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Bound Trichoderma resource chains and population mechanisms (batch116) - #1906
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Source-based self-adversarial review at exact head 44d2638; not independent approval.
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Retain resource delivery as cross-feeding without assigning an unmeasured neutral fungal fitness effect.; Represent E. coli product formation as a recipient outcome, not a second pairwise metabolite exchange.; Retain experimentally validated model support and equilibria with condition-bounded community scope, not unconditional stability.
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Retain carbohydrate cross-feeding while separating cellulose hexoses from supplied pentoses and unsupported commensalism.; Preserve LAB redox evidence alongside continuing fungal oxygen consumption, without reciprocal syntrophy or LAB-alone anoxia.; Restore experimentally supported co-substrate dependence and distinguish recipient production, alternative arms and pretreated three-member benchmark.
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Retain phase-specific hydrolysate cross-feeding without erasing the initial glucose phase or overgeneralizing cellulolytic incapacity.; Make recipient growth explicit, retain conditional commensalism interpretation, and remove dependence-as-mediator of all treatment responses.; Retain observed competition with viability, relative-growth and fluorescence-proxy limits; pigment mediation remains unresolved.
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Accounted for every original node and direction: 9 nodes retained, 5 of 6 arrows retained, 4 renames. Removed only the unisolated dependence-to-population-control mediation. No new topology; all target names and discussion anchors resolve.
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Isobutanol overcorrection check: experimental model validation is explicitly preserved from the abstract. Hydrolysis provides a resource basis, not sufficient proof of unconditional coexistence. E. coli product formation is a recipient outcome, not another metabolite exchange. Full-paper assumptions remain an open knowledge gap.
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Lactate overcorrection check: LAB-associated redox lowering is preserved alongside continued fungal oxygen consumption and membrane geometry. Neither LAB-alone anoxia nor reciprocal thermodynamic syntrophy is asserted. Cellulose hexoses are separated from pentose feedstock.
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Co-substrate controls: acetate depletion/feed rescue and glucose alternatives prevent lactate-alone production claims. The 19-word quotation is from accepted-manuscript main p6, not SI. Acetate-feed, low-OTR and L. brevis arms remain distinct. Clear Fig4 supports the three-member steam-pretreated beechwood benchmark; not an untreated/four-member claim.
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Filamentous controls: initial supplied glucose precedes hydrolysate dependence. The source conditional early competition/late commensalism interpretation is retained without universal neutral fungal fitness. Spore storage/viability is not fluorescence-tag causality. Relative osmolality advantage is not absolute bacterial stimulation; corrected fluorescence is not universal exact cell counting. Pigment mediation remains unresolved.
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Source matching: all 16 graph and 3 discussion quotations have fresh primary and cache literal matches, not entailment certification. Abstract and accepted-manuscript wording are bound to their actual matching versions. Only one bounded 19-word main-text cache excerpt added with provenance; 922 other caches unchanged, no publication PDF/body imports.
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Preservation: three guarded records and append-only histories; 457 other records, non-graph raw blocks and prior history/decisions unchanged. Canonical strain 1344414 is not replaced by species 51453. Three explicit participant-list users added. Measured census: 415 community-level, 137 mixed, 278 community-only, 1570 taxa, 1280 solely credited. Sole-credit survey is not actual coverage proof; logic and share guard unchanged.
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Seven real in-memory control/mutation/restored-control probes reject loss of experimental validation, unconditional stability, loss of joint redox, lactate-only conversion, assay conflation, unisolated mediation and absolute/proxy overclaims. Changed values and rejecting assertions recorded; canonical hashes unchanged. These are not extra pytest tests.
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Eleven focused and 1056 combined tests pass, including tests/test_datamodel.py after issue1899. All 3 records pass schema, strict, terms, full-record references, snippets, rank and history. 57 network warnings preserved, zero structural defects. 456 rendered pages, 1365 nodes and 527 arrows match exact source descriptions; deterministic rendering, not UI screenshot certification. Local reference passes do not certify Linux and corpus snippet audit remains informational.
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Graph repairs1901-1903 await protected-main merge; metadata1904/1905 remain open. No Edison extension/spend. Prior Ruegeria research1883 still needs a configured authenticated provider. Self-review is not independent approval. Postcommit docs-current and exact-head publication are separate gates. No protection bypass, artificial CI or premature branch deletion.
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Corpus: 372 reviewed, 34 pending, 54 needs_research across 460 records. Overall goal remains incomplete.
1056 passed in 441.55s (0:07:21); eleven focused tests and seven real in-memory mutation probes. All three edited records pass schema, strict, term, full-record reference, snippet and history checks. 34 gate outputs retain commands, output tails and digests. All 457 other records, 922 other caches and non-graph raw blocks are unchanged.
Nine nodes and five of six original directions remain, with four renames and no new topology. Experimental model validation is retained for isobutanol stability; the abstract does not resolve every condition. The lactate graph preserves joint fungal/LAB redox roles and acetate/glucose co-substrate controls, separating alternative arms from the steam-pretreated three-member benchmark. Filamentous recipient growth remains phase-specific; dependence does not isolate mediation of all population-control effects.
Fresh primary abstracts and identity metadata checked. Isobutanol full text remained inaccessible after bounded public attempts. Lactate accepted-manuscript main text, selected SI and source figures were read; filamentous main text and appendices were read from fresh XML. Exact read scopes and limitations are committed. All 19 graph/discussion quotations have fresh primary and cache literal matches, not entailment certification. One cache gains a bounded 19-word main-text excerpt and provenance; no publication PDF or full body imported.
