Correct source identity and metabolic-relay graph claims (batch93)

[realmarcin]

Scope

Closes #1750.
Closes #1751.
Closes #1752.
Non-graph #1753 remains open after the graph repair merges.

• Re-evidence community iron oxidation and retain the source-backed mineral-dissolution direction without COMMENSALISM, iron-transport misannotation or rate-limiting inference.; Re-evidence positive bulk/concentrate metal recovery using the exact Rammelsberg DOI; remove MUTUALISM and two unproven partner-specific recycling arrows.; Retain observed acidification and authors sulfur-oxidation interpretation without MUTUALISM, enzyme/passivation certainty or the untested sulfur-to-iron feedback.
• Retain directly supported YL-JM2C-to-JMP134 intermediate CROSS_FEEDING and its existing downstream direction.; Rename rescue to conversion, remove the unsupported reverse recipient-to-donor assignment and SYNTROPHY, and qualify the existing endpoint arrow to intermediate clearance.; Rename the existing consortium endpoint to distinguish parent disappearance from intermediate accumulation; retain positive removal/bromide evidence without SYNTROPHY or closed-carbon-balance certainty.
• Retain experimentally supported aromatic/aliphatic oxygenate division of labor. Preserve the existing unresolved succinate cross-feeding discussion without inventing a donor-recipient arrow or restoring removed outcome-only nodes.
• Retain NICHE_PARTITIONING as an explicit HYPOTHESIZED/PARTIAL interpretation; preserve SUPPORT for measured bulk removal and document contradictory control reporting without inventing cross-feeding.

Adversarial Review

• Initial combined regression output retained:855passed and one participant-set failure. The expected set now includes Rammelsberg after the measured census; the corrected full suite was rerun. Reference CLI success is macOS-only, not a Linux claim: existing DOI-cache casing issue1091 remains unresolved.
• Fresh both-root baseline preceded sources; four whole records and all nine original nodes/six arrows accounted for. Eight nodes/three directions retained, one intrinsic node/three feedback arrows removed, no new topology.
• Rammelsberg primary105443 is distinct from Finnish105484. Community chemistry and positive metal recovery remain; the dominant recorded taxa are not the entire enrichment or demonstrated pairwise beneficiaries. Correct iron-to-dissolution direction retained. Generic review chemistry cannot establish strain-specific recycling/passivation, and intrinsic carbon fixation is not exchange. Incorrect iron-transport annotation removed.
• BDE-47 retains supported forward intermediate CROSS_FEEDING, functional enzymes, transwell relay, sequential growth and wastewater endpoints. Both monoculture and mixed culture remove parent BDE-47; partner conversion prevents2,4-DBP accumulation. Reverse donor benefit/return transfer is not shown. SYNTROPHY does not require obligacy; feedback is the missing criterion. Pathway reconstruction/bromide release are not a closed carbon balance.
• RAMC graph and entire record remain unchanged: exact primary monoculture/pool comparisons support complementary utilization. Succinate exchange remains proposed, not an asserted arrow. WT and engineered RAMC-P claims remain separate; no protocol/design additions. Existing non-graph citation-marker omission yields one ASSEMBLED classification and one RENDERING; baseline/current counts measured equal, not silently called literal MATCH.
• PPOW roles remain an explicit HYPOTHESIZED/PARTIAL model while bulk removal retains SUPPORT. Methods2.4 describes controls but the conclusion says they are lacking; this source conflict is not resolved by choosing one statement. No directional cross-feeding invented. Existing member-mechanism discussion preserved.
• Three fresh PMC main bodies and complete public Rammelsberg pre-proof text read, with captions/table text but no figure pixels, raw data or complete supplements. One retained BDE FigureS16 caption has existing-cache-only provenance. All other21graph/new-discussion quotes freshly matched; quote matching is not entailment. Publisher metadata independently verifies Rammelsberg DOI/title/OA license but is not full text. No security challenge bypass.
• All921baselinecaches preserved; two independent full-text caches added: the public Rammelsberg pre-proof and freshly retrieved PPOW PMC text. PPOW initial31NoContent CLI failure is separately retained, not counted as a pass.457otherrecords, non-graph raw blocks and prior histories/decisions remain unchanged. Canonical IDs/labels preserved; Rammelsberg COMMUNITY_LEVEL scope and BDE recipient-step participants intentionally repaired. Legacy community-level census changes are measured, not used to claim mechanistic connectivity.
• Eight new regressions and focused schema/strict/term/reference/snippet/history checks executed, including the explicit RAMC baseline exception. Network remains56existingwarnings and zero structural defects. Deterministic rendering and exact HTML-description checks are not browser screenshots; generated-model loader1703 remains outside certification.
• Ignored-inclusive local and all-state issue dedup recorded with exclusions. Repairs1750-1752 remain open until protected-main merge; non-graph1753 remains unresolved. No provider spend, new wet-lab instructions, independent approval or corpus-completion claim. Prior denied/pending Edison scopes unchanged.

