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Correct transfer direction and outcome attribution (batch101) - #1802
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Source-based self-adversarial review at exact head cdc6df5; not independent approval.
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Retain donor electron harvesting without a separate SYNTROPHY classification.; Retain the reported electron-transfer direction while distinguishing author terminology, transcriptional response and unverified feedback.; Retain recipient nitrate reduction without assigning reciprocal syntrophic benefit.
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Retain one-way lactate provisioning with explicit sequential versus simultaneous scope.; Correct the reversed pairwise cross-feeding assignment to a Shewanella-scoped electrical outcome; preserve both configurations and their evidence.
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Scope coaggregation to both canonical members without a directed syntrophic classification.; Retain the reported donor-to-recipient transfer shift with PARTIAL causal attribution and no claim that mediated transfer disappears.; Retain the measured methane-indicator increase without equating the proxy to total flux or reciprocal fitness.
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Retain the whole-SynCom host-protection phenotype without inferring genus-to-pathogen antagonism or adding unsupported directions.
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Whole four-record/all10node/6direction review preceded edits. Nine nodes/five existing directions remain; one duplicate workflow node/arrow removed and three names updated. No new topology or Edison spend.
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Fe0 retains donor harvesting, reported electron transfer and recipient nitrate reduction. Author electro-syntrophy terminology and metatranscriptomics do not independently establish schema-specific product-removal feedback or causal necessity. The definition is not obligacy; direct electrons are not forced into metabolite CROSS_FEEDING.
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Starch retains one-way lactate provisioning and the real current outcome. EGT is a sequential broth handoff after fermenter removal, EGP is simultaneous cultivation. Correct the reverse source/target/type assignment and preserve both parallel-result snippets when removing the duplicate configuration node. EGT current maxima are not EGP values; source unit inconsistency is not silently repaired.
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PDA retains coaggregation, donor/recipient transfer direction and the measured roughly380% methane-indicator increase. Aggregation becomes two-member community-level; both arrows are causal but PARTIAL. Interface conductivity is not isolated aggregation mediation; proxy percentage is not calibrated total flux, natural methanogenesis or reciprocal fitness.
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Shrimp remains byte-identical: one community-level host-protection phenotype, no invented genus-to-pathogen antagonism or arrows. Existing closed1105/1106 corrections and discussion preserved; no new event/history for unchanged content.
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Fifteen graph and three new-discussion quotations match fresh primary abstracts and pre-existing whole caches. Main texts not independently verified, direct publisher403s and bounded searches disclosed. Shrimp independent publisher-indexed abstract support followed an empty EuropePMC query; absence of a query hit does not disprove historical access. No cache text added, no access bypass or source audit exception.
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Three changed records/histories;457otherrecords/all923caches and prior history/decisions unchanged. Non-graph raw blocks/taxonomy preserved, not recertified. Exact participant allowlist adds starch; measured CL census403to404 and mixed127to128, with solely-credited taxa1276unchanged. Only the CL census ceiling updates for the evidenced classification correction; no runtime rule or other bound changes.
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Seven new tests and919combined regressions passed, as did four full-record schema/strict/terms/reference/snippet checks and three histories. Network exactly matches baseline56warnings/zero structural defects. Deterministic rendering and description parser cover456pages/1388descriptions/560arrows, not browser screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Whole-corpus snippet audit is informational, not clean-corpus certification.
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Repairs1798-1800 are addressed locally and remain open until protected-main merge. Non-graph1801 remains open. Denied/unanswered Edison scopes, loader1703 and DOI-cache1091 remain outside certification. Self-review is not independent approval; no artificial CI, protection bypass, premature issue closure or branch deletion.
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Corpus320reviewed/92pending/48needs_research is not completion. Postcommit docs-current and exact-head publication are separate gates, not preasserted here.
919 passed in 264.17s (0:04:24); seven new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; three append-only histories validated.40 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. The complete corpus snippet audit remains informational, not clean-corpus certification. All18reviewed graph/discussion quotations match fresh primary abstracts and existing caches.
Nine of ten nodes and five of six directions remain, with three renames. Three records changed; shrimp and456otherrecords, all923caches, taxonomy and non-graph raw blocks preserved. Corpus320reviewed/92pending/48needs_research. Network56existingwarnings/zero structural defects. Participant census adds one exact stem; CL403to404,mixed127to128,solely-credited taxa1276unchanged. Only the measured CL census ceiling updated, no runtime connectivity-rule change.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with three append-only history records. Postcommit docs-current passed clean, SHA256 4bc4236a84ce014866b410a11dfb7ea8ec39861cfe3207a394e54b45b9084171. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; abstract-level source access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
No new topology or Edison spend. Non-graph1801 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
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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Exact-head self-adversarial restack review at 4b93535adab513fbc18a07bd32fc2400ab716dbf.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 66f6492e37c11ddf199538da0c01c8d03537b40770e4c5da38cf49b95324190e.
Tree a9b7ae74dd4081397ade12413751dde0209ed652 matches the independently computed clean merge.
Compared with historical tree 52d1f6e6c58e6e076db6bfd04e176f6a57d5e00d, 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 #1798.
Closes #1799.
Closes #1800.
Non-graph #1801 remains open.
Adversarial Review
Verification And Output Records
919 passed in 264.17s (0:04:24); seven new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; three append-only histories validated.40 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. The complete corpus snippet audit remains informational, not clean-corpus certification. All18reviewed graph/discussion quotations match fresh primary abstracts and existing caches.
Nine of ten nodes and five of six directions remain, with three renames. Three records changed; shrimp and456otherrecords, all923caches, taxonomy and non-graph raw blocks preserved. Corpus320reviewed/92pending/48needs_research. Network56existingwarnings/zero structural defects. Participant census adds one exact stem; CL403to404,mixed127to128,solely-credited taxa1276unchanged. Only the measured CL census ceiling updated, no runtime connectivity-rule change.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with three append-only history records. Postcommit docs-current passed clean, SHA256 4bc4236a84ce014866b410a11dfb7ea8ec39861cfe3207a394e54b45b9084171. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; abstract-level source access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
No new topology or Edison spend. Non-graph1801 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Source Limits
Dependency
Draft depends on #1797. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.