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Separate ecological observations from genomic candidates (batch95) - #1765
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Source-based self-adversarial review at exact head 69727be; not independent approval.
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Retain measured beta-diversity/composition response without colonization-facilitation or a mediation arrow.; Retain explicitly COMPUTATIONAL predicted fungal-guild shift, not measured fungal function or plant-growth mediation.
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Retain measured available-P response without MUTUALISM and qualify existing acquisition arrow.; Retain transport-associated root observations as PARTIAL, not measured transporter flux or necessary mediation.; Retain positive pot biomass/P outcome, distinguish the adverse field comparison and remove elemental-phosphorus grounding.
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Retain iron-oxidizing Leptospirillum contribution with group/sample scope and the existing ferric-oxidant arrow.; Retain Ferroplasma contribution and existing arrow without carbon fixation, competitive exclusion or pairwise CROSS_FEEDING.; Retain the real iron/mineral feedback with external supply and mine-wide flux scope, not MUTUALISM.; Retain generic observed ARMAN contact without species/subgroup pairing or SYNTROPHY.; Rename and bound the existing higher-pH node to observed A. ferrooxidans distribution, not COMPETITION or intrinsic genomic metabolism.
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Retain electroactive community enrichment, without NICHE_PARTITIONING or universal direct EET.; Retain observed biofilm dominance and genomic capacity without COMPETITION or analysis-order arrows.
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Fresh both-root graph baseline preceded paper reads. All four whole records,18originalnodes and9arrows accounted for.12nodes6existingdirections retained;6nodes3analysis-order arrows removed;1node renamed. No new causal topology.
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FSQN is byte-for-byte unchanged. Its microbiome-composition response and explicit COMPUTATIONAL fungal-guild prediction remain distinct and unconnected. Zero arrows is appropriate here; no invented mediation to rice growth. Primary evidence remains abstract-bounded, not complete-text certification.
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Rice phosphorus SynCom has a positive pot biomass/P outcome, distinct from the negative field rice/soybean intercropping comparison. Root morphology, IAA, soil-P fractions and transporter expression do not separately establish necessary mediation. Two existing arrows and the transport pathway remain PARTIAL; plant benefit does not establish MUTUALISM. Graph evidence was detached from non-graph aliases before source-classification changes. Elemental-P grounding removed from the phenotype node.
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Richmond Fe/mineral feedback remains in its actual directions. Oxygen and mineral supply bound the cycle; mine-outflow dissolution estimates are not individual-biofilm or species rates. Iron oxidation is not iron-ion transport, direct nutrient CROSS_FEEDING or pairwise MUTUALISM. Leptospirillum group/sample identity is bounded; Ferroplasma isolate mixotrophy is not field autotrophy or competitive exclusion.
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Richmond generic ARMAN contact remains positive, without unsupported F. acidarmanus/subgroup identification. Duplicate Parvarchaeota contact is removed. Nitrogen-fixing isolate capacity is preserved in a discussion, not promoted to measured partner transfer; proteomic nondetection does not deny capacity. SYNTROPHY does not require obligacy, but contact is not metabolic feedback. Higher-pH A. ferrooxidans distribution is retained under a renamed observation node, not COMPETITION or reference-genome functional proof.
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Adversarial diff review caught copied taxon narratives and GTDB metadata inside seven newly populated participant objects, which reintroduced unsupported non-graph claims. These were removed, leaving only canonical preferred_term/term identities. Issue1762, an additional curation event/history, and an explicit regression assertion record the fix. Initial verification was deliberately interrupted after10recorded outputs; all final gates were rerun. Prior outputs are retained separately, not counted as final verification.
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Rifle community electroactivity/enrichment and Geobacter biofilm dominance remain. Four genomic inventory/conclusion nodes and three analysis-order arrows are removed. MHC/PCC/e-pilus/OmcS predictions do not prove niche partitioning, competition, universal EET, natural mineral flux or syntrophic partners. The candidate set does not exclude all other aquifer organisms. The source leaves the dominant organism environmental niche unresolved and conflicts in near-complete-genome denominators; no silent reconciliation. Cultivation setup remains unchanged.
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Two complete fresh primary main texts and their captions read, selected Richmond geochemical sections and five further Richmond primary abstracts read; FSQN abstract read. No supplement/raw-data/figure-pixel review. EuropePMC XML failures and PMC challenges do not count as access and were not bypassed. Background Ferroplasma review is not exact-system proof; downloaded Acidithiobacillus/Parvarchaeota main texts were not read or used as functional proof.21retained/new-discussion quotations freshly match primary text and unchanged caches; lexical matching is not entailment.