Verification And Output Records

856 passed in 287.22s (0:04:47); eight new regressions. Four focused schema/strict/term/reference checks and three append-only history checks passed. Local snippet checks preserve RAMC's measured baseline exception:20MATCH,1RENDERING,1ASSEMBLED from a citation-marker omission. Four full-record CLI and local snippet checks executed. Literal matches do not establish entailment or independent provenance: RAMC selected cache quotes separately match fresh full text; the retained BDE FigureS16 caption has existing-cache-only provenance. Rammelsberg new cache is the complete public author pre-proof browser extraction, not a final PDF. CLI Total checks counts issues, not executed checks. Executed on macOS, not Linux: existing issue1091 remains open for the pinned DOI-cache reader casing mismatch on case-sensitive filesystems.

All nine original nodes and six arrows reviewed. Eight nodes and three supported directions remain; one intrinsic node and three unsupported feedback arrows removed. RAMC unchanged; Rammelsberg, BDE-47 and PPOW repaired. Coverage288reviewed/124pending/48needs_research across460records. All56network warnings unchanged, zero structural defects. Legacy community-level census changes are explicitly measured, not evidence of partner mechanisms.457otherrecordfiles and921baselinecaches preserved; two independent full-text caches added. Prior histories and decision ledgers unchanged.

Deterministic rendering and exact HTML-description parsing, not screenshots. Postcommit check-docs-current passed clean, SHA256 f5488dc374bedae3156b3092d9cf98b466e85f5d116b17edddf7f096082ae0fa. Decisions, 42 gate outputs plus two repaired failures (cache access and participant-census expectation), source provenance and self-adversarial dispositions committed under reports/causal_graph_review for batch93. Three fresh primary main bodies and one public Rammelsberg pre-proof read. The BDE bromide caption is existing-cache-only, not a fresh supplement or pixel review. Full-corpus snippet audit is informational, not clean-corpus certification. Loader1703 remains outside certification.

No new topology or paid Edison run. Non-graph issue1753 remains open. No independent approval or corpus completion. Protected-main merge pending.

Source Limits

• Reference CLI checks were executed on macOS, not Linux. Existing issue1091 documents the pinned validator's DOI-cache casing mismatch on case-sensitive filesystems. The new DOI cache follows repository convention; this graph repair does not resolve or certify that cross-platform reader contract.
• The first combined regression run passed855tests and failed the exact participating_taxa record-set assertion. Rammelsberg intentionally adds explicit community participants; the measured census supports updating the expected set. The failed output is retained separately from the corrected rerun.
• All four whole records, nine original nodes and six original arrows reviewed. Eight nodes and three qualified existing arrows remain; RAMC unchanged. No new node/direction, experimental protocol, provider submission or paid Edison job.
• Three fresh EuropePMC main bodies and the complete public Rammelsberg author pre-proof text read, including captions and available table text. No figure-pixel, raw-data or complete supplement review. Rammelsberg browser extraction is not a downloaded final PDF; repository challenge and direct403 were not bypassed. The official publisher API returned identifying metadata only.
• Rammelsberg105443 is the exact study;105484 is a different Finnish study and its caches remain unchanged. PMID39770610 is a background review, with only abstract/sections1-2 read. The corrected graph includes dominant recorded taxa without claiming they exhaust the enrichment. Non-graph source/community/industrial-scale errors remain issue1753.
• BDE-47 cross-feeding, functional pathway and removal remain positive. Parent disappearance alone does not need JMP134; the demonstrated contribution is clearing2,4-DBP. Current SYNTROPHY does not assert obligacy; donor feedback, reverse transfer, reciprocal fitness and closed carbon balance are not established by this comparison. The retained bromide quote matches the existing appended FigureS16 caption, read but not freshly retrieved or visually inspected. Thus21of22graph/new-discussion quotations have fresh independent primary matches, one is existing-caption-only. Non-graph partner roles remain issue1753.
• RAMC remains supported without asserting the proposed succinate cross-feed; WT versus RAMC-P distinctions and previous non-graph fixes stay intact. Its selected appended cache is not independent evidence, but both graph quotes separately match the fresh complete main body.
• PPOW retains a HYPOTHESIZED/PARTIAL complementarity model and the SUPPORT bulk-removal observation. Methods/control claims conflict with the conclusion; neither control adequacy nor total absence is certified. Abstract versus main-text concentration-unit conflict and non-graph member-role evidence remain issue1753.
• All921baselinecaches and457otherrecord files preserved; two new exact-source caches added with browser-extraction provenance. All prior histories/decision ledgers and all non-graph raw blocks are preserved. Canonical taxon IDs/labels remain, but Rammelsberg process scope and BDE recipient-step assignment are intentionally repaired.
• Dedup included ignored/hidden local files except.git/docs/site/references_cache, with relevant caches separately checked. All-state issue titles/bodies refreshed; six matching existing issues read. Comments/PRs not exhaustively searched. Repairs1750-1752 close only after protected-main merge; non-graph1753 remains open.
• Self-adversarial review is not independent approval, generated-model loader certification or corpus completion. Loader1703 and prior denied/pending Edison scopes remain unchanged. Subsequent test/render/publication gates are not preasserted.
• The initial PPOW reference CLI failed with31NoContent errors because its old text dump was not usable by that validator. A second new cache independently extracted from the freshly retrieved complete PMC primary text resolves cache access without changing the original dump. Two new caches total, all921baselinecaches unchanged. The failed attempt remains separately recorded, not represented as a pass.

