Bound mat carbon models, conditional floc assembly and Naica physiology (batch76)

[realmarcin]

Scope

Closes #1632.
Closes #1633.
Closes #1634.
Non-graph #1635 stays OPEN after graph-repair merge.

• Preserve measured diel expression, not metabolic flux or demonstrated niche partitioning.; Retain proposed polymer-to-photomixotrophy link as HYPOTHESIZED.; Bound diazotrophic potential and partial-genome absence; replace unsupported directional taxa with participants.; Preserve uneven overlapping mat structure; remove spatial-context arrow.
• Preserve microcolonies and their conditional contribution to mixed structures.; Preserve actual macroclusters with centrifugation/calcium and imaging boundaries; remove model-utility arrow.; Retain proof-of-concept utility without a second biological causal stage.
• Preserve aggregate NDC-6 removal and functional complementation; no mutualism, invented intermember flux, or new arrow. Existing1197/1198 boundaries between three-day10C performance and separate10.2C optimization remain unchanged.
• Retain lineage-specific inferred thermophily; remove environmental-context arrow.; Retain putative oxidation; correct GO grounding and remove unmeasured graph concentrations.; Retain proposed donor constraint with negative-PCR limits; remove co-occurrence arrow and unsupported competition.

Adversarial Review

• All four whole records and every original node/arrow reviewed after fresh both-root baseline. Three complete main bodies plus tables/captions; two abstract-bounded sources and only partial indexed diel Methods. Access errors and subscription barriers respected, not bypassed. No claim that unseen controls are absent.
• Retain measured Mushroom Spring RNA patterns. The metabolic endpoint remains putative carbon fixation so the polymer-reserve arrow does not spuriously become a cause of gene expression. This intermediate self-review finding was corrected, and complete verification rerun with superseded outputs preserved. Polymer flux is the explicit source model, not a measured flux assay.
• Thermodesulfovibrio nitrogen fixation is putative even with accessory nif genes; prior Synechococcus activity is not transferred to it. Remove source/target implication and preserve canonical participants. Partial genomes limit absence conclusions; mat layers overlap and distinct sampling campaigns are not a simultaneous intervention. Remove spatial restatement arrow without discarding measured community structure.
• Preserve real stable nitrifier microcolonies and mixed macroclusters. Release alone did not suffice; centrifugation plus calcium-rich resuspension and their unresolved separation are explicit. FISH-induced aggregation is a separate artefact, not a reason to deny later suspended clusters. Remove only the model-utility causal stage, not biological assembly.
• NDC6 is valid unchanged: measured aggregate low-temperature removal and functional complementation need no arbitrary arrow. Preserve1197/1198 no-mutualism and optimization-versus-three-day boundaries. Do not falsely recast reported gene-expression evidence as metagenomics or assert unmeasured per-member fitness.
• Naica thermophily is inferred from high GC in specified lineages, not universal OP3 growth measurements. AamoA detection supports putative oxidation but not flux or concentrations. Correct assimilation GO0019676 to oxidation GO0019329, verified against AmiGO, without taxonomy changes.
• Negative dsrA amplification does not establish absence. Preserve proposed donor scarcity and non-dominance interpretation with sampling/primer limits, unpublished H2S context and no claimed donor-rescue assay. Neither environmental context nor co-occurrence with AamoA creates a causal link. Unsupported competition label and two context arrows removed.
• Three case-inexact graph quotations corrected and the truncated negative-PCR quote shortened; all18 graph quotes match both fresh source and cache. Original erroneous cache-suffix search is not evidence of absence.920 caches and all raw non-graph blocks remain untouched; residual metadata claims tracked separately in1635.
• Every11 nodes and6 original arrows accounted for;11nodes2arrows remain. Three guarded writes and histories;457 records including NDC6 unchanged. Zero structural defects and44 baseline warnings unchanged. Connectivity census unchanged, not evidence of member-level effects.
• Actual schema, strict, terms, full-record references, snippets, histories, both-root inventory/network/rank, regression, lint and deterministic rendering checks retained. Exact descriptions parsed across456 generated pages, not browser screenshots. Postcommit docs-current is separate.
• No new topology or paid provider call. Earlier Edison authorization scopes are unchanged.916 issue bodies and27 ignored/hidden local matches deduplicated;1197/1198/939/396 preserved. No exhaustive PR-comment audit.1632-1634 stay OPEN until protected-main merge;1635 stays OPEN afterward. Self-review is not independent approval or corpus completion.

