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Bound causal profiles, predictions and process outcomes (batch98) - #1783
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Source-based self-adversarial review at exact head af0cc46; not independent approval.
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Retain the proposed organic-matter electron-acceptor mechanism without commensalism or flux certainty.; Retain hypothesized acetate cross-feeding while separating deep potential from surface activity and hydrogenotrophy.; Retain depth stratification and its hypothesized supply direction without asserting competition reduction or vertical transport.
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Retain the measured root-zone decomposer response at community scope, not fungal-bacterial mutualism.; Retain increased ECM colonization and PARTIAL community-assembly association without named molecular transfers.; Retain root-trait mediation as PARTIAL and distinguish contrasting treatment effects.; Retain predicted bacterial hosts and depth associations without experimental viral predation or methane-host assignment.
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Retain nitrite cross-feeding as a supported model hypothesis, not direct transfer measurement.; Retain complementary nitrous oxide reduction without unmeasured competition reduction.; Retain both redox-driven model directions with steady-state and spatial-scope limits.
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Retain detoxification benefit and PARTIAL productivity mediation without neutral-partner fitness.; Retain inferred carbon routing with residual-feedstock and one-replicate limits.; Retain two-member community outcome while distinguishing productivity, yield and variable wax-ester production.
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Fresh both-root baseline preceded source reads. Four whole records and all13nodes/8directions reviewed and retained, with4renames. No topology extension or provider spend.
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SPRUCE methane: retain organic-matter electron acceptor and acetate interpretations as hypotheses. Gene abundance is not flux; deep acetate accumulation does not prove transport to surface methanogens, and acetate is not the direct hydrogenotrophic substrate.
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SPRUCE warming: retain measured root-zone community response and ECM colonization, but not fungal-bacterial mutualism, unmeasured compound exchange or enzyme activity. Existing directions are PARTIAL and cannot propagate a uniformly positive effect because warming and elevatedCO2 have contrasting saprotroph responses.
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SPRUCE virus: keep computational bacterial host predictions and depth associations, not experimentally demonstrated predation, lysis or methane-cycler host links. Entire sampled peat column was saturated. No new infection mechanism is inferred.
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Saanich: retain the calibrated model and its observational support, while distinguishing fitted nitrite leakage from direct transfer measurement. Complementary denitrification co-occurs at the transition zone; it is not demonstrated spatial separation or competition reduction.
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Detox coculture: retain positive inhibitor conversion and lactic-acid productivity. The proposed mediator is PARTIAL; neutral ADP1 fitness is not established. Residual feedstock is distinct from secreted yeast carbon. Wax esters were reliably quantified in only one of four replicates; similar lactic-acid yield is not enhanced yield.
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Adversarial diff review found residual stronger evidence explanations in Saanich and the coculture. Corrected competition-reduction and direct-carbon-transfer/isolated-mediation wording, preserving four initial histories and adding two correction histories before final gates.
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All24graph and4new-discussion quotations match fresh primary text and maintained caches. Primary access boundaries and exact read sections are recorded, including Saanich XML500/normal PMC HTML and Wiley direct403/public web-rendered text. No challenge solved. No full cache-body, figure-pixel, supplement or raw-data certification.
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Four records changed;456otherrecords,923caches and all non-graph raw blocks preserved. Scope-specific participant identities use only existing canonical labels/IDs. Two exact participant-list users added; existing connectivity bounds and equality checks unchanged. Census stays402community-level/128mixed/1542taxa; solely community-credited taxa1266->1268 after unsupported fungal-bacterial and viral pairwise claims are re-scoped. No runtime connectivity-rule change.
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Eight focused tests and896combined regressions passed.44gate output records/digests retained, including six history validations. Network comparison and measured census are recorded in validation. Deterministic HTML-description validation is not browser screenshots; postcommit docs-current is separate.
