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Correct exact-system dechlorination and biochar causality (batch 31) - #1393
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Source-based self-adversarial review at exact head e62e9da; not independent approval.
Addressed #1388/#1389/#1390 after reading actual diffs against the recorded primary-source access. Eleven nodes retained, six arrows retained and one common-amendment outcome arrow removed. Preserve exact strain-195 acetylene rescue without importing ANAS/BAV1 results; disclose PARTIAL abstract-only evidence. Assign recipient phenotypes without reverse nutrient transfer.
Separate SEM aggregates from modeled hydrogen diffusion, keep uncertain mediation PARTIAL, and distinguish butyrate/crotonate/threshold conditions and cometabolism. Biochar sorption is not degradation; lower VC is inoculum-dependent. Composition alone does not demonstrate functional flux, DIET or field stability. CWV2 body access is an author-uploaded proof, not the final published body.
354 passed in 182.27s (0:03:02); six new tests. Schema, strict, terms, independent snippet/history gates, deterministic rendering, exact descriptions across 456 pages and actual post-commit docs-current passed. All three reference-validator commands performed zero checks despite exit 0; this is no-op, not evidence validation. Zero structural errors; 31 unchanged warnings. Registry 174 to 175, measured connectivity unchanged, no numeric bounds or algorithms altered. Three guarded writes/histories; 457 other records and 920 caches unchanged.
Metadata #765/#1391 and CO research #1392 remain open. Syntrophomonas remains needs_research, not a completed graph review. Edison dry run only; no provider job/charge. No article bodies/PDFs committed, no uninspected figure/supplement claims. Protected CI/main merge and full-corpus completion are not claimed. Preserve dependencies until main merges.
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 bb70b30363645bad9823ea3a4c3bf95eb4baec7a
after protected main merge of #1312. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 356ed655f362fe54f3076e3fa1593f2ce0ac7e7d
after protected main merge of #1315. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 2ff0be594df169b9291d9bc9976ebbf3d814e580
after protected main merge of #1318. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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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Reference-counter correction (#1469) The earlier statement that linkml-reference-validator 0.1.7's The source-backed correction and historical candidate inventory are committed in #1470 at The new Fucoidan batch separately retains 14 baseline reference-CLI failures and 15 baseline snippet-audit mismatches for supplement-sidecar excerpts. Those are not failures attributed to this older PR. This correction is self-review, not independent approval or merge authorization beyond the existing protected workflow. |
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Self-adversarial review refreshed at exact head ba35f58dcd24f7d6fb4fcd8fba8f87e9bc7810fa
after protected main merge of #1323. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 6740149bac82c82c19b609dcb55c8a03061bb8d6
after protected main merge of #1328. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 bde32d7d420667e3c874f26610766f2a721a0636
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 427600baeb60d3bb1aedd436a68b0239fc9b77af
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 3200ac1a5ccb7c63968575e6e7843e5fa1bd2746
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 ec33b5807e34c6ac566042eea8625e72fbeb69bf
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 f91d467f407626eef920bd370af7086706bead6b
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree fcd538f72078d9b7d359d76e6ef226cca1eb06c3.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 e89d913e7d1a370a4e2d685ff355c87891565f8d. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head f91d467f407626eef920bd370af7086706bead6b, 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 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce). 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 28809c5c776195e351a0405d1f0ab14fe3a14e92
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 7b24f9ffb9d438f9f622d09d902f9aef62a35771.
The batch-owned binary patch is byte-identical
(SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce); 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 6ed5001c2430f2a5675ba6c9a4f5605d59144a79. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 28809c5c776195e351a0405d1f0ab14fe3a14e92, 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 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce). 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 c47ee0df3a621bff7a5d5d0bc0897490994cc0b7.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 4cadb305f15e304789622c4e848d315153827f1c6a3abb9463fa4febc77cabce.
Tree 01e98573022e7e86b7eef6ca62ce70799ffbdd94 matches the independently computed clean merge.
Compared with historical tree bf320eed2dbf3913d57017a2e3ba3b6f91b822e5, 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. |
Scope
Three changed records: Pelobacter SFB93/Dhc195, Syntrophomonas wolfei/Dhc195 and the CWV2/D345 biochar consortium. Two graph reviews completed; Syntrophomonas remains needs_research for possible CO structure. Corpus: 137 reviewed / 318 pending / 5 needs_research across all 460 records in both roots.
Closes #1388. Closes #1389. Closes #1390. Non-graph #765/#1391 and graph research #1392 remain open.
Changes And Adversarial Review
All eleven nodes retained; six arrows retained and one unsupported TCE-outcome-to-VC-outcome arrow removed. Recipient dechlorination is no longer reverse nutrient transfer. Preserve directly demonstrated strain-195 acetylene rescue, distinguishing it from the ANAS abstract phrase, ANAS methanogenesis and BAV1 outcomes. The cached rescue snippet is PARTIAL for this exact pair; no copyrighted body is restored.
Joint Syntrophomonas/Dhc aggregates are observed by SEM, while their hydrogen-flux contribution is modeled. Mark modeled evidence COMPUTATIONAL and the arrow PARTIAL; do not infer experimental necessity, directional colonization or conductive electron transfer. Preserve positive butyrate-fed hydrogen support, external cobalamin and separate assay conditions. VC-to-ethene cometabolism is not growth-coupled respiration.
For biochar, retain positive amendment/activity support with selective mediation unresolved. Adsorption is not biological transformation, BC600 is not necessarily the strongest sorbent, and lower-VC effects differ by inoculum. Relative-abundance guild profiles do not demonstrate flux, DIET, guild necessity or long-term field stability. The body read is an author-uploaded uncorrected proof, not the final published body.
Verification
354 passed in 182.27s (0:03:02); six new tests. Schema, strict, terms, independent snippet and history gates passed. Reference-validator commands returned 0 but performed zero checks: they are no-op, not evidence validation. Raw diagnostics and actual snippet counts are recorded separately; a textual MATCH is not scientific endorsement.
Zero structural errors; all 31 prior network warnings unchanged. Measured connectivity survey unchanged. Exact participant registry 174 to 175 users, adding only the Syntrophomonas record; no numeric bounds or algorithms changed.
Three guarded edits, llm-assisted events, append-only histories and regenerated pages. All non-graph raw blocks, 457 other records and 920 caches preserved. Repeat rendering deterministic; exact descriptions checked across all 456 pages. Actual post-commit docs-current passed with a clean tree. No screenshot QA claimed.
Decision, validation and self-adversarial records are committed under reports/causal_graph_review, dated 20261006, batch31. This is source-based self-adversarial review, not independent approval. Source-access limits and uninspected figures/supplements are explicit. No article bodies/PDFs committed. One-community Edison dry run only, no provider job or charge; a failed LiteLLM pricing-map request is disclosed. New CO structure awaits authorized research and primary-source assessment under #1392.
Stacking
Draft dependency on #1387. Do not merge into the topic parent. Require exact-head protected main checks/queue after parents merge; move dependents before branch deletion. This batch does not complete the full-corpus goal.