Verification And Output Records

677 passed in 244.49s (0:04:04); eight new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All18 graph quotations independently match fresh primary XML/abstract and existing caches. Cache matching is not entailment. Diel and NDC sources remain abstract-bounded; all920 caches unchanged, not recertified. Prior batch73 non-graph reference exception is outside this batch.

All11 original nodes and6 arrows reviewed;11 nodes and2 arrows retained. Three records repaired; NDC6 unchanged. Measured RNA, uneven overlapping mat populations, stable microcolonies and true mixed macroclusters remain. Polymer-to-putative-fixation link retained without implying a cause of gene expression. No new structure or paid provider run. Non-graph #1635 stays OPEN.

All457 unchanged records,920 caches and raw non-graph blocks verified. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings preserved exactly; connectivity census unchanged. Repeat renders deterministic, exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 fd9022806e955b1ecad52f6d69f2e52de1df97035302940c33543cdd05bf979f. Every-node/every-arrow decisions,39 final actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch76. Initial validation outputs preserved as superseded after correcting an intermediate endpoint rename. Final focused rerun:17 passed. Corpus:246 reviewed,188 pending,26 needs_research. Not independent approval or corpus completion.

Source Limits

• Fresh pre-paper baseline covered460 records and920 caches across both roots including ignored/hidden YAML. All11 original nodes and6 arrows reviewed;11 nodes and2 arrows retained. Three records repaired with three histories; NDC6 byte-for-byte unchanged.
• Full primary main bodies, embedded tables and captions read for undermat, bioflocculation and Naica. Diel and NDC6 fresh primary abstracts read; diel indexed publisher view was only partially read through early Results. Diel XML returned500, PMC challenge and normal publisher403; NDC publisher is a subscription preview. No access-barrier bypass or full-Methods claim for those two. Separate supplements, raw data and original figure pixels not audited.
• All graph quotations match fresh primary and existing caches with whitespace-only normalization. Three case-inexact Naica graph quotes corrected to source text, and a misleadingly truncated negative-PCR quote shortened. This is not entailment proof or recertification of920 unchanged caches. Original search using two incorrect cache suffixes errored and truncated; corrected structured exact-reference matching supersedes it. No complete paper uploaded.
• Mushroom measured diel transcripts and uneven overlapping mat populations retained. Polymer flux remains the explicitly proposed model; Thermodesulfovibrio nitrogen fixation is putative, not Synechococcus-to-Thermodesulfovibrio transfer. nifHDK alone and partial-genome absence are insufficient. Distinct sampling campaigns are not merged into a simultaneous experiment.
• Biofloc microcolonies and positive mixed macroclusters retained with calcium-rich resuspension and centrifugation conditions. Release alone did not suffice; FISH preparation caused separate artefacts. Calcium versus centrifugation remains unresolved. Model utility is not a second biological causal event; no full-scale performance equivalence or isolated EPS mechanism inferred.
• NDC6 aggregate removal and functional complementation retained unchanged. Existing1197/1198 fixes preserve no unsupported mutualism and the distinction between three-day10C performance and separate10.2C optimization. Gene-expression evidence is actually reported, not reclassified as metagenomics. Sparse valid graph does not require invented topology.
• Naica high-GC thermophily and AamoA capacity remain positive but inferred, not growth/flux measurements. Correct GO0019676 assimilation to GO0019329 oxidation, confirmed against AmiGO. Negative dsrA PCR is not absence; donor scarcity is proposed, not competition or causal promotion of oxidation. No taxonomy edits, including396 near-tie and curated groundings.
• Dedup scanned916 all-state issue titles/bodies and27 local matching files with ignored/hidden-inclusive search excluding git/docs/site/cache. Matching1197/1198/939/396 bodies read and preserved. No exhaustive PR-comment audit or global source-absence claim.
• No new topology: repairs and evidence qualification require no Edison extension. Zero provider submissions/credits. Earlier scoped paid questions and the AM_AB denial are not overridden.
• Three repair issues stay OPEN until protected-main merge; separate metadata issue stays OPEN afterward. Non-graph blocks are preserved, not certified. Self-adversarial review is not independent approval; corpus review remains unfinished.
• Self-adversarial review corrected an intermediate endpoint rename: the retained polymer link targets putative carbon fixation, not gene expression. Measured RNA remains positive evidence; no new node or arrow, no second curation event, and initial validation outputs are retained as superseded.

