Repair pyrene, syntrophy and pepper causal claims (batch83)

[realmarcin]

Scope

Closes #1685.
Closes #1686.
Closes #1687.
Closes #1688.
Research #1689/#1690 and non-graph #1691 stay OPEN after graph-repair merge.

• Retain observed bottleneck and qualify the candidate intermediate handoff.; Preserve extracellular emulsification without asserting reciprocal fitness or measured pyrene mediation.; Preserve near-complete pyrene removal without equating it with carbon mineralization.
• Preserve propionate syntrophy and correct universal dependence and evidence attribution.; Preserve alternative-substrate coculture growth without universal product stoichiometry.; Preserve the hydrogen sink and source-bound coaggregation evidence while separating observations and diffusion modeling.
• Preserve measured diversity changes while qualifying the proposed enrichment direction.; Preserve relative OTU associations without converting predictive importance into causation.; Preserve directly measured whole-plant growth without reciprocal-fitness inference.
• Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.; Preserve T14/A6 inhibition and distinguish it from a demonstrated host-protection mechanism.; Preserve measured growth and visible symptoms without inventing direct disease-severity quantification.

Adversarial Review

• Fresh both-root460record/920cache baseline preceded paper review. Four whole records,13nodes and9arrows assessed including missing structures. Twelve retained nodes/eight arrows and one removed workflow node/arrow all have dispositions. No new topology or paid provider submission.
• PES retains near-complete50mg/Lpyrene removal in10days at5%salinity and N7monoculture49.95%in14days. Removal is not complete carbon mineralization. Intermediate profiles and hphtC-5annotation/modeling/transcripts support a candidate handoff, not traced transfer or enzyme necessity. Published Figure8correction fixes reversed structures; the record already has the corrected chemical direction.
• A11-associated extracellular emulsification remains positive:68%soybean-oil index under assay-specific growth conditions. A11yeast-extract and N7/PESpyrene conditions differ. Emulsion phenotype and genomic capacity do not isolate pyrene mass-transfer mediation, export apparatus or reciprocal fitness. Both removal arrows remain explicitly hypothesized.
• Syntrophy retains growth on propionate and alternative substrates with the hydrogenotrophic partner and the directly implied donor-to-methanogen direction. Pure-culture pyruvate/fumarate growth and fumarate-to-succinate exception disallow universal obligate dependence. Alternative-substrate products are not assumed identical. A copied evidence explanation now explicitly includes propionate.
• The2005primary abstract/captions add real coaggregation and2-BEShydrogen-consumption inhibition evidence, not direct electron conduction. Stronger association on propionate and modeled diffusion limits are distinct findings. Full methods and missing feedback/coaggregation topology remain1689research; no fabricated negative control claim or uninspected full-text certification.
• Peppergrowth workflow node/arrow removed, while all three biological nodes and the authors proposed diversity-to-native-taxa-to-growth model remain. Both arrows are hypotheses, not inferred necessity from correlations/random-forest importance. Figure3visually confirms increased fungal AND bacterial Chao richness; same-letter Shannon/Simpson panels do not support a blanket evenness increase.
• Preserve fungalBray-Curtis increase and bacterialBray-Curtis decrease, measured plant/root outcomes and selected native relative-abundance changes. Scedosporium genus decreases while OTU451increases; do not collapse these resolutions or claim absolute expansion, inoculated-strain colonization, symbiosis or reciprocal microbial fitness. Prior taxonomy decisions1216/1217remain untouched.
• Biocontrol individual trait screens are heterogeneous. Table1places strongest pathogen inhibition withT14andA6at58.4%and17.6%; canonical participating taxa narrow to those two. Narrative/tableIAAandammonia rankings conflict. Separate siderophore/enzyme screens are not demonstrated inhibition mechanisms; oomyceteP.capsici does not establish a host antifungal-defense or chitin-wall-degradation claim.
• Preserve challenged-host growth and visible wilting/necrosis response. Section3.5explicitly says no direct disease severity/pathogen-load quantification and no SynCom-only control. Both trait/antagonism-to-host arrows remain hypotheses. Additional positive soil nitrate/K/Ca and community responses stay in discussion pending1690; predicted functions are not measured flux.
• PESindexed full main text/tables/captions, its correction and two pepper full main texts read. Fresh public primary PDFs inspected on growthpages6/7/8andbiocontrol3/4. Two syntrophy studies are abstract/caption limited. Other original figures, separate supplements and raw data remain uninspected. Failed/captcha downloads are not evidence; public source access respected.
• Eighteen graph quotations and new discussion quotations independently checked against fresh primary artifacts. One new cache has20quoted words from two primary excerpts, not full paper text. Full-corpus just audit-snippets executed with actual counts; its informational exit0 is not a clean-corpus claim. Four focused snippet gates contain no weak/mismatched/no-content/assembled evidence.
• Four guarded history events,456otherrecords920originalcaches and all raw non-graph blocks preserved. Final Chao/explanation fixes retain24superseded passing outputs;14unchanged record gates reused by hash, affected gates rerun. Forty-one final checks recorded. Deterministic rendering and exact descriptions across456pages are parser checks, not browser screenshots.47network warnings unchanged,zero new structural/connectivity findings; taxonomy/auditor rules and global connectivity census unchanged.
• Dedup searched962all-state issue titles/bodies,six matched bodies and62localfiles with ignored/hidden inclusion and declared exclusions. One13736character Edison causal dry run is not paid authorization or a report. Pending/denied scopes remain unchanged. Repairs1685-1688close only on protected-main merge; research1689/1690andmetadata1691remain OPEN. Self-adversarial COMMENT is not independent approval or corpus completion. Move dependents before deleting parents.

