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Correct evidence modality and community outcome scope (batch97) - #1777
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Source-based self-adversarial review at exact head f74410c; not independent approval.
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Retain supported mutualism and a PARTIAL rodent-outcome direction.; Retain positive Candida-to-S. mutans biofilm facilitation with the correct in-vitro source.; Retain the positive rodent carriage/lesion outcome at community scope, not pairwise colonization.
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Retain supported directional colonization facilitation and the existing structural link, correcting modality.; Retain community structure and acidogenesis, with positive perturbation evidence and PARTIAL in-vivo mediation.; Retain the rodent disease comparison at two-member community scope.
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Retain measured expression and EPS, not direct enzyme activity or colonization.; Retain in-vitro composite phenotypes at community scope with correct modality.; Retain the positive rodent outcome, not proven human adult causation.
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Retain detoxification and its leaching direction without an unsupported neutral-partner fitness claim.; Retain the primary EET interpretation while distinguishing perturbation support from quantitative flux partition.
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Fresh both-root baseline preceded source reads. Four whole records and all11nodes/7directions accounted for; all retained,5nodes renamed. No new topology or provider spend.
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Candida mutualism and directional biofilm facilitation remain. EPS evidence is IN_VITRO; the rodent carriage/lesion endpoint is COMMUNITY_LEVEL. The existing lesion arrow is PARTIAL mediation, not a proven human causal effect.
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Selenomonas entrapment and structure evidence is IN_VITRO. Retain experimentally supported S. mutans-to-S. sputigena facilitation and the structural direction. The primary matrix-disruption and ex-vivo evidence must not be erased as mere association. Mixed acidogenesis and rodent lesions are not recipient colonization measurements.
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Veillonella gtf expression and EPS fluorescence remain, without independently quantified enzyme activity or species-resolved cell abundance. Correct the in-vitro source, use named community participants for composite outcomes, and distinguish rodent intervention from adult human association. Both mediator directions are PARTIAL.
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Battery detoxification, EET and leaching remain. Beneficial detoxification does not establish neutral fitness of BS3 in the exact pair, so COMMENSALISM is removed. Predecessor comparisons and the final-consortium interpretation are distinguished; perturbation and riboflavin evidence is not a quantitative partition of direct/shuttle flux. Earlier scale-up discussion preserved.
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Adversarial diff review found that two newly explicit interpretation statements lacked direct result quotations at the node. Added source-matched Selenomonas structural and SO3 perturbation quotations, with two new correction histories referencing and preserving the initial histories. Both fixes preceded final validation; no interrupted attempt.
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All16graph and4new-discussion quotations match fresh primary text and unchanged caches. Candida XML retrieval failed; fresh abstract/PubMed captions and selected primary sections for the other sources were read. Truncated flattened cache output is not a complete cache-body read. No figure pixels, supplements or raw-data certification.
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Four records changed;456otherrecords,923caches, canonical taxonomy and all non-graph raw blocks preserved. Six append-only histories. No culture procedures, genetic designs or pathogen-enhancement instructions added. Non-graph1776 remains separate.
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Connectivity census: records with community scope399->402,mixed125->128,taxa1536->1542,solely credited1266 unchanged. Exactly named two-member participant lists explain the change; narrow bounds updated with dedicated scope tests. Initial regression found an incomplete participant allowlist (887passed/1failed). Added exactly the three intentional users; equality guard retained. Failed output and initial snapshot preserved, complete regression rerun; unchanged earlier gates digest-checked on resume.
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Eight focused tests and888combined regressions passed;44output records and digests retained. Whole-record gates and six history gates ran.56network warnings unchanged,zero structural defects. Deterministic rendering and exact HTML description parsing are not screenshots; postcommit docs-current remains a separate gate.
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Fresh all-state issue title/body and ignored/hidden-inclusive local dedup with stated exclusions performed;941/942 read and distinct. PRs/comments not exhaustive. Repairs1772-1775 close only after protected-main merge;1776 remains open. Linux DOI-cache1091 and loader1703 not certified.