Dependency

Draft depends on #1631. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head a74e8e8; not independent approval.

Repairs #1632-#1634 addressed; non-graph #1635 unresolved.

• Preserve measured diel expression, not metabolic flux or demonstrated niche partitioning.; Retain proposed polymer-to-photomixotrophy link as HYPOTHESIZED.; Bound diazotrophic potential and partial-genome absence; replace unsupported directional taxa with participants.; Preserve uneven overlapping mat structure; remove spatial-context arrow.

• Preserve microcolonies and their conditional contribution to mixed structures.; Preserve actual macroclusters with centrifugation/calcium and imaging boundaries; remove model-utility arrow.; Retain proof-of-concept utility without a second biological causal stage.

• Preserve aggregate NDC-6 removal and functional complementation; no mutualism, invented intermember flux, or new arrow. Existing1197/1198 boundaries between three-day10C performance and separate10.2C optimization remain unchanged.

• Retain lineage-specific inferred thermophily; remove environmental-context arrow.; Retain putative oxidation; correct GO grounding and remove unmeasured graph concentrations.; Retain proposed donor constraint with negative-PCR limits; remove co-occurrence arrow and unsupported competition.

• All four whole records and every original node/arrow reviewed after fresh both-root baseline. Three complete main bodies plus tables/captions; two abstract-bounded sources and only partial indexed diel Methods. Access errors and subscription barriers respected, not bypassed. No claim that unseen controls are absent.

• Retain measured Mushroom Spring RNA patterns. The metabolic endpoint remains putative carbon fixation so the polymer-reserve arrow does not spuriously become a cause of gene expression. This intermediate self-review finding was corrected, and complete verification rerun with superseded outputs preserved. Polymer flux is the explicit source model, not a measured flux assay.

• Thermodesulfovibrio nitrogen fixation is putative even with accessory nif genes; prior Synechococcus activity is not transferred to it. Remove source/target implication and preserve canonical participants. Partial genomes limit absence conclusions; mat layers overlap and distinct sampling campaigns are not a simultaneous intervention. Remove spatial restatement arrow without discarding measured community structure.

• Preserve real stable nitrifier microcolonies and mixed macroclusters. Release alone did not suffice; centrifugation plus calcium-rich resuspension and their unresolved separation are explicit. FISH-induced aggregation is a separate artefact, not a reason to deny later suspended clusters. Remove only the model-utility causal stage, not biological assembly.

• NDC6 is valid unchanged: measured aggregate low-temperature removal and functional complementation need no arbitrary arrow. Preserve1197/1198 no-mutualism and optimization-versus-three-day boundaries. Do not falsely recast reported gene-expression evidence as metagenomics or assert unmeasured per-member fitness.

• Naica thermophily is inferred from high GC in specified lineages, not universal OP3 growth measurements. AamoA detection supports putative oxidation but not flux or concentrations. Correct assimilation GO0019676 to oxidation GO0019329, verified against AmiGO, without taxonomy changes.

• Negative dsrA amplification does not establish absence. Preserve proposed donor scarcity and non-dominance interpretation with sampling/primer limits, unpublished H2S context and no claimed donor-rescue assay. Neither environmental context nor co-occurrence with AamoA creates a causal link. Unsupported competition label and two context arrows removed.