Verification And Output Records

746 passed in 437.51s (0:07:17); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.18graph quotations independently match fresh primary content and caches. Literal matching is not entailment or whole-record provenance certification; non-graph claims and original920caches are preserved, not globally recertified.

All13 original nodes and9arrows reviewed. Four records repaired:12nodes/8qualified arrows retained,one workflow node/arrow removed. Positive pyrene removal, syntrophic growth/coaggregation, plant growth and isolate traits remain. Additional positive soil/community responses remain in discussion pending research #1690; syntrophy extension #1689 and metadata #1691 stay OPEN.

All456 other records,920 original caches and raw non-graph blocks verified unchanged. One new short coaggregation cache contains20quoted words. Canonical taxa and auditor rules unchanged. Zero structural defects;47baseline warnings preserved with no new findings. Connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Full-corpus just audit-snippets executed; its informational exit0 is not a clean-corpus claim, and actual counts are committed.

Postcommit just check-docs-current passed with clean tree; log SHA256 5956db740beade5c69729dba96c815708f7650d0b2bc03372ab58c32c7aff03a. Every-node/every-arrow decisions,41final actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch83.24superseded passing checks preserved after final Chao richness/evidence-explanation corrections. Final focused rerun:10 passed. Corpus:259reviewed,160pending,41needs_research. One syntrophy Edison dry run; zero paid submissions/credits, scoped question unanswered. Not independent approval or corpus completion.

Source Limits

• Fresh before-paper baseline across both roots:460records/920caches,47warnings,zero structural defects. Four whole records,13nodes9arrows reviewed;12nodes8arrows retained,one workflow node/arrow removed. No new topology.
• PES full primary indexed main text/tables/captions and correction read; corrected chemical direction agrees with record. Two pepper full main texts read, with fresh public primary PDFs and cached growth text. Selected original PDF pages visually checked: growth6/7/8, biocontrol3/4. Separate supplements, remaining original figures and raw data not audited.
• Species-description paper2002 and coaggregation2005 remain primary-abstract/caption limited. Preserve observed coculture growth, coaggregation and inhibitor-caption evidence without claiming full methods reviewed. Modeled distances are not measured flux. Missing feedback/coaggregation structure tracked in1689.
• Europe PMC returned502/503 service errors; publisher/PMC routes returned403 or browser checks. Public primary PDFs retrieved from Semantic Scholar; no access control bypass. One erroneous initial growth PMC URL was rejected for no article content and is not evidence. Failed retrieval receipts remain outside repository.
• PGPR screens differ among isolates; no direct disease score/pathogen load or SynCom-only control in biocontrol study. Positive host growth and visible symptoms survive. Soil nitrate/K/Ca and community changes retained in discussion pending1690 extension workflow; predicted functions are not flux. Protocol/identity conflicts remain1691.
• Source evidence is not a blanket causality certificate. Original920caches and456otherrecords and raw non-graph blocks preserved. One new cache contains20quoted words from primary abstract/caption, not complete copyrighted article. Canonical taxonomy/auditor rules unchanged.
• Dedup962all-state issue titles/bodies,6matched bodies read,62local files with hidden/ignored inclusion excluding.git/docs/site/references_cache; additional exact coaggregation-reference search matched none in that scope. No exhaustive issue-comment/PR audit. Truncated combined outputs reread where claim-critical.
• One13736character single-community Edison causal dry run; scoped paid question unanswered,zero provider jobs/credits. Earlier denied/pending scopes unchanged. Repairs1685-1688close only after protected-main merge; research1689/1690andmetadata1691remainOPENafterward.
• Four append-only history artifacts. Validation and rendering receipts are separate gates, not preasserted here. Self-adversarial review is not independent approval or whole-corpus completion.
• Final original Figure3 inspection preserves increased fungal AND bacterial Chao richness; a copied propionate evidence explanation was corrected. Affected gates rerun and earlier passing outputs retained. Four original append-only histories unchanged.

