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Bound methanogen DIET evidence; keep acetate extensions open (batch46) - #1484
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Source-based self-adversarial review at exact head b59f9d6; not independent approval.
Repairs #1480/#1481 addressed after primary-text, graph-diff and validation-output review. Extensions #1482/#1483 remain OPEN.
Two existing DIET graphs repaired after exact-system primary-source review:
- Methanosaeta: distinguish the donor reaction, defined-coculture transfer and CO2 methane route. Replace environmental-expression excerpts with checked defined-coculture evidence; bound aggregate necessity and unresolved receiver proteins. Resolve the obsolete primary-access question without declaring the missing acetate branch complete.
- Methanosarcina: preserve DIET and condition-dependent pilin/GAC evidence, while correcting the donor carbon reaction, total-methane attribution and timeless uniqueness. Retain the hcp lag phenotype and explicitly HYPOTHESIZED negative establishment arrow; remove NICHE_PARTITIONING and unmeasured secretion annotations. Do not import G. sulfurreducens controls or Methanosaeta radiotracer evidence into this pair.
All six original nodes and four arrows retained with bounded source/target/direction decisions. Both acetate branches remain missing under #1482 and #1483; both records remain needs_research. Two separate Edison dry runs spent no credits; specific paid-job authorization and report review remain pending.
461 passed in 211.31s (0:03:31); six new focused tests. Schema, strict, term, reference, snippet and history checks pass for both records. All 31 excerpts match preserved caches: Methanosaeta 12, Methanosarcina 19. Text matching is not scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage (#476), Linux DOI-cache casing (#1091), and selected-cache provenance (#1362) remain limitations.
Pre-source batch45 and fresh pre-edit batch46 baselines are distinguished; selected records and all caches match across them. Zero structural errors; all 34 existing network warnings unchanged. All 458 other records, all 920 source caches, taxonomy, non-graph raw blocks and prior history preserved, not certified. Participant registry and corrected census unchanged; no production logic or census-bound changes. Repeat renders deterministic and descriptions parser-checked across all 456 pages, without a browser screenshot claim.
Actual post-commit just check-docs-current exited 0 with clean tree; log SHA256 9fe518e4132281c5a9452d0d8a0941af14b10b49b2ca7e00a755b7b687825a08.
Whole records and every original node/arrow reviewed. Complete primary main bodies, Methods and captions read for both 2014 studies and the 2023 T6SS study; selected 2014 figures inspected with scope and rendering limitations in the ledger. No 2023 figure images, separate supplements, raw data or analysis code audited. Full copyrighted PDFs remain temporary, not committed. The cached composite Methanosaeta Content is not certified as a faithful complete abstract; updated excerpts were checked independently against the primary paper.
Decisions, actual validation outputs/digests and limitations are committed under reports/causal_graph_review, batch46. Source-based self-adversarial review, not independent approval.
Protected main merge, missing-branch implementation and full-corpus completion remain 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 c52efa3ed75e43812b394a62cbcd5559c3c634ab
after protected main merge of #1328. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 review refreshed at exact head a9353133c07b434bb6ce663134e7e80d4c0b5a2f
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 review refreshed at exact head 3eff0bc90e131a22af4a081786c0997b6203d0a6
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 review refreshed at exact head fcb59eb5643329e07e954ad78cc098c00fd2d010
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 review refreshed at exact head e23c099138c709c8cc5eada0e6d2e4068cea0093
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 review refreshed at exact head 27ea3f3edb94c8f03fe1dbf1095e37184aa1179f
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0f7d6ff2043a642b918cfa9f30b87075f715efe4.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 integration review at exact head 5865f7d8f820b282b19afd8e8ed8483bdc55cd50. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 27ea3f3edb94c8f03fe1dbf1095e37184aa1179f, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.
Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.
An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.
Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.
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Self-adversarial review refreshed at exact head 3cfcf62c0616ed97493deb39280553eaaa908236
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 1c032d9a342e22dfc9e49f9b4b9073bc88fa4bc5.
The batch-owned binary patch is byte-identical
(SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4); 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 a19a2dc6eee1d586fce2e4921910409f299c9224. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 3cfcf62c0616ed97493deb39280553eaaa908236, 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 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4). 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 828d20e5adcb5fdeefc24287155f86bbcbb693bd.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 d0bc5b3ffdb8319a5909636ef14c752b916d6231c0d3b7041b66188de3182ec4.
Tree 0af33a16c63e8eca53529991cf6011a29fb85e80 matches the independently computed clean merge.
Compared with historical tree 1ec30a6f566d69fd0c1d7501b50f151a20e893d5, 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. |
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Scope
Closes #1480. Closes #1481.
Related unfinished work: #1482 and #1483 remain OPEN. This PR does not close them.
Two existing DIET graphs repaired after exact-system primary-source review:
All six original nodes and four arrows retained with bounded source/target/direction decisions. Both acetate branches remain missing under #1482 and #1483; both records remain needs_research. Two separate Edison dry runs spent no credits; specific paid-job authorization and report review remain pending.
Verification And Output Records
461 passed in 211.31s (0:03:31); six new focused tests. Schema, strict, term, reference, snippet and history checks pass for both records. All 31 excerpts match preserved caches: Methanosaeta 12, Methanosarcina 19. Text matching is not scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage (#476), Linux DOI-cache casing (#1091), and selected-cache provenance (#1362) remain limitations.
Pre-source batch45 and fresh pre-edit batch46 baselines are distinguished; selected records and all caches match across them. Zero structural errors; all 34 existing network warnings unchanged. All 458 other records, all 920 source caches, taxonomy, non-graph raw blocks and prior history preserved, not certified. Participant registry and corrected census unchanged; no production logic or census-bound changes. Repeat renders deterministic and descriptions parser-checked across all 456 pages, without a browser screenshot claim.
Actual post-commit just check-docs-current exited 0 with clean tree; log SHA256 9fe518e4132281c5a9452d0d8a0941af14b10b49b2ca7e00a755b7b687825a08.
Whole records and every original node/arrow reviewed. Complete primary main bodies, Methods and captions read for both 2014 studies and the 2023 T6SS study; selected 2014 figures inspected with scope and rendering limitations in the ledger. No 2023 figure images, separate supplements, raw data or analysis code audited. Full copyrighted PDFs remain temporary, not committed. The cached composite Methanosaeta Content is not certified as a faithful complete abstract; updated excerpts were checked independently against the primary paper.
Decisions, actual validation outputs/digests and limitations are committed under reports/causal_graph_review, batch46. Source-based self-adversarial review, not independent approval.
Corpus: 168 reviewed / 278 pending / 14 needs_research across 460 records. Existing-node repair is not completion of either missing branch or of the corpus.
Dependency
Draft depends on #1479. Do not merge into the topic parent. Require eligible exact-head checks and the protected main queue after parents merge; move dependents before deleting merged branches.