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Nine matching all-state issue bodies read after ignored/hidden-inclusive dedup with recorded exclusions. Graph1778-1781 are addressed but await protected-main merge; non-graph1782 and ontology463 stay open. Linux DOI-cache1091 and loader1703 not certified.
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Self-adversarial COMMENT is not independent approval. No protection bypass, fabricated CI or premature issue closure. Corpus308reviewed/104pending/48needs_research is not complete.
896 passed in 412.41s (0:06:52); eight focused regressions. Four whole records passed schema, strict, term, reference and snippet gates; six append-only histories validated. All 44 gate outputs and digests are committed with decisions, source provenance and adversarial findings. Residual stronger evidence explanations were corrected before final gates while preserving the original histories. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; primary access and section limits are recorded in the ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All 13 nodes and eight directions retained, with four node renames. Four records changed; 456 other records and 923 caches preserved. Non-graph raw blocks and canonical taxonomy are unchanged, not recertified. Coverage: 308 reviewed, 104 pending and 48 needing research across 460 records. Network comparison and the measured connectivity census are recorded. The exact participant allowlist was extended by two stems; no connectivity bounds were loosened.
All 28 graph and discussion quotations matched fresh sources and unchanged caches. Primary read sections and access limits are recorded: Saanich XML returned HTTP500 but its normal PMC page worked; the direct Wiley fetch returned HTTP403, while public web-rendered publisher text was available. Figure pixels, supplements, raw data and complete cache bodies are not certified. Deterministic rendering and exact HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 7ad3fd3bb85e58ffb442836eee4e5c4ba4b1b67f3f6518a41ce62d5c301d0f6f.
No topology extension, culture or strain-design instructions, or Edison spend. Non-graph #1782 and ontology #463 remain open. Self-adversarial review is not independent approval. 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 governance integration review at exact head 39cfd1c9cbbd22ee481753e93c6d357b4cf939b0. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head af0cc46dc2b6438010297cea796110a22ed78771, 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 13ca8d070b5fce47ff321608301be8e1bcbf102ea2ee992417f8fbe6b98efdba). 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 dee5baa5912ab85200549c836cc5ca7cf0f3e99b.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 13ca8d070b5fce47ff321608301be8e1bcbf102ea2ee992417f8fbe6b98efdba.
Tree 5763794ea3516c876215dc9bde0c39fe0f6620c7 matches the independently computed clean merge.
Compared with historical tree 3a38cf843bf02b2b6d7ed8c9e4d04797516f52d8, 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 #1778.
Closes #1779.
Closes #1780.
Closes #1781.
Non-graph #1782 remains open after this graph repair merges.
Adversarial Review
Verification And Output Records
896 passed in 412.41s (0:06:52); eight focused regressions. Four whole records passed schema, strict, term, reference and snippet gates; six append-only histories validated. All 44 gate outputs and digests are committed with decisions, source provenance and adversarial findings. Residual stronger evidence explanations were corrected before final gates while preserving the original histories. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; primary access and section limits are recorded in the ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All 13 nodes and eight directions retained, with four node renames. Four records changed; 456 other records and 923 caches preserved. Non-graph raw blocks and canonical taxonomy are unchanged, not recertified. Coverage: 308 reviewed, 104 pending and 48 needing research across 460 records. Network comparison and the measured connectivity census are recorded. The exact participant allowlist was extended by two stems; no connectivity bounds were loosened.
All 28 graph and discussion quotations matched fresh sources and unchanged caches. Primary read sections and access limits are recorded: Saanich XML returned HTTP500 but its normal PMC page worked; the direct Wiley fetch returned HTTP403, while public web-rendered publisher text was available. Figure pixels, supplements, raw data and complete cache bodies are not certified. Deterministic rendering and exact HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 7ad3fd3bb85e58ffb442836eee4e5c4ba4b1b67f3f6518a41ce62d5c301d0f6f.
No topology extension, culture or strain-design instructions, or Edison spend. Non-graph #1782 and ontology #463 remain open. Self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1777. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.