• Three case-inexact graph quotations corrected and the truncated negative-PCR quote shortened; all18 graph quotes match both fresh source and cache. Original erroneous cache-suffix search is not evidence of absence.920 caches and all raw non-graph blocks remain untouched; residual metadata claims tracked separately in1635.

• Every11 nodes and6 original arrows accounted for;11nodes2arrows remain. Three guarded writes and histories;457 records including NDC6 unchanged. Zero structural defects and44 baseline warnings unchanged. Connectivity census unchanged, not evidence of member-level effects.

• Actual schema, strict, terms, full-record references, snippets, histories, both-root inventory/network/rank, regression, lint and deterministic rendering checks retained. Exact descriptions parsed across456 generated pages, not browser screenshots. Postcommit docs-current is separate.

• No new topology or paid provider call. Earlier Edison authorization scopes are unchanged.916 issue bodies and27 ignored/hidden local matches deduplicated;1197/1198/939/396 preserved. No exhaustive PR-comment audit.1632-1634 stay OPEN until protected-main merge;1635 stays OPEN afterward. Self-review is not independent approval or corpus completion.

677 passed in 244.49s (0:04:04); eight new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All18 graph quotations independently match fresh primary XML/abstract and existing caches. Cache matching is not entailment. Diel and NDC sources remain abstract-bounded; all920 caches unchanged, not recertified. Prior batch73 non-graph reference exception is outside this batch.

All11 original nodes and6 arrows reviewed;11 nodes and2 arrows retained. Three records repaired; NDC6 unchanged. Measured RNA, uneven overlapping mat populations, stable microcolonies and true mixed macroclusters remain. Polymer-to-putative-fixation link retained without implying a cause of gene expression. No new structure or paid provider run. Non-graph #1635 stays OPEN.

All457 unchanged records,920 caches and raw non-graph blocks verified. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings preserved exactly; connectivity census unchanged. Repeat renders deterministic, exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 fd9022806e955b1ecad52f6d69f2e52de1df97035302940c33543cdd05bf979f. Every-node/every-arrow decisions,39 final actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch76. Initial validation outputs preserved as superseded after correcting an intermediate endpoint rename. Final focused rerun:17 passed. Corpus:246 reviewed,188 pending,26 needs_research. Not independent approval or corpus completion.

Protected-main merge pending.

[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, 44 warning across 16 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)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

KBase_Models_for_Zahmeeth_Original_PLOS
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Klebsiella' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas fluorescens' has no interactions

Total: 2 issues (0 error, 2 warning)

Lake_Washington_Methane_Oxygen_Methylotroph_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylosarcina' has no interactions

Total: 1 issues (0 error, 1 warning)

Lotus_LjSC3
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Burkholderiaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule210' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule215' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule218' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Oxalobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Phyllobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonadaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobiaceae bacterium' has no interactions

Total: 9 issues (0 error, 9 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 integration review at exact head 85a1a7b0b52f7779d17aabeddcac57037dcf4a9d. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head a74e8e81dc708280fedbf1fe63453275b3d53394, 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 ddc201330bd56eef86f378fc07322be51883e4fb15222e7e1dda4ccd901557a7). 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 4357c2a0a3649cfc1a7cba3164a2af34c04e98ca
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree dcbcdececc216d6adcc05ebedde18ab59c489abc.
The batch-owned binary patch is byte-identical
(SHA-256 ddc201330bd56eef86f378fc07322be51883e4fb15222e7e1dda4ccd901557a7); 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 6c3dee20c873b175f43ede45babbcff53814f8b7. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 4357c2a0a3649cfc1a7cba3164a2af34c04e98ca, 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 ddc201330bd56eef86f378fc07322be51883e4fb15222e7e1dda4ccd901557a7). 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 7d579b724265208e0b5e8efe40ce835143d86d69.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 ddc201330bd56eef86f378fc07322be51883e4fb15222e7e1dda4ccd901557a7.
Tree a82606d6b95edc0be5f679d3d2c936c0e9a8f04f matches the independently computed clean merge.
Compared with historical tree e0bb46749b05ae321bd90b980aa420211c90e8d2, 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 d6016b3de911cca9a2ce3751c1917d9ad0961990 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.