Bound SC2 MFC and Mars panel causal claims to measured assays (batch68)

[realmarcin]

Scope

Closes #1582.
Closes #1583.
Closes #1584.
Closes #1585.
Related #1586 non-graph metadata and existing #573 panel-model question remain OPEN after graph repair merge; coordinate #1580.

• Retain plate inhibition and plant protection, not competition or immune mechanism.; Retain plant benefit under challenge, not reciprocal mutualism or demonstrated IAA mediation.; Retain Salkowski/CAS outputs with chemical-identity, pathway and host-transfer limits.
• Retain relative genus response at partial-roster scope, not partitioning or isolated catalytic mediation.; Retain positive whole-system removal and power with cycle-specific voltage and unresolved member flux.
• Retain bounded abiotic resource hypothesis from cited leachate chemistry, not niche partitioning.; Retain hydration-dependent viable-recovery observations; remove assay-order causation.; Retain strain-specific positive persistence with late-time and water-control exceptions.
• Retain measured extract chemistry with speciation, carryover and phosphorus limits.; Retain species-specific optical growth/photophysiology, not measured nitrogen flux; remove workflow arrow.; Retain processed-culture plant benefit with endpoint and treatment specificity, not live commensalism.

Adversarial Review

• Verification also caught ruff B023 in the new mapping test helper after619 tests passed. Explicitly bind the per-record rename map, preserve pre-fix regression/formatting outputs and rerun the full suite on final content. No scientific record changed for these verification fixes.
• Read four whole records and all11 original nodes/six arrows, four complete fresh primary main texts/captions and both main tables. Retain11 nodes, qualifyfour arrows and remove two assay-order arrows. No new causal structure. Original figure pixels, separate supplements, raw data and external papers cited in the four studies were not independently audited.
• SC2: retain seven-day PDA inhibition comparable to C7 and14-day B73 height/fresh-root-mass improvement. The plate and plant assays do not isolate competition, pathogen-load mediation or host immunity. Keep the existing inhibition-to-growth hypothesis explicitly HYPOTHESIZED, not causal certainty or proof of no contribution.
• SC2: Salkowski with pure-IAA calibration and CAS halo assays support the reported45/65ugmL and0.50cm outputs. Keep chemical interpretations with their assay limits, not exact siderophore identity, pathway perturbation, in-planta delivery or reciprocal benefit. Preserve host/pathogen as external participants and prior Mark maize SC2 siderophore evidence as incidental metal relevance #887-Keep maize SC2 design rationale out of ecological_interactions #889 repairs; do not resolve strain aliases from species-list order.
• MFC: retain positive98.7% benzene removal, product observations, sustained biotic voltage and higher power density than acetate.902.3mV belongs to250mgL cycleVI,899.9mV to330mgL cycleVII;390.1 versus238.8mWm2 is not100fold. The awkward removal sentence is resolved against abstract, main Table1 and Conclusion, not interpreted as98.7% residual benzene.
• MFC: relative genus enrichment does not resolve absolute expansion, niche partitioning or member catalytic necessity. Keep composition-to-output as the authors HYPOTHESIZED route, with confounded substrate/acclimation context. Four named genera are a partial roster. DET/MET and traced partner exchange remain unresolved. Preserve Adversarial review: Mangrove MFC Bacillus role is over-typed as PRIMARY_DEGRADER #1124 Bacillus role correction; existing Arcobacter role and Daphnia metadata remain follow-up.
• Meteorite: shared abiotic substrate and separate growth/persistence results are not a coculture. Earlier leachate chemistry does not prove current ion-specific uptake or carbon source. Low-perchlorate meteorite and terrestrial conditions are not general Martian habitability. Water controls, unequal initial phototroph counts, MPN recovery and heterotroph CFUs bound inference.
• Meteorite: preserve positive Chr20 persistence and early Planococcus growth while stating most Planococcus ratios lose late recoverability, E.coli survives in water-only controls, and below quantification is not extinction. Remove the assay-to-persistence workflow arrow, not the measured endpoint. Keep qualified substrate support rather than erase the positive resource hypothesis.
• MGS-1: retain TXRF elemental chemistry, separate OD440/PSII growth and Nostoc/Anabaena performance with Anabaena late decline and Arthrospira clumping/mild-growth limits. Element totals are not speciation/uptake. No direct N2 or O2 flux measured; undetected extract phosphorus, inoculum and reserves/carryover matter.
• Lemna: preserve seven-day positive dry-weight outcomes for Arthrospira filtered/sonicated and Chlorella filtered culture material. Lower frond yields, nonsignificant filtered/sonicated differences and nonequivalence caveat retained. Processed-material benefit is not live commensalism. Growth-advantage mediation of fertilizer advantage is not established: Nostoc grows well but supplies the weakest material treatment. Remove that workflow arrow while retaining resource-transfer observations.
• Panel-model caveat remains unresolved, not hidden by graph status. Existing COMMUNITY_LEVEL is retained only as the current container for shared abiotic/panel observations; Mars_Meteorite_EETA79001_Growth_Panel is a panel of monocultures modelled as a community #573 is still OPEN for record-model placement. No new schema convention, coculture or emergent microbial community is certified. Prior PR574 and graph-adding commit fa3f1a8 read.
• Read complete biological diff. Remove unsupported specific interaction/process annotations but preserve supported growth/photosynthesis context, positive endpoints and author-proposed routes. Renames retarget every retained edge and prior discussion anchor. Detach graph aliases; preserve explicit benzene and benzene_term anchors needed by untouched non-graph references.456 other records and920 caches preserved; append one history/event per target. Initial regressions found one exact-registry failure with618 passing: add the two deliberately named Mars panel records to USERS after measuring the census. Retain all test logic, preserve the failed output/digest in superseded_checks, and rerun the complete suite.
• Actual focused schema/strict/terms/references/snippets/history gates, network/rank, repeat rendering, regressions and formatting outputs recorded.17 graph excerpts independently primary-matched with whitespace normalization. Coarse scope census unchanged; network warnings46->44 because two observed MFC genera are now explicitly named in whole-biofilm nodes, not because their catalytic roles were established. Initial verifier no-delta assumption was corrected after inspecting actual output; no scientific edits made to satisfy the gate. Other44 warnings preserved exactly, no auditor-rule changes. Exact descriptions parsed over456 pages, not screenshots; postcommit docs-current is a separate gate.
• Dedup874 all-state issue titles/bodies and47 scoped ignored/hidden local files; matching issue bodies, relevant histories, prior PR574 and graph-adding commit read, not every PR/comment/local match. Bound SC2 maize biocontrol mechanisms to separate measured assays #1582-Separate regolith growth panel from processed-culture biofertilization #1585 addressed but OPEN until protected-main merge. Reconcile SC2 MFC and Mars-panel non-graph assay metadata #1586/Mars_Meteorite_EETA79001_Growth_Panel is a panel of monocultures modelled as a community #573 remain OPEN afterward. No provider spend; exact-head COMMENT self-review is not independent approval or corpus completion.

