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Bound field outcomes and model-derived ecological claims (batch96) - #1771
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Source-based self-adversarial review at exact head c33f689; not independent approval.
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Retain initial genus-level enrichment and coincident reduction with a PARTIAL removal arrow, not cross-feeding or species-resolved enzymology.; Retain measured early groundwater uranium loss, not nanoparticle identity or mutualism.; Retain sulfate/sulfide observations and the adverse later uranium response; remove the contradicted immobilization arrow.; Retain community succession and a PARTIAL process link, with the Fe(III)/acetate explanation explicitly hypothetical.
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Retain substrate-driven composition and the existing PARTIAL phenotype direction, not within-community niche partitioning.; Retain CMC core selection without asserting complementary resource use.; Retain measured caproate and genus associations without demonstrated hydrogen flux or methane effects.
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Retain supported metabolite cross-feeding and the existing oxygen-consumption direction.; Retain reciprocal positive oxygen/metabolite feedback without an absolute zero-oxygen or syntrophy claim.; Retain FG4-associated inhibition and its negative arrow, not reciprocal competition or isolated-target toxicity.; Retain Brevibacillus-to-Bordetella growth suppression without reciprocal-harm classification.
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Retain measured community SCFA outcomes without donor-recipient or BP5 attribution.; Retain community-only detection with cultivation confounding, not colonization facilitation.; Retain explicit predicted exchange following neighboring-enzyme perturbation; remove both bridges to observed expression and output.
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Fresh both-root baseline preceded paper reads. All four whole records,16originalnodes and10arrows accounted for;14nodes6existingdirections retained,2nodes4arrows removed,4nodes renamed. No new topology.
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Rifle early uranium loss and Geobacter association are retained separately from later sulfate/sulfide observations and increasing groundwater uranium. The prior sulfide-to-continued-immobilization arrow is contradicted. No nanoparticle size/product, pairwise mutualism or species-resolved enzymatic flux survives in graph attributes.
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Rifle Anaeromyxobacter evidence points to a Geobacter uraniireducens transcriptome and another field site; two Oak Ridge sources, high-salinity enrichment and a D. hippei isolate are not exact Rifle membership or exchange evidence. Two unsupported nodes are removed without asserting these organisms/reactions can never occur. Succession is measured; Fe(III)/acetate mediation remains hypothetical. Unspecified participants do not certify all canonical taxa.
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Rumen composition, CMC core selection and xylan caproate remain positive evidence. Separate enrichment lines do not resolve within-community niche partitioning, reduced competition or hydrogen/methane flux. The existing direction remains PARTIAL. Earlier discussions and non-graph evidence are preserved.
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SF356 positive metabolite/oxygen feedback and its existing directions remain, as do FG4 acid-associated inhibition and Brevibacillus suppression. Reciprocal harm is not established by suppression alone, so COMPETITION is removed. Current SYNTROPHY requires product-removal metabolic feedback, not obligacy; oxygen facilitation is not automatically syntrophy. Aerotolerance prevents an absolute zero-oxygen assertion.
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Adversarial diff review caught the FG4 node retaining a CSK1 pairwise target despite a community-level endpoint. It is now COMMUNITY_LEVEL with FG4 source and no target. A second curation/history event records the fix, preserving the initial history. The initial validation was interrupted after23completed outputs; all final gates rerun. A focused regression protects the corrected scope.
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SIHUMIx small-protein expression, computational exchange and transit-study SCFA output remain separate observations. rxn15467 is a neighboring-enzyme perturbation, not a BP5 knockout. Genomic proximity does not establish BP5 mediation; remove both causal bridges. Exchange remains explicitly COMPUTATIONAL/PARTIAL, bulk SCFA is not measured cross-feeding, and community-only detection is confounded by cultivation conditions.
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The positive synthetic-CR2 lag/cell-size finding is acknowledged without claiming native-community action or colonization facilitation. No new CR2 graph node is added. Transit Results/abstract support the output direction; inconsistent discussion BCFA wording is explicitly recorded, not silently combined.
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Rumen complete fresh main text and captions, selected SIHUMIx/transit primary sections, cached Rifle main text and fresh primary abstracts read with explicit access limits. No figure-pixel, supplement or raw-data certification.28graph/new-discussion quotes match fresh primary text and unchanged caches; literal matches are not entailment. Rifle cached body is not fresh independent full-text verification; XML failures and PMC challenge were not bypassed.
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Four records changed;456unchangedrecords,923unchangedcaches and all non-graph raw blocks preserved. Five append-only histories including the scope correction. Canonical taxonomy not recertified. No participant-slot fixture change is needed. Actual connectivity census is recorded, not treated as ecological evidence.
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Eight focused tests and880combined regressions passed, all four whole-record gates and five history gates executed.56network warnings unchanged and zero structural defects. Deterministic rendering and exact HTML description checks are not screenshots; postcommit docs-current is a separate gate. macOS passes do not certify Linux DOI-cache casing1091 or loader1703.