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Three changed records,457unchangedrecords and923unchangedcaches; four append-only histories including the adversarial participant repair. All non-graph raw blocks and canonical taxonomy remain unchanged, not recertified. Richmond participant-set fixture is updated. Unspecified contact participants still receive coarse legacy connectivity credit, which is not evidence for every member.
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Eight focused tests and872combined regressions pass, with four-record schema/strict/term/reference/snippet gates and four history gates.56network warnings unchanged,zero structural defects. Deterministic HTML rendering and exact description parsing are not screenshots. macOS reference passes do not certify Linux DOI-cache handling1091 or loader1703.
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Ignored/hidden-inclusive local dedup and refreshed all-state issue titles/bodies have explicit exclusions; matching prior issues read, no exhaustive PR/comment claim. Repairs1761-1763 remain open until protected-main merge;1764 remains non-graph follow-up. Exact-head COMMENT is self-adversarial review, not independent approval. No provider spend, new wet-lab protocol or branch-protection bypass; corpus remains incomplete.
872 passed in 505.26s (0:08:25); eight focused regressions. Four records passed schema, strict, term, reference and snippet checks, and four history artifacts passed.42 final gate output records/digests are committed with decisions, source provenance and self-adversarial findings. Ten preliminary outputs are preserved separately: that attempt was deliberately interrupted after adversarial diff review found copied participant narratives. Seven entries were narrowed to canonical identity only, an additional history was appended, and all final gates 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; FSQN and five Richmond primary sources are abstract bounded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All18originalnodes and9arrows reviewed;12nodes6existingdirections retained,6nodes3analysis-order arrows removed,1node renamed. Three records changed and FSQN unchanged;457unchangedrecords and923baselinecaches preserved. All non-graph raw blocks and canonical taxonomy remain unchanged, not recertified. Coverage296reviewed/116pending/48needs_research across460records. All56network warnings unchanged,zero structural defects. Legacy participant connectivity is not ecological evidence.
Two complete primary main texts/captions, selected Richmond geochemical sections and primary abstracts read.21retained/new-discussion quotations freshly matched; no figure pixels, supplements or raw-data review. Downloaded background main texts were not read or used as exact-system functional proof; failures/challenges were not bypassed. Deterministic rendering and exact HTML-description parsing are not screenshots. Postcommit check-docs-current passed clean, SHA256 72d1fe8d28da09ea89013f3e8dce320a8be1d15c7d8f5bf6b4ec416b7417868e.
No new topology or Edison submission/spend. Non-graph1764 remains open. 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 7eeb5350744dd9af9f42beeafadab8aab7526915. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 69727bed5e54f9de9d60323de0fb5879ae18c509, 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 0dd545d74e53fe6f97d8dee80239d3a6cbd65177160811b65aa66cd66f99b087). 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 a7952f0be74dd576e54cff92b81f60e3d5d7caa0.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 0dd545d74e53fe6f97d8dee80239d3a6cbd65177160811b65aa66cd66f99b087.
Tree 3812026d387b0daf3a04a153af5b0ad82f96be5e matches the independently computed clean merge.
Compared with historical tree 5024a3eb4835ef20d3ac24e91fba1d9939a3e13f, 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 #1761.
Closes #1762.
Closes #1763.
Non-graph #1764 remains open after this graph repair merges.
Adversarial Review
Verification And Output Records
872 passed in 505.26s (0:08:25); eight focused regressions. Four records passed schema, strict, term, reference and snippet checks, and four history artifacts passed.42 final gate output records/digests are committed with decisions, source provenance and self-adversarial findings. Ten preliminary outputs are preserved separately: that attempt was deliberately interrupted after adversarial diff review found copied participant narratives. Seven entries were narrowed to canonical identity only, an additional history was appended, and all final gates 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; FSQN and five Richmond primary sources are abstract bounded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All18originalnodes and9arrows reviewed;12nodes6existingdirections retained,6nodes3analysis-order arrows removed,1node renamed. Three records changed and FSQN unchanged;457unchangedrecords and923baselinecaches preserved. All non-graph raw blocks and canonical taxonomy remain unchanged, not recertified. Coverage296reviewed/116pending/48needs_research across460records. All56network warnings unchanged,zero structural defects. Legacy participant connectivity is not ecological evidence.
Two complete primary main texts/captions, selected Richmond geochemical sections and primary abstracts read.21retained/new-discussion quotations freshly matched; no figure pixels, supplements or raw-data review. Downloaded background main texts were not read or used as exact-system functional proof; failures/challenges were not bypassed. Deterministic rendering and exact HTML-description parsing are not screenshots. Postcommit check-docs-current passed clean, SHA256 72d1fe8d28da09ea89013f3e8dce320a8be1d15c7d8f5bf6b4ec416b7417868e.
No new topology or Edison submission/spend. Non-graph1764 remains open. Self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1760. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.