Verification And Output Records

619 passed in 201.31s (0:03:21); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 80 record snippets match selected caches;17 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;17 graph excerpts independently match fresh primary text after whitespace normalization. #1586 metadata, #573 panel modeling and broader #476/#1091/#1095 source limitations persist.

Eleven original nodes retained;6 arrows reviewed,4 qualified/retained and2 workflow arrows removed. No new structure or provider spend. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural errors;44 baseline findings preserved and two MFC DISCONNECTED findings removed after explicitly including the observed Pelobacter/Pseudomonas genera. This denotes observed membership, not established catalytic function. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure narrowed participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 e2d952aed2ba7e0aaef8647b67e57c82270a6c3b462814fd57d1717befee8201. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch68. Corpus218 reviewed /220 pending /22 needs_research: unfinished, not independent approval.

Source Limits

• All11 original nodes and6 arrows reviewed;11 nodes retained/qualified and renamed where needed,4 arrows qualified,2 workflow arrows removed. No new causal structure or provider submission.
• Four complete primary main texts/captions and both main tables read. No original figure-pixel, separate supplement, raw-data or executable-analysis audit. Numerical results not independently recomputed. Source statements about other papers are not independent reviews of those papers.
• SC2 positive inhibition, plant growth and Salkowski/CAS outputs retained without competition, immune activation, reciprocal benefit or selectively established mediator. Preserve external participants and prior Mark maize SC2 siderophore evidence as incidental metal relevance #887-Keep maize SC2 design rationale out of ecological_interactions #889 repairs.
• Mangrove whole-biofilm removal/electrochemistry remain positive. Relative genus response is not member activity or isolated mediation; DET/MET, partner exchange and carbon balance unresolved. Preserve Adversarial review: Mangrove MFC Bacillus role is over-typed as PRIMARY_DEGRADER #1124 Bacillus role removal. Named genera are a partial roster.
• Both Mars records remain separate-organism panels, not cocultures. Existing COMMUNITY_LEVEL containers preserve shared abiotic/assay observations but do not settle Mars_Meteorite_EETA79001_Growth_Panel is a panel of monocultures modelled as a community #573 model placement or prove emergent interactions. Do not count this repair as resolution of that open modeling issue.
• Meteorite hydration, unequal inocula and different viable-recovery assays bound persistence comparisons; E.coli water-only survival and late Planococcus loss at most ratios retained. Regolith composition is not universal Mars habitability or resolved uptake.
• MGS-1 growth is optical/photophysiological, not direct N2 or O2 flux; inoculum/carryover and undetected extract phosphorus matter. Processed-culture Lemna benefits are treatment/endpoint specific, not live commensalism or equivalence. Worst phototroph growth does not preclude positive material benefit.
• Canonical taxonomy and raw non-graph blocks preserved, not recertified; Reconcile SC2 MFC and Mars-panel non-graph assay metadata #1586 remains OPEN and coordinates Reconcile maize SynCom rosters roles and assay-specific non-graph metadata #1580 and Mars_Meteorite_EETA79001_Growth_Panel is a panel of monocultures modelled as a community #573. No new taxon mappings or experimental roles inferred. Preserve graph-owned benzene anchors required by unchanged non-graph aliases.
• All920 caches unchanged;17 graph excerpts match fresh primary text after whitespace normalization. Not historical cache/non-graph provenance certification. Public primary XML available without access bypass; full sources remain scratch-only.
• Dedup874 all-state issue titles/bodies and47 scoped ignored/hidden local matches; seven matching issue bodies and prior PR574, relevant histories and graph-adding commit read, not every PR/comment/local match. Self-review is not independent approval. Repair issues remain OPEN pending protected-main merge.

