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Review removal evidence and social-spreading graph (batch89) - #1737
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Source-based self-adversarial review at exact head f63d0b9; not independent approval. Repairs1732-1735addressed; metadata1736remains unfinished.
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Preserve reported interface and precursor facilitation with explicit evidence bounds.; Preserve the multilayer model without asserting mediator necessity or mutual fitness.; Preserve measured wax removal without mineralization or fitness inference.
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Preserve nitrate removal and reported abundance shifts without verified flux or niche partitioning.
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Preserve complementary transformations and qualify hydrolase-specific mediation.; Preserve directed intermediate coupling without asserting growth dependence or traced assimilation.; Preserve superior removal without equating the endpoint with cross-feeding or fitness.
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Preserve emergent spreading without a one-way inducer or resolved motor.; Preserve measured comigration without mutual-fitness or initiation-feedback inference.; Repair the existing initiation arrow source and preserve the tested association requirement.
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Fresh both-root baseline preceded papers; all10originalnodes6arrows retained with dispositions. One existing source endpoint corrected; its target and causal wording are unchanged. No new biological causal claim.
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Waxy-oil removal measurements and both existing directions survive. Proposed transfer and cooperation are PARTIAL; multi-omics and docking do not establish mediator necessity or reciprocal fitness. Unavailable methods are not evidence that perturbations were absent.
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Nitrogen preserves improved nitrate-N removal and reported abundance shifts. Metagenomic versus transcript wording is unresolved, not silently converted into verified expression or flux. Nitrate disappearance does not certify whole-system nitrogen loss or niche partitioning.
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Bifenthrin sequential transformations and positive consortium comparison remain. Intermediate coupling does not establish traced assimilation, growth dependence or reciprocal fitness. Hydrolase-specific mediation stays qualified.
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Social spreading, comigration and association requirement remain distinct positive findings. The existing initiation arrow text names contact, so its attachment changes from Comigration to the already-existing Contact-Dependent Initiation node. This repairs a mechanical source mismatch rather than extending the graph with a new claim.
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Primary membrane and adjacent-colony experiments support the association requirement; conditioned-medium and heat-killed-cell results do not identify a molecular trigger or motor. Follow-up differences among other isolate pairs do not override the canonical pair.
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Explicit canonical participants replace unsupported one-way inducer and mutual-fitness typing in social nodes. Non-graph temperature, timing and cross-feeder-role claims are preserved outside certification under1736.
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One fresh primary main text and four fresh abstracts read. Follow-up XML500 after bounded retries. No separate supplements, raw data or original figure pixels audited. No new growth-optimization details, strain combinations, genetic designs or experimental procedures added.
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All921caches456otherrecords and raw non-graph blocks preserved; four append-only histories and ten focused tests. Four explicit-participant users added, measured census updated, all56oldwarnings retained, zero structural defects. No taxonomy or auditor-rule change.
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Executed gates and deterministic HTML-description checks are not browser screenshots or generated-model loader certification. Loader1703remains open. Repairs1732-1735await protected-main merge;1736remains open. No paid Edison job or inferred authorization. Self-review is not independent approval or corpus completion.
806 passed in 278.00s (0:04:38); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Eighteen graph and eight discussion quotations match independent fresh-primary and cache text. Literal matching is not entailment or full-text certification.
All10originalnodes6arrows retained. One existing arrow reattached from Comigration to Contact-Dependent Initiation, preserving its target and wording. No new biological causal claim. Positive treatment comparisons and joint movement remain distinct from inferred mediation, traced assimilation, niche partitioning and reciprocal fitness.
456otherrecords, all921caches and raw non-graph blocks unchanged. All56existing network warnings preserved, zero structural defects. Four explicit participant users added with measured census. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and metadata #1736 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 c1ec120a5aac594e3d209f1d10707804204186e5c23149f6ecbc52e617cc0483. Decision ledger,42actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch89. Corpus276reviewed/136pending/48needs_research. No Edison dry run or paid submission; no new biological mechanism or experimental design. Not independent approval or corpus completion.
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 review refreshed at exact head 14f193477d80110cd729f6626cb0043ba6704e92
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 8323cd500b8d327c50030d13c9bfea0dd3f8d903.
The batch-owned binary patch is byte-identical
(SHA-256 e660550aea97adae52d37ea02e42587361d7415318a3313de0cfc70ad806d927); 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.
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Self-adversarial governance integration review at exact head f9e98185d201fdd2fa910b43097cc07c0f55e84b. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 14f193477d80110cd729f6626cb0043ba6704e92, 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 e660550aea97adae52d37ea02e42587361d7415318a3313de0cfc70ad806d927). 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 435a37279a486485b34f2378b9b3c4f8a2de3647.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 e660550aea97adae52d37ea02e42587361d7415318a3313de0cfc70ad806d927.
Tree 957e92dfd5992f4586278c82773c5d891529ec72 matches the independently computed clean merge.
Compared with historical tree 43df5faba3721a5830ac10c16943bf75b2c9ca8b, 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 #1732.
Closes #1733.
Closes #1734.
Closes #1735.
Metadata #1736 remains OPEN after graph-repair merge.
Adversarial Review
Verification And Output Records
806 passed in 278.00s (0:04:38); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Eighteen graph and eight discussion quotations match independent fresh-primary and cache text. Literal matching is not entailment or full-text certification.
All10originalnodes6arrows retained. One existing arrow reattached from Comigration to Contact-Dependent Initiation, preserving its target and wording. No new biological causal claim. Positive treatment comparisons and joint movement remain distinct from inferred mediation, traced assimilation, niche partitioning and reciprocal fitness.
456otherrecords, all921caches and raw non-graph blocks unchanged. All56existing network warnings preserved, zero structural defects. Four explicit participant users added with measured census. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and metadata #1736 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 c1ec120a5aac594e3d209f1d10707804204186e5c23149f6ecbc52e617cc0483. Decision ledger,42actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch89. Corpus276reviewed/136pending/48needs_research. No Edison dry run or paid submission; no new biological mechanism or experimental design. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1731. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.