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Recheck interaction semantics and preserve review history (batch91) - #1745
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Source-based self-adversarial review at exact head 8263b03; not independent approval. Repair1744addressed; research1715 and metadata follow-ups remain unfinished.
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Retain CROSS_FEEDING: the existing explanation already distinguishes source syntrophy wording from product-removal benefit.; Preserve binary electricity and substrate-conversion comparisons without a unique feedback or reciprocal-fitness claim.; Preserve substrate-dependent spatial observations without restoring a causal localization arrow.
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Preserve predominantly autotrophic carbon evidence and qualified community supply.; Retain the hypothesized CROSS_FEEDING model: direct host acquisition, scavenging and unknown biosynthesis remain alternatives; product-removal feedback is not established.; Preserve mixed-fraction lysolipid findings and qualified curvature interpretation.
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Preserve heterogeneous genome-inferred producer roles without new member assignments.; Preserve substrate-distinct proposed chain elongation and terminal-product limits.; Type the existing hypothesized lactate-transfer model CROSS_FEEDING with primary Discussion evidence; distinguish product-removal feedback from obligacy.
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Preserve measured methane/comparator outcomes and the qualified staged-transfer model.; Keep the metagenomically inferred transfer node untyped for unresolved product-removal feedback, not unproven obligacy.; Preserve environmental selection interpretation and function/stability distinction.
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Keep the positive degradation endpoint distinct from a product-removal mechanism; obligacy is not required by SYNTROPHY.; Preserve proposed products/pathways without treating metabolomic differences as partner feedback; unresolved topology remains #1715.
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Fresh both-root baseline preceded papers. Five previous reviews rechecked, three records changed and two unchanged. All14nodes7arrows retained with identical arrow wording/endpoints and participant assignments. No new direction, topology or inflated completed-review count.
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Current schema explicitly does not assert obligacy for SYNTROPHY. Its additional criterion is product-removal feedback making the first partner metabolism favourable. Cross-feeding and cooperative outcomes do not automatically demonstrate that feedback.
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UFMP primary main text supports an inferred producer-consumer connection. The existing transfer node receives CROSS_FEEDING with PARTIAL COMPUTATIONAL evidence; heterogeneous donor/substrate roles and both hypothesized arrows remain. No direct flux, stereochemistry, complete conversion or additional species assignment is claimed.
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Digestion retains reported methane increases, propionate reduction and function/stability trade-off. Metagenomic association is not transcript abundance or measured electron transfer. Its untyped mechanism node is justified by unresolved feedback, not unproven obligacy; primary access is abstract-only.
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Pleuromutilin retains its positive community endpoint and proposed-products evidence. These nodes do not resolve product-removal feedback and remain untyped; existing needs_research status and issue1715 remain. A discussion reference to nonexistent engineering_design is corrected to the record description. No new antibiotic-selection, growth optimization, genetic design, pathway or protocol details.
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MFC and Crystal Geyser already distinguished substrate provision from product-removal feedback, so their record bytes remain unchanged. MFC current/CMC outcomes and spatial observations stay separate; Crystal Geyser lipid/genome/isotope associations do not isolate a donor-recipient route. Missing fresh MFC full text is not absence of controls.
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Two complete main bodies, embedded table text and captions read, plus four other primary abstracts. No original figure pixels, raw data or complete supplement audit. Earlier pleuromutilin supplement notes/boundary rows reread, not newly downloaded or visually rendered; inconsistent S3 scale/subset/table labels are recorded in existing research1715, not reconciled.
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An initial PMID33125214 lookup was unrelated and explicitly excluded. Correct exact-system PMID42133144 was retrieved and read before edits. Target proofs reference only six correct primary sources; unrelated lookup artifacts remain for transparency, not evidence.
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Inventory previously rejected any repeated record review. Explicit parent ledger, record hash, original hash and ID links now select one linear tip independent of ordering. Tests reject duplicate, missing, self, mismatched, unlinked, forked, cyclic and disconnected histories. Current record hash and node/edge coverage checks remain mandatory; needs_research is not promoted.
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All previous tracked history and decision artifacts are byte-identical to the parent commit. Three append-only histories, eight record regressions and sixteen new inventory cases. All921caches457unchangedrecords/raw non-graph blocks preserved. Coverage280reviewed132pending48research;1420nodes584arrows, all56oldwarnings, zero structural defects and unchanged legacy census.