Dependency

Draft depends on #1581. 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 1c08cfa; not independent approval.

Repairs #1582-#1585 addressed; #1586/#573 unresolved.

• Retain plate inhibition and plant protection, not competition or immune mechanism.; Retain plant benefit under challenge, not reciprocal mutualism or demonstrated IAA mediation.; Retain Salkowski/CAS outputs with chemical-identity, pathway and host-transfer limits.

• Retain relative genus response at partial-roster scope, not partitioning or isolated catalytic mediation.; Retain positive whole-system removal and power with cycle-specific voltage and unresolved member flux.

• Retain bounded abiotic resource hypothesis from cited leachate chemistry, not niche partitioning.; Retain hydration-dependent viable-recovery observations; remove assay-order causation.; Retain strain-specific positive persistence with late-time and water-control exceptions.

• Retain measured extract chemistry with speciation, carryover and phosphorus limits.; Retain species-specific optical growth/photophysiology, not measured nitrogen flux; remove workflow arrow.; Retain processed-culture plant benefit with endpoint and treatment specificity, not live commensalism.

• Verification also caught ruff B023 in the new mapping test helper after619 tests passed. Explicitly bind the per-record rename map, preserve pre-fix regression/formatting outputs and rerun the full suite on final content. No scientific record changed for these verification fixes.

• Read four whole records and all11 original nodes/six arrows, four complete fresh primary main texts/captions and both main tables. Retain11 nodes, qualifyfour arrows and remove two assay-order arrows. No new causal structure. Original figure pixels, separate supplements, raw data and external papers cited in the four studies were not independently audited.

• SC2: retain seven-day PDA inhibition comparable to C7 and14-day B73 height/fresh-root-mass improvement. The plate and plant assays do not isolate competition, pathogen-load mediation or host immunity. Keep the existing inhibition-to-growth hypothesis explicitly HYPOTHESIZED, not causal certainty or proof of no contribution.

• SC2: Salkowski with pure-IAA calibration and CAS halo assays support the reported45/65ugmL and0.50cm outputs. Keep chemical interpretations with their assay limits, not exact siderophore identity, pathway perturbation, in-planta delivery or reciprocal benefit. Preserve host/pathogen as external participants and prior #887-#889 repairs; do not resolve strain aliases from species-list order.

• MFC: retain positive98.7% benzene removal, product observations, sustained biotic voltage and higher power density than acetate.902.3mV belongs to250mgL cycleVI,899.9mV to330mgL cycleVII;390.1 versus238.8mWm2 is not100fold. The awkward removal sentence is resolved against abstract, main Table1 and Conclusion, not interpreted as98.7% residual benzene.

• MFC: relative genus enrichment does not resolve absolute expansion, niche partitioning or member catalytic necessity. Keep composition-to-output as the authors HYPOTHESIZED route, with confounded substrate/acclimation context. Four named genera are a partial roster. DET/MET and traced partner exchange remain unresolved. Preserve #1124 Bacillus role correction; existing Arcobacter role and Daphnia metadata remain follow-up.

• Meteorite: shared abiotic substrate and separate growth/persistence results are not a coculture. Earlier leachate chemistry does not prove current ion-specific uptake or carbon source. Low-perchlorate meteorite and terrestrial conditions are not general Martian habitability. Water controls, unequal initial phototroph counts, MPN recovery and heterotroph CFUs bound inference.

• Meteorite: preserve positive Chr20 persistence and early Planococcus growth while stating most Planococcus ratios lose late recoverability, E.coli survives in water-only controls, and below quantification is not extinction. Remove the assay-to-persistence workflow arrow, not the measured endpoint. Keep qualified substrate support rather than erase the positive resource hypothesis.