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Fresh all-state issue title/body and ignored/hidden-inclusive local dedup have stated exclusions; matching prior issues read, PRs/comments not exhaustive.1766-1769 stay open until protected-main merge;1770 remains separate non-graph work. No provider spend, new wet-lab protocol or protection bypass. Self-review COMMENT is not independent approval; corpus remains incomplete.
880 passed in 285.17s (0:04:45); eight focused regressions. All four records passed schema, strict, term, reference and snippet gates; five history artifacts passed.43 final gate output records/digests are committed with decisions, source provenance and self-adversarial findings.23 preliminary outputs remain separate: that attempt was interrupted when diff review caught an unsupported CSK1 target in the FG4 node. Community scope and FG4 source now replace that pairwise claim, with an additional immutable history and a complete rerun. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; SF356 and Rifle-context fresh sources are abstract bounded; the Rifle main text was read from the maintained cache. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All16originalnodes/10arrows reviewed;14nodes6existingdirections retained,2nodes4arrows removed,4nodes renamed. Four records changed;456unchangedrecords and923baselinecaches preserved. Non-graph raw blocks and canonical taxonomy remain unchanged, not recertified. Coverage300reviewed/112pending/48needs_research across460records.56network warnings unchanged,zero structural defects. Coarse connectivity is not membership or mechanism evidence.
Rumen fresh main text, selected SIHUMIx/transit sections, cached Rifle main text and fresh primary abstracts read, with explicit access limits.28retained/new-discussion quotations freshly matched; no figure pixels, supplements or raw-data certification. Rifle cached body is not fresh independent full-text verification. Failed XML retrieval and PMC challenge were not bypassed. Deterministic rendering and HTML-description parsing are not screenshots. Postcommit check-docs-current passed clean, SHA256 bcc2c032b14c4efcc3c284397064cbe997a27bc9cbd672ad304ba5d9b72cd656.
No new topology or Edison spend. Non-graph1770 remains open. Source-based self-adversarial review is not independent approval. Protected-main merge pending.
Network integrity findingsWarnings 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. The full report is attached to the workflow run as an artifact. |
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Self-adversarial governance integration review at exact head d003b2fd538c958de68d8d46d4b440e214e15ef8. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head c33f6896716f6cfa4ccaac9b3ad97359de0674f9, 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 3aa7010fe2a0fe2a2ff0af80fcb050a4a34042525b6699c06bf46642500e33e1). 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.
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Exact-head self-adversarial restack review at 651a9ba7a1a04e2a0dd24ef7f463d4a755d9b06e.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 3aa7010fe2a0fe2a2ff0af80fcb050a4a34042525b6699c06bf46642500e33e1.
Tree a295e719f5cc4b3aee99dcddffa197bb600c0f25 matches the independently computed clean merge.
Compared with historical tree 7eaebe3a224a2b1a963722314f7ad145e5d8ce83, 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.
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Superseded by the protected cumulative merge #1975 at 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. |
1 participant
Scope
Closes #1766.
Closes #1767.
Closes #1768.
Closes #1769.
Non-graph #1770 remains open after this graph repair merges.
Adversarial Review
Verification And Output Records
880 passed in 285.17s (0:04:45); eight focused regressions. All four records passed schema, strict, term, reference and snippet gates; five history artifacts passed.43 final gate output records/digests are committed with decisions, source provenance and self-adversarial findings.23 preliminary outputs remain separate: that attempt was interrupted when diff review caught an unsupported CSK1 target in the FG4 node. Community scope and FG4 source now replace that pairwise claim, with an additional immutable history and a complete rerun. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; SF356 and Rifle-context fresh sources are abstract bounded; the Rifle main text was read from the maintained cache. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All16originalnodes/10arrows reviewed;14nodes6existingdirections retained,2nodes4arrows removed,4nodes renamed. Four records changed;456unchangedrecords and923baselinecaches preserved. Non-graph raw blocks and canonical taxonomy remain unchanged, not recertified. Coverage300reviewed/112pending/48needs_research across460records.56network warnings unchanged,zero structural defects. Coarse connectivity is not membership or mechanism evidence.
Rumen fresh main text, selected SIHUMIx/transit sections, cached Rifle main text and fresh primary abstracts read, with explicit access limits.28retained/new-discussion quotations freshly matched; no figure pixels, supplements or raw-data certification. Rifle cached body is not fresh independent full-text verification. Failed XML retrieval and PMC challenge were not bypassed. Deterministic rendering and HTML-description parsing are not screenshots. Postcommit check-docs-current passed clean, SHA256 bcc2c032b14c4efcc3c284397064cbe997a27bc9cbd672ad304ba5d9b72cd656.
No new topology or Edison spend. Non-graph1770 remains open. Source-based self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1765. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.