Corpus: 372 reviewed, 34 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Three explicit participant-list users added; no increase in the measured solely-credited census. Connectivity logic and share guard unchanged. Rendering is deterministic and all 456 pages' descriptions match YAML, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 d3af6394db29f1ec5d12eea5978296267909616ba0fa53d1d52e83b7e8b0a803. Local reference passes are macOS, not Linux certification; corpus snippets remain informational.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. Metadata #1904/#1905 remain open. No Edison invocation; prior Ruegeria extension #1883 still needs a configured provider. This COMMENT is self-review, not independent approval. Root blocker #1836 must be resolved through actual protected checks; no artificial CI, protection bypass or premature branch deletion.
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 review at exact head aa10cc1 after real palette correction #1913. Not independent approval.
The prior116 strict run failed only the palette frequency guard: commensalism and predation had two occurrences each. Source-backed scientific labels were not reverted. The actual template now folds rare commensalism into Other, preserving exact type text. FOLD_HEADROOM=2 and MIN_SEPARATION=15 remain unchanged; six common colours are unchanged. Enum overlap and rare/untyped/common legend fixtures are tested. Parent correction passed1077selected tests,21palette tests and four inspected desktop/mobile light/dark browser views.
All canonical records,caches,prior histories/decisions and non-palette source files are byte-identical to the previously reviewed tree. Only template,palette tests,generated HTML and the new CI report/review/infrastructure history change. Each branch's patch excluding those palette paths remains byte-identical (SHA256 35c2347d25bc9c42dba639727db14a6e03c555e49909977e3539afb03d82408d). Original heads are preserved by archive refs and earlier publication receipts. Generated conflicts,if any,were resolved only by rendering from unchanged canonical YAML.
Fresh head-specific tests: ................................ [100%]
32 passed in 2.51s
Test log SHA256 55d29b4552ff39562e42a841d78536a16ebc74768abdcf71cdaff93d18bd4315. Fresh docs-current passed clean; log SHA256 d3af6394db29f1ec5d12eea5978296267909616ba0fa53d1d52e83b7e8b0a803.
Reports: reports/causal_graph_review/ci-regression-1913-20261008.json and ci-review-1913-20261008.yaml. Their propagation-pending state and batch117's original CI-pending record are historical; this review documents subsequent verified propagation. Selected local tests are not full-suite/Linux CI certification. Actual protected checks remain required; #1836 independently blocks the root. Keep #1913 and scientific repair issues open until protected-main merge. No dispatch,rerun,artificial CI,protection bypass,merge or branch deletion.
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Exact-head self-adversarial restack review at d1d05f02bd84e7d578036a38ce69365b62e566ad.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 5e9fc064bd0b61d1b83cce831aac47d9e5845c485dce2b64fabe60577769d296.
Tree 4f019603be298b7c6363d0ea344e70a74d74f8cd matches the independently computed clean merge.
Compared with historical tree d2e813cf186ee41c01203869337f2299aaf1d475, 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 #1901.
Closes #1902.
Closes #1903.
Metadata #1904/#1905 remain open; this batch does not resolve prior research extensions.
Adversarial Review
Verification And Output Records
1056 passed in 441.55s (0:07:21); eleven focused tests and seven real in-memory mutation probes. All three edited records pass schema, strict, term, full-record reference, snippet and history checks. 34 gate outputs retain commands, output tails and digests. All 457 other records, 922 other caches and non-graph raw blocks are unchanged.
Nine nodes and five of six original directions remain, with four renames and no new topology. Experimental model validation is retained for isobutanol stability; the abstract does not resolve every condition. The lactate graph preserves joint fungal/LAB redox roles and acetate/glucose co-substrate controls, separating alternative arms from the steam-pretreated three-member benchmark. Filamentous recipient growth remains phase-specific; dependence does not isolate mediation of all population-control effects.
Fresh primary abstracts and identity metadata checked. Isobutanol full text remained inaccessible after bounded public attempts. Lactate accepted-manuscript main text, selected SI and source figures were read; filamentous main text and appendices were read from fresh XML. Exact read scopes and limitations are committed. All 19 graph/discussion quotations have fresh primary and cache literal matches, not entailment certification. One cache gains a bounded 19-word main-text excerpt and provenance; no publication PDF or full body imported.
Corpus: 372 reviewed, 34 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Three explicit participant-list users added; no increase in the measured solely-credited census. Connectivity logic and share guard unchanged. Rendering is deterministic and all 456 pages' descriptions match YAML, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 d3af6394db29f1ec5d12eea5978296267909616ba0fa53d1d52e83b7e8b0a803. Local reference passes are macOS, not Linux certification; corpus snippets remain informational.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. Metadata #1904/#1905 remain open. No Edison invocation; prior Ruegeria extension #1883 still needs a configured provider. This COMMENT is self-review, not independent approval. Root blocker #1836 must be resolved through actual protected checks; no artificial CI, protection bypass or premature branch deletion.
Dependency
Draft depends on #1900. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.
Verified Palette Correction #1913
Closes #1913.
Real palette fix propagated at aa10cc1. Exact-head self-review supersedes the earlier propagation-pending state, not source-history records. Required protected CI and root #1836 remain outstanding; no merge or deletion.