• MGS-1: retain TXRF elemental chemistry, separate OD440/PSII growth and Nostoc/Anabaena performance with Anabaena late decline and Arthrospira clumping/mild-growth limits. Element totals are not speciation/uptake. No direct N2 or O2 flux measured; undetected extract phosphorus, inoculum and reserves/carryover matter.

• Lemna: preserve seven-day positive dry-weight outcomes for Arthrospira filtered/sonicated and Chlorella filtered culture material. Lower frond yields, nonsignificant filtered/sonicated differences and nonequivalence caveat retained. Processed-material benefit is not live commensalism. Growth-advantage mediation of fertilizer advantage is not established: Nostoc grows well but supplies the weakest material treatment. Remove that workflow arrow while retaining resource-transfer observations.

• Panel-model caveat remains unresolved, not hidden by graph status. Existing COMMUNITY_LEVEL is retained only as the current container for shared abiotic/panel observations; #573 is still OPEN for record-model placement. No new schema convention, coculture or emergent microbial community is certified. Prior PR574 and graph-adding commit fa3f1a8 read.

• Read complete biological diff. Remove unsupported specific interaction/process annotations but preserve supported growth/photosynthesis context, positive endpoints and author-proposed routes. Renames retarget every retained edge and prior discussion anchor. Detach graph aliases; preserve explicit benzene and benzene_term anchors needed by untouched non-graph references.456 other records and920 caches preserved; append one history/event per target. Initial regressions found one exact-registry failure with618 passing: add the two deliberately named Mars panel records to USERS after measuring the census. Retain all test logic, preserve the failed output/digest in superseded_checks, and rerun the complete suite.

• Actual focused schema/strict/terms/references/snippets/history gates, network/rank, repeat rendering, regressions and formatting outputs recorded.17 graph excerpts independently primary-matched with whitespace normalization. Coarse scope census unchanged; network warnings46->44 because two observed MFC genera are now explicitly named in whole-biofilm nodes, not because their catalytic roles were established. Initial verifier no-delta assumption was corrected after inspecting actual output; no scientific edits made to satisfy the gate. Other44 warnings preserved exactly, no auditor-rule changes. Exact descriptions parsed over456 pages, not screenshots; postcommit docs-current is a separate gate.

• Dedup874 all-state issue titles/bodies and47 scoped ignored/hidden local files; matching issue bodies, relevant histories, prior PR574 and graph-adding commit read, not every PR/comment/local match. #1582-#1585 addressed but OPEN until protected-main merge. #1586/#573 remain OPEN afterward. No provider spend; exact-head COMMENT self-review is not independent approval or corpus completion.

619 passed in 201.31s (0:03:21); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 80 record snippets match selected caches;17 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;17 graph excerpts independently match fresh primary text after whitespace normalization. #1586 metadata, #573 panel modeling and broader #476/#1091/#1095 source limitations persist.

Eleven original nodes retained;6 arrows reviewed,4 qualified/retained and2 workflow arrows removed. No new structure or provider spend. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural errors;44 baseline findings preserved and two MFC DISCONNECTED findings removed after explicitly including the observed Pelobacter/Pseudomonas genera. This denotes observed membership, not established catalytic function. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure narrowed participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 e2d952aed2ba7e0aaef8647b67e57c82270a6c3b462814fd57d1717befee8201. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch68. Corpus218 reviewed /220 pending /22 needs_research: unfinished, not independent approval.

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 3f446041348e0ab461dd1cad55affa46290e3e6d. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 1c08cfa2a72756659fcb2d051be343941d45d729, 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 3ba5b3384cf01da513bd6e29b79d313bbcaa36d99da86b58beced57ff01ec266). 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 04e728a324cb66ecdbb05519dd42faf6b7ea7369
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3a8154795495f3110721c204c349c0eb69381f69.
The batch-owned binary patch is byte-identical
(SHA-256 3ba5b3384cf01da513bd6e29b79d313bbcaa36d99da86b58beced57ff01ec266); 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 fb9cdcca6a1440ea98a17b3036768e2ff4221160. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 04e728a324cb66ecdbb05519dd42faf6b7ea7369, 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 3ba5b3384cf01da513bd6e29b79d313bbcaa36d99da86b58beced57ff01ec266). 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 eba66c8aeafcc8065cb26efe5dcacc8c1611ec81.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 3ba5b3384cf01da513bd6e29b79d313bbcaa36d99da86b58beced57ff01ec266.
Tree 96a683d862bdddc7f3b78432c44b89401d4898ae matches the independently computed clean merge.
Compared with historical tree f355e99a977ec91bb3be1ce12d7edcb90bca2ee9, 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 d53c42c5e8fd0f3635b455809d6a82b97d03a4a5 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.