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No Edison dry run, provider submission or spend. Executed gates and deterministic HTML parser checks are not browser screenshots or generated-model loader certification; loader1703 remains open. Repair1744 awaits protected-main merge; research1715 and metadata183/1327/1366/1716 stay open. Source-based self-review is not independent approval or corpus completion.
841 passed in 329.80s (0:05:29); eight new record regressions and sixteen inventory cases. Five per-record schema/strict/term/reference/snippet gates and three append-only history gates passed. Five full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Twenty-three graph and two discussion quotations match fresh target-specific primary text and cache text. Literal matching is not entailment; two main bodies and four other abstracts were read, not six full papers.
Five previous reviews rechecked: three record edits and two unchanged records. All14nodes7arrows retained, including arrow wording/endpoints and participant assignments. UFMP's existing transfer hypothesis receives CROSS_FEEDING with PARTIAL evidence. Digestion and pleuromutilin remain untyped for unresolved product-removal feedback or outcome scope, not for unproven obligacy.
Explicit hash-linked review supersession preserves old ledgers and histories and rejects unlinked duplicates, forks and cycles. Existing current-record hash, node and edge coverage checks remain. Coverage is unchanged at280reviewed/132pending/48needs_research; re-review does not add completed records.
457record files and all921caches unchanged. All56existing network warnings preserved, zero structural defects; measured legacy census unchanged. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703, research #1715 and non-graph #183/#1327/#1366/#1716 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 8025412f87dc8271f6f0d028dc3cff600e5af404469a4218b807fbf60062f0c8. Decision ledger,47actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch91. Two complete primary main bodies and four other abstracts read; an unrelated initial lookup is explicitly excluded. No new topology, paid Edison submission, genetic design, antibiotic-selection or experimental protocol. 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 5fb1fb3d8fa26c4f424be17f7a380e3f9c0eaee6
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 449355448ac2337a465440fd87013586a21eb45d.
The batch-owned binary patch is byte-identical
(SHA-256 e0b80bf0599aef056110e6266eef18c52d092fa507f39cd994659563c1485f34); 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 2050459dc01231b52741502fea473f8196e11fa6. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 5fb1fb3d8fa26c4f424be17f7a380e3f9c0eaee6, 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 e0b80bf0599aef056110e6266eef18c52d092fa507f39cd994659563c1485f34). 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 694ecc87177f520a10fc664ce2e6f1b668e076e7.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 e0b80bf0599aef056110e6266eef18c52d092fa507f39cd994659563c1485f34.
Tree decbbb82a03e1b13ca793790cac7555507230ea6 matches the independently computed clean merge.
Compared with historical tree d69372d97c0c36a91f669d537d25a92eccb35540, 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 #1744.
Research #1715 and non-graph #183/#1327/#1366/#1716 remain OPEN after the rationale repair.
Adversarial Review
Verification And Output Records
841 passed in 329.80s (0:05:29); eight new record regressions and sixteen inventory cases. Five per-record schema/strict/term/reference/snippet gates and three append-only history gates passed. Five full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Twenty-three graph and two discussion quotations match fresh target-specific primary text and cache text. Literal matching is not entailment; two main bodies and four other abstracts were read, not six full papers.
Five previous reviews rechecked: three record edits and two unchanged records. All14nodes7arrows retained, including arrow wording/endpoints and participant assignments. UFMP's existing transfer hypothesis receives CROSS_FEEDING with PARTIAL evidence. Digestion and pleuromutilin remain untyped for unresolved product-removal feedback or outcome scope, not for unproven obligacy.
Explicit hash-linked review supersession preserves old ledgers and histories and rejects unlinked duplicates, forks and cycles. Existing current-record hash, node and edge coverage checks remain. Coverage is unchanged at280reviewed/132pending/48needs_research; re-review does not add completed records.
457record files and all921caches unchanged. All56existing network warnings preserved, zero structural defects; measured legacy census unchanged. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703, research #1715 and non-graph #183/#1327/#1366/#1716 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 8025412f87dc8271f6f0d028dc3cff600e5af404469a4218b807fbf60062f0c8. Decision ledger,47actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch91. Two complete primary main bodies and four other abstracts read; an unrelated initial lookup is explicitly excluded. No new topology, paid Edison submission, genetic design, antibiotic-selection or experimental protocol. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1743. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.