Dependency

Draft depends on #1749. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 65716e7; not independent approval.

• Re-evidence community iron oxidation and retain the source-backed mineral-dissolution direction without COMMENSALISM, iron-transport misannotation or rate-limiting inference.; Re-evidence positive bulk/concentrate metal recovery using the exact Rammelsberg DOI; remove MUTUALISM and two unproven partner-specific recycling arrows.; Retain observed acidification and authors sulfur-oxidation interpretation without MUTUALISM, enzyme/passivation certainty or the untested sulfur-to-iron feedback.

• Retain directly supported YL-JM2C-to-JMP134 intermediate CROSS_FEEDING and its existing downstream direction.; Rename rescue to conversion, remove the unsupported reverse recipient-to-donor assignment and SYNTROPHY, and qualify the existing endpoint arrow to intermediate clearance.; Rename the existing consortium endpoint to distinguish parent disappearance from intermediate accumulation; retain positive removal/bromide evidence without SYNTROPHY or closed-carbon-balance certainty.

• Retain experimentally supported aromatic/aliphatic oxygenate division of labor. Preserve the existing unresolved succinate cross-feeding discussion without inventing a donor-recipient arrow or restoring removed outcome-only nodes.

• Retain NICHE_PARTITIONING as an explicit HYPOTHESIZED/PARTIAL interpretation; preserve SUPPORT for measured bulk removal and document contradictory control reporting without inventing cross-feeding.

• Initial combined regression output retained:855passed and one participant-set failure. The expected set now includes Rammelsberg after the measured census; the corrected full suite was rerun. Reference CLI success is macOS-only, not a Linux claim: existing DOI-cache casing issue1091 remains unresolved.

• Fresh both-root baseline preceded sources; four whole records and all nine original nodes/six arrows accounted for. Eight nodes/three directions retained, one intrinsic node/three feedback arrows removed, no new topology.

• Rammelsberg primary105443 is distinct from Finnish105484. Community chemistry and positive metal recovery remain; the dominant recorded taxa are not the entire enrichment or demonstrated pairwise beneficiaries. Correct iron-to-dissolution direction retained. Generic review chemistry cannot establish strain-specific recycling/passivation, and intrinsic carbon fixation is not exchange. Incorrect iron-transport annotation removed.

• BDE-47 retains supported forward intermediate CROSS_FEEDING, functional enzymes, transwell relay, sequential growth and wastewater endpoints. Both monoculture and mixed culture remove parent BDE-47; partner conversion prevents2,4-DBP accumulation. Reverse donor benefit/return transfer is not shown. SYNTROPHY does not require obligacy; feedback is the missing criterion. Pathway reconstruction/bromide release are not a closed carbon balance.

• RAMC graph and entire record remain unchanged: exact primary monoculture/pool comparisons support complementary utilization. Succinate exchange remains proposed, not an asserted arrow. WT and engineered RAMC-P claims remain separate; no protocol/design additions. Existing non-graph citation-marker omission yields one ASSEMBLED classification and one RENDERING; baseline/current counts measured equal, not silently called literal MATCH.

• PPOW roles remain an explicit HYPOTHESIZED/PARTIAL model while bulk removal retains SUPPORT. Methods2.4 describes controls but the conclusion says they are lacking; this source conflict is not resolved by choosing one statement. No directional cross-feeding invented. Existing member-mechanism discussion preserved.

