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Bound resource loops, community profiles and treatment effects (batch99) - #1790
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Source-based self-adversarial review at exact head 91808da; not independent approval.
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Retain yeast-to-alga carbon supply without requiring fermentation as its sole route.; Retain algal reduced-nitrogen supply and the conditional reciprocal resource loop; mediation strength remains PARTIAL.
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Retain condition-dependent coauxotrophic mutualism, distinct from product formation.; Retain the intended divided-pathway handoff and PARTIAL production direction without direct flux certainty.; Retain the measured titer comparison without assigning mutualism or conversion-efficiency benefit to the aggregate endpoint.
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Retain observed community differences at community scope; remove unmeasured pairwise benefit and physiological causation.
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Retain full-community antagonism with all twelve inoculum identities, without competition/defense ontology overclaims.; Retain the dropout-supported pairwise MC contribution and its direction, without universal necessity or additivity.; Retain measured spatial timing and scoped participants, without niche-partitioning or colonization-causality claims.; Keep the MC dropout result at community-contribution scope with only MC as participant and the fungal challenge as external context; do not assert a pairwise consortium-membership relation.
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Fresh both-root baseline preceded source reads. Four whole records/all14nodes/6directions reviewed. Nine nodes/four existing directions remain; five unsupported nodes/two arrows removed, one rename. No new topology/provider spend.
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Yeast-alga: retain reciprocal carbon/nitrogen dependence and both directions with PARTIAL mediation bounds. Oxygen release alone does not establish a yeast benefit. Do not infer fermentation as the sole carbon-dioxide source.
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Resveratrol: coauxotrophy remains MUTUALISM, pathway handoff remains CROSS_FEEDING, but aggregate titer is not mutualistic fitness. Retain controls, precursor accumulation and biomass tradeoff; the existing pathway-to-production direction is PARTIAL, not an isolated explanation of the FLO1 increment.
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Atacama: retain the community composition comparison without lithium-only causation. Taxon presence is not demonstrated exchange, nutrient recycling, phototrophy or functional redundancy. Four functional nodes and both arrows removed; no claim that these processes are biologically impossible.
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Sclerotia: retain laboratory treatment effects and the MC dropout contribution, but not resource competition, defense-process ontology, niche-partitioning or colonization-only causation. Preserve nonadditivity and time dependence. The fungal challenge remains external to the twelve-member consortium.
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Adversarial preflight identified an UNKNOWN_TARGET error after initially assigning MC pairwise scope. Corrected to a one-participant community-contribution node; appended a fifth history, preserving the original four. Failed preflight exit3/output digest is recorded. Audit rules were not weakened.
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All12graph and4new-discussion quotations match maintained caches. Fourteen match fresh primary text after normalization. Two spatial excerpts have explicit accepted-manuscript/final-article wording equivalences, with final text separately checked; they are not mislabeled literal matches. No full-cache, figure-pixel, supplement or raw-data certification.
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Four records changed;456otherrecords,923caches and all non-graph raw blocks preserved. Exactly one participant-list user added. Community-level census402->403 reflects Atacama, with exactly six existing members; mixed128unchanged, community-only274->275, taxa1542->1548 and solely community-credited1268->1274. Only the community-level bound increases by one; no runtime connectivity rule changes.
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Eight focused tests and904combined regressions passed.43finalgate records/digests include five history validations. Network retains56pre-existing warnings and zero structural defects. HTML-description parsing/deterministic rendering is not screenshots; postcommit docs-current is separate.
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Six matching all-state issue bodies read after ignored/hidden-inclusive dedup with recorded exclusions. Graph1784-1787 await protected-main merge; non-graph1788/provenance1789 and broader765 stay open. Access limits include XML500 and direct403; normal public pages were used without bypass. Loader1703/Linux DOI-cache1091 not certified.
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Self-adversarial COMMENT is not independent approval. No protection bypass, fabricated CI or premature closure. Corpus312reviewed/100pending/48needs_research is not complete.
904 passed in 453.95s (0:07:33); eight focused regressions. Four whole records passed schema, strict, term, reference and snippet gates; five append-only histories validated. All 43 final gate outputs and digests are committed with decisions, source provenance and adversarial findings. The initial MC external-target scope error was corrected before final gates, preserving the failed preflight and 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.
Nine of fourteen nodes and four of six directions remain, with one rename. Four records changed; 456 other records and 923 caches preserved. Non-graph raw blocks and taxonomy are unchanged, not recertified. Coverage: 312 reviewed, 100 pending and 48 needing research across 460 records. Network retains 56 existing warnings and zero structural defects. One exact participant-list user added; the community-level census ceiling increases by one to reflect the brine profile, without changing runtime rules.
All 16 graph/discussion quotations matched unchanged caches. Fourteen match fresh primary text literally after normalization; two spatial quotations have documented manuscript/final-version differences and separately matched final text. Primary read sections and access limits are recorded, including XML HTTP500 and direct publisher HTTP403. Normal public pages were read without bypass. No figure-pixel, supplement, raw-data or full-cache-body certification. Deterministic rendering and HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 400779f42004aff7ea9d16edd6fcdaa6472df57d910774a1b02ed90cc993983f.
No new topology, experimental instructions or Edison spend. Non-graph #1788, cache provenance #1789 and broader re-evidencing #765 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 f98c2fec808fffa43e66965a291a00c0cf43df9a. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 91808dab93ea3f44cb933761e6e178e260070909, 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 f54e93a1ed73f073a0294debd93242be87fbd935f952279276dbecb0d745978f). 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 03ec662b917cc02de59ce592f5a09b2358208fb5.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 f54e93a1ed73f073a0294debd93242be87fbd935f952279276dbecb0d745978f.
Tree 00a0d0b188d8e2110738e607f22b56ed93c835d3 matches the independently computed clean merge.
Compared with historical tree 1268b22a96ae2e3a4712c5d105bd802af3d9e15e, 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 #1784.
Closes #1785.
Closes #1786.
Closes #1787.
Non-graph #1788 and provenance #1789 remain open after this graph repair merges.
Adversarial Review
Verification And Output Records
904 passed in 453.95s (0:07:33); eight focused regressions. Four whole records passed schema, strict, term, reference and snippet gates; five append-only histories validated. All 43 final gate outputs and digests are committed with decisions, source provenance and adversarial findings. The initial MC external-target scope error was corrected before final gates, preserving the failed preflight and 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.
Nine of fourteen nodes and four of six directions remain, with one rename. Four records changed; 456 other records and 923 caches preserved. Non-graph raw blocks and taxonomy are unchanged, not recertified. Coverage: 312 reviewed, 100 pending and 48 needing research across 460 records. Network retains 56 existing warnings and zero structural defects. One exact participant-list user added; the community-level census ceiling increases by one to reflect the brine profile, without changing runtime rules.
All 16 graph/discussion quotations matched unchanged caches. Fourteen match fresh primary text literally after normalization; two spatial quotations have documented manuscript/final-version differences and separately matched final text. Primary read sections and access limits are recorded, including XML HTTP500 and direct publisher HTTP403. Normal public pages were read without bypass. No figure-pixel, supplement, raw-data or full-cache-body certification. Deterministic rendering and HTML-description checks are not screenshots. Postcommit docs-current passed clean, SHA256 400779f42004aff7ea9d16edd6fcdaa6472df57d910774a1b02ed90cc993983f.
No new topology, experimental instructions or Edison spend. Non-graph #1788, cache provenance #1789 and broader re-evidencing #765 remain open. Self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1783. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.