Dependency

Draft depends on #1684. 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 f29d929; not independent approval.

Repairs #1685-#1688 addressed; non-graph #1691 unresolved.

• Retain observed bottleneck and qualify the candidate intermediate handoff.; Preserve extracellular emulsification without asserting reciprocal fitness or measured pyrene mediation.; Preserve near-complete pyrene removal without equating it with carbon mineralization.

• Preserve propionate syntrophy and correct universal dependence and evidence attribution.; Preserve alternative-substrate coculture growth without universal product stoichiometry.; Preserve the hydrogen sink and source-bound coaggregation evidence while separating observations and diffusion modeling.

• Preserve measured diversity changes while qualifying the proposed enrichment direction.; Preserve relative OTU associations without converting predictive importance into causation.; Preserve directly measured whole-plant growth without reciprocal-fitness inference.

• Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.; Preserve T14/A6 inhibition and distinguish it from a demonstrated host-protection mechanism.; Preserve measured growth and visible symptoms without inventing direct disease-severity quantification.

• Fresh both-root460record/920cache baseline preceded paper review. Four whole records,13nodes and9arrows assessed including missing structures. Twelve retained nodes/eight arrows and one removed workflow node/arrow all have dispositions. No new topology or paid provider submission.

• PES retains near-complete50mg/Lpyrene removal in10days at5%salinity and N7monoculture49.95%in14days. Removal is not complete carbon mineralization. Intermediate profiles and hphtC-5annotation/modeling/transcripts support a candidate handoff, not traced transfer or enzyme necessity. Published Figure8correction fixes reversed structures; the record already has the corrected chemical direction.

• A11-associated extracellular emulsification remains positive:68%soybean-oil index under assay-specific growth conditions. A11yeast-extract and N7/PESpyrene conditions differ. Emulsion phenotype and genomic capacity do not isolate pyrene mass-transfer mediation, export apparatus or reciprocal fitness. Both removal arrows remain explicitly hypothesized.

• Syntrophy retains growth on propionate and alternative substrates with the hydrogenotrophic partner and the directly implied donor-to-methanogen direction. Pure-culture pyruvate/fumarate growth and fumarate-to-succinate exception disallow universal obligate dependence. Alternative-substrate products are not assumed identical. A copied evidence explanation now explicitly includes propionate.

• The2005primary abstract/captions add real coaggregation and2-BEShydrogen-consumption inhibition evidence, not direct electron conduction. Stronger association on propionate and modeled diffusion limits are distinct findings. Full methods and missing feedback/coaggregation topology remain1689research; no fabricated negative control claim or uninspected full-text certification.

• Peppergrowth workflow node/arrow removed, while all three biological nodes and the authors proposed diversity-to-native-taxa-to-growth model remain. Both arrows are hypotheses, not inferred necessity from correlations/random-forest importance. Figure3visually confirms increased fungal AND bacterial Chao richness; same-letter Shannon/Simpson panels do not support a blanket evenness increase.

• Preserve fungalBray-Curtis increase and bacterialBray-Curtis decrease, measured plant/root outcomes and selected native relative-abundance changes. Scedosporium genus decreases while OTU451increases; do not collapse these resolutions or claim absolute expansion, inoculated-strain colonization, symbiosis or reciprocal microbial fitness. Prior taxonomy decisions1216/1217remain untouched.

• Biocontrol individual trait screens are heterogeneous. Table1places strongest pathogen inhibition withT14andA6at58.4%and17.6%; canonical participating taxa narrow to those two. Narrative/tableIAAandammonia rankings conflict. Separate siderophore/enzyme screens are not demonstrated inhibition mechanisms; oomyceteP.capsici does not establish a host antifungal-defense or chitin-wall-degradation claim.

• Preserve challenged-host growth and visible wilting/necrosis response. Section3.5explicitly says no direct disease severity/pathogen-load quantification and no SynCom-only control. Both trait/antagonism-to-host arrows remain hypotheses. Additional positive soil nitrate/K/Ca and community responses stay in discussion pending1690; predicted functions are not measured flux.

