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Bound process outcomes and ecological mechanisms (batch100) - #1797
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Source-based self-adversarial review at exact head 17dbd4b; not independent approval.
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Retain substrate specialization, with a PARTIAL link to the retention-dependent improvement.; Retain the controlled batch-duration result without an additional niche-partitioning label.; Retain near-simultaneous depletion as a measured process outcome.
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Retain inferred nitrite cross-feeding with PARTIAL partner/pathway attribution and metagenomic limits.; Retain the measured treatment gradient without categorical competition or a universal dosing optimum.
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Retain the time-resolved initial-richness association and distinguish its nitrate-disappearance endpoint.; Retain larger lower-richness functional increases without proven mutational causation or endpoint equivalence.; Retain statistical complementarity as biomass-yield partitioning, not a resolved interaction mechanism.; Retain mixture/monoculture relative-yield inference without species-pair or transfer assignments.
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Retain stable mixed biofilm formation without colonization-facilitation overclassification.; Retain the two-taxon transcriptional response within the three-member culture at scoped community level.; Retain the measured current advantage without syntrophy, mutualism or superadditivity claims.
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Fresh both-root baseline preceded sources. Four whole records and all14originalnodes/5directions reviewed;12nodes/4arrows retained,2workflow nodes/1arrow removed,5renames. No new topology or provider submission.
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Yeast: preserve substrate specialization,29%shorter batch time and near-simultaneous depletion; retention and timing outcomes are not additional niche-partitioning interactions or intrinsic-growth benefits. The specialization-to-retention direction is PARTIAL.
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Anammox: preserve conditional nitrite supply and measured treatment performance. Metagenomic abundance is not expression or pathway-resolved flux; dosage-associated competition is HYPOTHESIZED. Culture-volume ratios are not cell-number ratios or universal optima.
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Richness: remove construction/serial-transfer workflow nodes. Keep initial-richness associations with endpoint-specific time bounds, larger lower-richness gains, statistical complementarity and relative yields. Nitrate disappearance does not establish complete denitrification; complementarity does not identify exchanged substrates or beneficial mutations.
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Biofilm: retain real higher current than each solitary culture and both existing uncertain directions. Do not upgrade that result to superadditivity, reciprocal fitness or demonstrated product-removal feedback. Transcript comparison is scoped within the three-member community, not a binary-pair perturbation.
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All23graph and4new-discussion quotations match fresh primary text and maintained cache bytes. Exactly one15word selected excerpt was appended with provenance and rights limits. It remains excluded by the independent cache audit, which correctly reports one MISMATCH for that quote. This is not a clean-cache claim or a changed audit rule.
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Four records and one selected-excerpt cache appendix changed;456otherrecords and922othercaches preserved. All non-graph raw blocks, taxonomy, prior histories and earlier decisions preserved. Four append-only histories; exact participant-list census adds one stem. Connectivity bounds and runtime/schema/audit code unchanged.
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Focused checks,912broad regressions, source/cache digest checks and full-record schema/strict/terms/reference validation are recorded with actual outputs. Ruff then detected stdlib import order in the new test; that formatting-only fix has before/after hashes, preserved failure output and final focused/full Black/Ruff reruns. Final mypy explicitly selects the Python3.13 package environment because plain just-lint autodetects a separate system Python3.10 and fails four imports; failed attempts remain recorded. Type target/rules unchanged. The broad run preceded the import-formatting fix. Network retains56existingwarnings and zero structural defects. HTML parser checks/deterministic rendering are not screenshots; postcommit docs-current remains separate.
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Issues1791-1794 addressed locally, close only after protected-main merge. Non-graph1795 and provenance1796 remain open. Source section and access limits, including rights-reserved primary pages, are recorded. No full-cache-body, figure-pixel, supplement or raw-data certification; loader1703 and DOI-cache1091 not certified.
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Source-based self-adversarial review is not independent approval. No protection bypass, artificial CI, premature issue closure or branch deletion. Corpus316reviewed/96pending/48needs_research is not complete.
912 passed in 314.50s (0:05:14); eight final focused regressions after a stdlib-import-order fix. Four full-record schema, strict, ontology-term and reference checks passed; four append-only histories validated.43final gate records plus preserved failed attempts. Full Black/Ruff passed. Plain just-lint failed four imports because mypy autodetects a separate system Python3.10; explicit Python3.13 package-environment mypy passed with the configured type target and rules unchanged. The independent cache snippet audit correctly excludes the selected15word biofilm excerpt and reports one MISMATCH for it. All27reviewed quotations separately match fresh primary text. No audit-rule changes or clean-corpus claim.
Twelve of fourteen nodes and four of five directions remain, with five renames. Four records and one clearly labeled selected-excerpt cache appendix changed;456otherrecords and922othercaches preserved. Non-graph raw blocks and taxonomy unchanged, not recertified. Corpus316reviewed/96pending/48needs_research. Network56existingwarnings/zero structural defects. Participant census adds one exact stem, with no connectivity-bound or runtime changes.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 af6821d94f56ddd740f20f6a06fc6118438ebc461576c28673bf6b6ca0ba56ab. 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; primary access and section limits are recorded in the ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
No new topology or Edison spend. Non-graph1795/provenance1796 remain 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 98f1628c7b074b4d7e6c82a56d9030a608321a64.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 a7d837958530796038900633a3ccd36af0512006c080e2d262a63168b5f35be3.
Tree 510f6d97680417c72d5dbf8d38e0c38bbef06c52 matches the independently computed clean merge.
Compared with historical tree cc8ab5502ca8b7462ee3e27d57c0bd5196a4271d, 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 #1791.
Closes #1792.
Closes #1793.
Closes #1794.
Non-graph #1795 and provenance #1796 remain open.
Adversarial Review
Verification And Output Records
912 passed in 314.50s (0:05:14); eight final focused regressions after a stdlib-import-order fix. Four full-record schema, strict, ontology-term and reference checks passed; four append-only histories validated.43final gate records plus preserved failed attempts. Full Black/Ruff passed. Plain just-lint failed four imports because mypy autodetects a separate system Python3.10; explicit Python3.13 package-environment mypy passed with the configured type target and rules unchanged. The independent cache snippet audit correctly excludes the selected15word biofilm excerpt and reports one MISMATCH for it. All27reviewed quotations separately match fresh primary text. No audit-rule changes or clean-corpus claim.
Twelve of fourteen nodes and four of five directions remain, with five renames. Four records and one clearly labeled selected-excerpt cache appendix changed;456otherrecords and922othercaches preserved. Non-graph raw blocks and taxonomy unchanged, not recertified. Corpus316reviewed/96pending/48needs_research. Network56existingwarnings/zero structural defects. Participant census adds one exact stem, with no connectivity-bound or runtime changes.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 af6821d94f56ddd740f20f6a06fc6118438ebc461576c28673bf6b6ca0ba56ab. 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; primary access and section limits are recorded in the ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
No new topology or Edison spend. Non-graph1795/provenance1796 remain open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Source Limits
Dependency
Draft depends on #1790. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.