• Three fresh PMC main bodies and complete public Rammelsberg pre-proof text read, with captions/table text but no figure pixels, raw data or complete supplements. One retained BDE FigureS16 caption has existing-cache-only provenance. All other21graph/new-discussion quotes freshly matched; quote matching is not entailment. Publisher metadata independently verifies Rammelsberg DOI/title/OA license but is not full text. No security challenge bypass.

• All921baselinecaches preserved; two independent full-text caches added: the public Rammelsberg pre-proof and freshly retrieved PPOW PMC text. PPOW initial31NoContent CLI failure is separately retained, not counted as a pass.457otherrecords, non-graph raw blocks and prior histories/decisions remain unchanged. Canonical IDs/labels preserved; Rammelsberg COMMUNITY_LEVEL scope and BDE recipient-step participants intentionally repaired. Legacy community-level census changes are measured, not used to claim mechanistic connectivity.

• Eight new regressions and focused schema/strict/term/reference/snippet/history checks executed, including the explicit RAMC baseline exception. Network remains56existingwarnings and zero structural defects. Deterministic rendering and exact HTML-description checks are not browser screenshots; generated-model loader1703 remains outside certification.

• Ignored-inclusive local and all-state issue dedup recorded with exclusions. Repairs1750-1752 remain open until protected-main merge; non-graph1753 remains unresolved. No provider spend, new wet-lab instructions, independent approval or corpus-completion claim. Prior denied/pending Edison scopes unchanged.

856 passed in 287.22s (0:04:47); eight new regressions. Four focused schema/strict/term/reference checks and three append-only history checks passed. Local snippet checks preserve RAMC's measured baseline exception:20MATCH,1RENDERING,1ASSEMBLED from a citation-marker omission. Four full-record CLI and local snippet checks executed. Literal matches do not establish entailment or independent provenance: RAMC selected cache quotes separately match fresh full text; the retained BDE FigureS16 caption has existing-cache-only provenance. Rammelsberg new cache is the complete public author pre-proof browser extraction, not a final PDF. CLI Total checks counts issues, not executed checks. Executed on macOS, not Linux: existing issue1091 remains open for the pinned DOI-cache reader casing mismatch on case-sensitive filesystems.

All nine original nodes and six arrows reviewed. Eight nodes and three supported directions remain; one intrinsic node and three unsupported feedback arrows removed. RAMC unchanged; Rammelsberg, BDE-47 and PPOW repaired. Coverage288reviewed/124pending/48needs_research across460records. All56network warnings unchanged, zero structural defects. Legacy community-level census changes are explicitly measured, not evidence of partner mechanisms.457otherrecordfiles and921baselinecaches preserved; two independent full-text caches added. Prior histories and decision ledgers unchanged.

Deterministic rendering and exact HTML-description parsing, not screenshots. Postcommit check-docs-current passed clean, SHA256 f5488dc374bedae3156b3092d9cf98b466e85f5d116b17edddf7f096082ae0fa. Decisions, 42 gate outputs plus two repaired failures (cache access and participant-census expectation), source provenance and self-adversarial dispositions committed under reports/causal_graph_review for batch93. Three fresh primary main bodies and one public Rammelsberg pre-proof read. The BDE bromide caption is existing-cache-only, not a fresh supplement or pixel review. Full-corpus snippet audit is informational, not clean-corpus certification. Loader1703 remains outside certification.

No new topology or paid Edison run. Non-graph issue1753 remains open. No 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, 56 warning across 20 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)

Phormidium_Alkaline_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacteroidota members' has no interactions

Total: 1 issues (0 error, 1 warning)

Polaromonas_Vanadium_Reduction_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Desulfitobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Desulfovibrio species' has no interactions
  [warning] DISCONNECTED: Taxon 'Geobacter species' has no interactions

Total: 3 issues (0 error, 3 warning)

Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa MDR6-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa NfxB-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa OrfN' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa PA14' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa mexZ' has no interactions

Total: 5 issues (0 error, 5 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 governance integration review at exact head f3de201e83724133c15a2852adaedc78b853e386. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 65716e7454538e9749b65bcbbb6fc233b6c6b8f8, 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 45f1b32b9908468aa727eb27c7974b2619abd7377f5f3b91180a7650bef35ef7). 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 5756e8e244d1c6e04d9797e91f97b709e41ae619.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 45f1b32b9908468aa727eb27c7974b2619abd7377f5f3b91180a7650bef35ef7.
Tree 77bf52b8bb8b90d503825bba8b1e910e8dd21138 matches the independently computed clean merge.
Compared with historical tree 1cb01fb64d13bf9992d73176f5f71e15cb16825f, 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 9404a41700332c3a8e248cb62aee7bd968139a01 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.