero structural errors. All 25 existing warnings remain; six newly exposed DISCONNECTED warnings reflect explicit participant subsets and removal of unsupported relationships. They are documented against #1378/#1379, not hidden by fabricated interactions. The exact participant registry changes from 170 to 173 users; before/after connectivity is measured and no numeric bounds or algorithms are changed.

Three guarded edits, three llm-assisted events, three append-only histories and three regenerated pages. Non-graph raw blocks, 457 other records and all 920 reference caches are byte-preserved. Repeated rendering is deterministic and exact descriptions were checked on all 456 pages. Actual post-commit just check-docs-current passed with a clean tree. No browser screenshot QA is claimed.

Review records: reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml, validation-20261006-batch29.json, and adversarial-review-20261006-batch29.yaml. Source access is recorded separately for each paper, including abstract-only limits and the author-proof status. Enamel Tables 1-2 and Dombrowski Figure 3 were inspected visually. No new full article/PDF, new graph structure or paid Edison job is introduced. This is source-based self-adversarial review, not independent approval.

Stacking

Draft dependency on #1374. Do not merge into the topic parent. Require exact-head protected main checks/queue after parents merge, and move dependents before deleting branches. This batch does not complete the full-corpus goal.

[realmarcin]

Source-based self-adversarial review at exact head a4ca06d433a89666e12c662b24e7fa488c200355, not independent approval.

Addressed #1375, #1376 and #1377. The actual diffs were read against primary evidence, not only validator output. Preserve positive immune/colonization, degradation/SIP and enamel outcomes. Remove three unsupported SynCom35 relationship nodes, the duplicate Deepwater oxygen node, its restatement arrow and two enamel workflow arrows. Retain four arrows, with both Deepwater links explicitly hypothetical. Strain/community scope, incomplete canonical rosters, alternative explanations and source-access limits remain explicit.

All fourteen original nodes and seven arrows have decisions. WRKY detail was read in the primary body, not established by its broad cached snippet. Non-graph #1378, #1379 and #1380 remain open; those blocks are preserved, not certified. The six newly exposed DISCONNECTED warnings are expected evidence gaps, not a reason to invent participant relationships.

342 passed in 165.07s (0:02:45); six new tests, all focused validation, deterministic rendering, exact description checks on 456 pages and actual post-commit docs-current passed. Zero structural errors; 25 prior plus six new warnings. Three guarded changes/histories, 457 other records and all 920 caches preserved. Exact participant census 170 to 173; measured connectivity and unchanged bounds.

Decisions, validation and this adversarial review output are committed. Enamel Tables 1-2 and the Dombrowski Figure 3 were visually inspected; remaining source access is described per paper. No independent approval, new Edison job, protected CI success or full-corpus completion is claimed. Require protected main merge; do not merge into the topic parent or delete branches with dependents.

[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 a6e03707b786427157618b2ee1174719d9675068
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 61b30331a625dcd74c2e332865037fcd89cc0a12
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 1f1d4683cbd734d3a81345225e5e0f408660d460
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 6cde012f51a9e8cf7c17c967e2e4c07216627829
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 655dd72bb33f3053b9b1eeee74631fa90644fd90
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 2be033711223fccd2e59c7ab46e2b3623bab9290
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 7798bc86e3fe684bd3e5160dc03123aa5a25f021
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 4ff3fa1d814cf70043ecf7dd528b77c1d918766d
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 7a2c786d8f1d9328b20aae303a1b86e1c78d2d97
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 91af21e78e931c1edb8bbcda8844d319694406ea
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 7bd1b8c5da7f64d28a8eea627c11bf2d8583fdd3.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 902c72772aaf6b778b28f4a59155d59f14ecd526. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 91af21e78e931c1edb8bbcda8844d319694406ea, 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 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5). 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 a84f68f1bcdfbe3ff7a43d7de975086db974f1fd
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 6c7fc9ba5f70b53f64752addd9212514aee4f815.
The batch-owned binary patch is byte-identical
(SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5); 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 46ca547a9fa0686c19734f09bf21263bf0c76599. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head a84f68f1bcdfbe3ff7a43d7de975086db974f1fd, 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 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5). 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 bb47fac8bea5832e7fd5c56aa390cfe31cf77540.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 5df1f68d8e79c10a74425997ca256a943cfc32d6d15b42fb55df735f27ef51c5.
Tree 3f151f563be77bc3363e26ac39fce30db76b5d74 matches the independently computed clean merge.
Compared with historical tree 9b520cb41979feff9d1603c394c437f2669933e3, 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 649f80fe6bf86da88a7a2acfc5e8114a27f610b8 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.