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Bound CL95 biocontrol and S11 nitrogen-removal causal claims (batch48) - #1489
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Source-based self-adversarial review at exact head e3864bd; not independent approval.
Issues #1487 and #1488 addressed.
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Bound CL95 antagonism, host growth and marker recovery; remove unproven ecological labels and the suppression-to-growth correlation arrow.
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Retain S11 nitrogen-removal performance without unmeasured mutualism or resolved consortium flux routes.
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Whole CL95 and S11 records and every original node/arrow read. CL95 complete cached primary body, Methods, Tables1-2 and captions; selected cached S3/S5/S6/S7 text. S11 primary abstract only; full article unavailable. No original supplemental DOCX, figure images, raw data or code inspected.
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Positive CL95 73% plate inhibition, 66.67% field control and growth phenotypes remain. No resource-competition mechanism, reciprocal fitness or causal suppression-to-growth mediation is inferred from those measurements. The sole correlation-only arrow is removed rather than converted into a demonstrated link.
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Both Bacillus velezensis strains remain distinct by canonical strain labels despite sharing a species CURIE. All five CL95 members and the external pathogen or host are unchanged. No generic helper drops the host/pathogen or collapses the strain identities.
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Table S5 plate zones remain exact CL95 proxy endpoints, not nutrient transfer to ginseng. Preserve earlier phosphate-removal and broad-process fixes #892/#893 and the prior cache fix #894.
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Labeled NJ13/NT35/FG14 recovery does not independently track every CL95 member or demonstrate directed movement of individual cells. Separate soil enzyme activity from its organism of origin and causal mediation; broaden symbiosis GO to the existing interspecies process. Preserve the abstract/main-text catalase percentage discrepancy rather than silently choosing a new value.
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Defense-gene transcription and microbiome associations are positive observations but not pathway-blockade, recruitment or nutrient-flux proof. Their unresolved mediation remains in the existing anchored knowledge gap, with no unsupported new causal structure or paid Edison run.
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S11 improved bulk removal remains positive. Retain authors HNAD isolate characterization while removing resolved graph-level oxidation/denitrification assignments and unmeasured MUTUALISM. Do not infer percentage-point improvement or confuse residual industrial nitrite with removal efficiency.
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Graph evidence aliases were deep-copied before changing explanations. Engineering-design and taxonomy aliases, non-graph raw blocks, prior history values and #1027 modeled_environment are unchanged. Six focused tests cover these risks and exact all-node/arrow ledger coverage.
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Inspected record/test diff. All four nodes retained; one arrow removed. Two guarded records, two append-only histories and two regenerated pages. All 458 other records and 920 caches preserved, not certified. All participant scopes and measured connectivity census unchanged; no registry, range-bound or production matching changes.
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Initial472-regression pass and Ruff B905 failure retained with output digests. Corrected the new ledger test to zip(..., strict=True), then reran the regression suite, Black and Ruff. No scientific record, source cache or history was changed by this test-only correction.
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Actual schema, strict, labels, references, snippets, rank and history gates passed; network equals baseline with34 pre-existing findings and zero structural defects. Repeat HTML renders and all descriptions parser-checked without claiming browser screenshots. Actual post-commit docs-current remains a separate gate.
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Dedup includes799 all-state issue titles/bodies and ignored/hidden local files. Closed issues892/893/894/1027 concern distinct earlier fixes; no duplicate found in inspected scope. Not every comment or PR review inspected. Source-based self-adversarial review is not independent approval.
472 passed in 181.86s (0:03:01); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 36 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All four nodes retained, one correlation-only arrow removed. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All458 other records and920 caches preserved, not certified. Participant scopes and connectivity census unchanged; no production, registry or census-bound changes.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 0d822276d941b0cbbd64eb67a0f9bf425c8cdbb4942c4e3c4175715cab36eda1.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch48. Not independent approval. Corpus171 reviewed /275 pending /14 needs_research, not complete.
Protected main merge remains 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 8c89ddf173808307354644c7842c69cce8e5a9f6
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree affd939b0a8cf19217bf113d7fb469a7413849d0.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 09cb71416cacb51b09d9470853048941861427ff
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree affd939b0a8cf19217bf113d7fb469a7413849d0.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 4c58d1bd4422f1003084ac49e0f46d12603ddb6a
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree affd939b0a8cf19217bf113d7fb469a7413849d0.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 efbd11745044926e7edac94c65564a90e9b6323c
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree affd939b0a8cf19217bf113d7fb469a7413849d0.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 7063cd8e3f3c664f055cdc36bdd070bed96f147c
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree affd939b0a8cf19217bf113d7fb469a7413849d0.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 5b4dbe2e29d9fc3dfca93cafb0a5244e26cfae81. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 7063cd8e3f3c664f055cdc36bdd070bed96f147c, 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 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74). 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 8b7fa6bcd5eaedebef3f9b9647da062f82c75c42
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 33763fbb300c6fb13e7695f622a1210c37afb5a8.
The batch-owned binary patch is byte-identical
(SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74); 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 38d9bb9434252e4162bf867771b0cd0c5cf154e3. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 8b7fa6bcd5eaedebef3f9b9647da062f82c75c42, 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 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74). 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 fc091ae1237f7370a34efc6bf3985aae1ab22f63.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 dca742e09aa8148bed35de4b558cd9fe3f80d315412532fd4d9a8666d6bffe74.
Tree 49ff3824dbf7f63bef53bb4fbeaac659dd7b23c6 matches the independently computed clean merge.
Compared with historical tree 8e9d010cef9da2d7bf2a8abf465445080f511c6d, 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
Closes #1487. Closes #1488.
Adversarial Review
Verification And Output Records
472 passed in 181.86s (0:03:01); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 36 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All four nodes retained, one correlation-only arrow removed. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All458 other records and920 caches preserved, not certified. Participant scopes and connectivity census unchanged; no production, registry or census-bound changes.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 0d822276d941b0cbbd64eb67a0f9bf425c8cdbb4942c4e3c4175715cab36eda1.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch48. Not independent approval. Corpus171 reviewed /275 pending /14 needs_research, not complete.
Dependency
Draft depends on #1486. Do not merge into the topic parent. Require eligible exact-head CI and the protected main queue after parent merges. Move dependents before deleting merged branches. No Edison job or provider spend for this existing-structure repair.