• PESindexed full main text/tables/captions, its correction and two pepper full main texts read. Fresh public primary PDFs inspected on growthpages6/7/8andbiocontrol3/4. Two syntrophy studies are abstract/caption limited. Other original figures, separate supplements and raw data remain uninspected. Failed/captcha downloads are not evidence; public source access respected.

• Eighteen graph quotations and new discussion quotations independently checked against fresh primary artifacts. One new cache has20quoted words from two primary excerpts, not full paper text. Full-corpus just audit-snippets executed with actual counts; its informational exit0 is not a clean-corpus claim. Four focused snippet gates contain no weak/mismatched/no-content/assembled evidence.

• Four guarded history events,456otherrecords920originalcaches and all raw non-graph blocks preserved. Final Chao/explanation fixes retain24superseded passing outputs;14unchanged record gates reused by hash, affected gates rerun. Forty-one final checks recorded. Deterministic rendering and exact descriptions across456pages are parser checks, not browser screenshots.47network warnings unchanged,zero new structural/connectivity findings; taxonomy/auditor rules and global connectivity census unchanged.

• Dedup searched962all-state issue titles/bodies,six matched bodies and62localfiles with ignored/hidden inclusion and declared exclusions. One13736character Edison causal dry run is not paid authorization or a report. Pending/denied scopes remain unchanged. Repairs1685-1688close only on protected-main merge; research1689/1690andmetadata1691remain OPEN. Self-adversarial COMMENT is not independent approval or corpus completion. Move dependents before deleting parents.

746 passed in 437.51s (0:07:17); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.18graph quotations independently match fresh primary content and caches. Literal matching is not entailment or whole-record provenance certification; non-graph claims and original920caches are preserved, not globally recertified.

All13 original nodes and9arrows reviewed. Four records repaired:12nodes/8qualified arrows retained,one workflow node/arrow removed. Positive pyrene removal, syntrophic growth/coaggregation, plant growth and isolate traits remain. Additional positive soil/community responses remain in discussion pending research #1690; syntrophy extension #1689 and metadata #1691 stay OPEN.

All456 other records,920 original caches and raw non-graph blocks verified unchanged. One new short coaggregation cache contains20quoted words. Canonical taxa and auditor rules unchanged. Zero structural defects;47baseline warnings preserved with no new findings. Connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Full-corpus just audit-snippets executed; its informational exit0 is not a clean-corpus claim, and actual counts are committed.

Postcommit just check-docs-current passed with clean tree; log SHA256 5956db740beade5c69729dba96c815708f7650d0b2bc03372ab58c32c7aff03a. Every-node/every-arrow decisions,41final actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch83.24superseded passing checks preserved after final Chao richness/evidence-explanation corrections. Final focused rerun:10 passed. Corpus:259reviewed,160pending,41needs_research. One syntrophy Edison dry run; zero paid submissions/credits, scoped question unanswered. 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, 47 warning across 17 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)

Panzhihua_Vanadium_Titanium_Tailings
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Polaromonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium pisi' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium selenitireducens' has no interactions

Total: 3 issues (0 error, 3 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 469dd6db095c87a7a715091a3a90094900580880. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head f29d9295102b2cac41dd1a8269ed340823a35d3b, 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 7a1593e0d7b420ed74a2585f541b455396c2dbaddf113e8341da75e94d2a671c). 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 07bd4d4329e3413391d3d98c9a16bd403cb478d1
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 0c71f4ab8759620a3e1af2db137bb50544d4d75b.
The batch-owned binary patch is byte-identical
(SHA-256 7a1593e0d7b420ed74a2585f541b455396c2dbaddf113e8341da75e94d2a671c); 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 bc897b4f4d244663103d76fe43b1db721646db2a. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 07bd4d4329e3413391d3d98c9a16bd403cb478d1, 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 7a1593e0d7b420ed74a2585f541b455396c2dbaddf113e8341da75e94d2a671c). 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 c088d3dba246014f7d964bc5c708cb1c10fb80cd.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 7a1593e0d7b420ed74a2585f541b455396c2dbaddf113e8341da75e94d2a671c.
Tree be92ed2a8cf1008be0741e569b42da0154e014ec matches the independently computed clean merge.
Compared with historical tree 26c7a898f883b80888b2bcde691fdd6562a16bb1, 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 69ef4cd9ad54f0e7a9ac4a8836952c531d96b671 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.