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Self-adversarial review is COMMENT, not independent approval. No protection bypass, CI fabrication or automatic issue closure. Corpus304reviewed/108pending/48needs_research remains incomplete.
888 passed in 507.98s (0:08:27); eight focused regressions. Four complete records passed schema, strict, term, reference and snippet gates, plus six append-only histories.44 gate output records/digests are committed with decisions, provenance and self-adversarial findings. Two evidence-attachment findings were corrected before final validation, preserving initial 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; Candida full text unavailable and other sources read in stated sections. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All 11 nodes and 7 directions retained, with 5 node renames. Four records changed; 456 other records and 923 caches preserved. Non-graph blocks and canonical taxonomy unchanged, not recertified. Coverage: 304 reviewed, 108 pending and 48 needs_research across 460 records. The 56 network warnings are unchanged, with zero structural defects. Measured connectivity changed with three newly community-scoped records, but solely credited taxa stayed at 1266. The initial regression found 887 passing tests and one incomplete participant-allowlist fixture; exactly the three intentional users were added after measured census, preserving the equality guard. Failed output and the initial snapshot are preserved; the complete regression suite was rerun and unchanged earlier gates digest-checked.
Selected fresh primary sections for Selenomonas,Veillonella,battery and the Candida abstract/PubMed captions read.20graph/discussion quotations matched to fresh source text and unchanged caches. Candida full-text XML failed. No figure-pixel,supplement or raw-data certification; truncated cache output is not a complete cache-body read. Deterministic rendering and HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 e62ce7e51d47edcd4cd57538a7721538a8736fd83614564116b656679c86d6f3.
No new topology, wet-lab instructions, pathogen-enhancement design or Edison spend. Non-graph1776 remains open. Source-based 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 bc8085a8118646f06183896d6aad36c6b448feac. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head f74410c51a59c6c5690b6c4e4fe732772ba37bd4, 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 fb415b9a93055634d3876b22697fddc4a257e519a197a1af124e29574bb3c6d3). 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 f7c939629cf55a46e6c0113bef4f4f1bab73e661.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 fb415b9a93055634d3876b22697fddc4a257e519a197a1af124e29574bb3c6d3.
Tree 1599059c880b6544c28f6ee035aff8ab1c074a9f matches the independently computed clean merge.
Compared with historical tree 5c7cecfcd7952ac40fb8c20ea5f6b6c45e0ee6bd, 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 #1772.
Closes #1773.
Closes #1774.
Closes #1775.
Non-graph #1776 remains open after this graph repair merges.
Adversarial Review
Verification And Output Records
888 passed in 507.98s (0:08:27); eight focused regressions. Four complete records passed schema, strict, term, reference and snippet gates, plus six append-only histories.44 gate output records/digests are committed with decisions, provenance and self-adversarial findings. Two evidence-attachment findings were corrected before final validation, preserving initial 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; Candida full text unavailable and other sources read in stated sections. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All 11 nodes and 7 directions retained, with 5 node renames. Four records changed; 456 other records and 923 caches preserved. Non-graph blocks and canonical taxonomy unchanged, not recertified. Coverage: 304 reviewed, 108 pending and 48 needs_research across 460 records. The 56 network warnings are unchanged, with zero structural defects. Measured connectivity changed with three newly community-scoped records, but solely credited taxa stayed at 1266. The initial regression found 887 passing tests and one incomplete participant-allowlist fixture; exactly the three intentional users were added after measured census, preserving the equality guard. Failed output and the initial snapshot are preserved; the complete regression suite was rerun and unchanged earlier gates digest-checked.
Selected fresh primary sections for Selenomonas,Veillonella,battery and the Candida abstract/PubMed captions read.20graph/discussion quotations matched to fresh source text and unchanged caches. Candida full-text XML failed. No figure-pixel,supplement or raw-data certification; truncated cache output is not a complete cache-body read. Deterministic rendering and HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 e62ce7e51d47edcd4cd57538a7721538a8736fd83614564116b656679c86d6f3.
No new topology, wet-lab instructions, pathogen-enhancement design or Edison spend. Non-graph1776 remains open. Source-based self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1771. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.