Bound phototrophic carbon, lipid and attachment evidence (batch111)

[realmarcin]

Scope

Closes #1865.
Closes #1866.
Closes #1867.
Non-graph culture metadata #1868 and membership #1869 remain open.

• Preserve acetate-supported carbon feeding with explicit nonexclusive, untraced attribution.; Retain measurable butanol as a community endpoint with time-course and adaptation bounds.
• Retain strain-bounded sucrose feeding and whole-culture production support.; Preserve demonstrated ROS protection and conditional mutualism without exclusive mediation or obligacy.; Retain mixed-culture fatty-acid and biomass outcomes without duplicate exchange typing.
• Retain source-attributed EPS attachment role without an isolated effect size or persistent donor claim.; Retain early diatom attachment as an untyped, participant-bounded phenotype.; Retain combined AB diatom development without intergroup facilitation typing.; Retain mature community establishment with observed-versus-introduced membership boundaries.; Retain reproducibility and stress phenotypes without niche-partitioning or proven redundancy.

Adversarial Review

• Whole original targets and complete graph/discussion diffs reviewed. All 11 original nodes and three directions have dispositions. Ten nodes and all three directions remain; one assembly-only node is removed and three outcome nodes are renamed. No new topology or Edison job/spend.
• Challenge overcorrection: retain acetate-supported feeding and butanol production, sucrose feeding, conditional lichen mutualism, measured peroxide relief, catalase rescue, whole-culture fatty-acid increase, periphyton attachment, mature establishment and stress responses. Positive outcomes do not establish exclusive carbon attribution, obligate dependence or isolated mediation.
• Butanol: lower extracellular acetate supports consumption, not isotope-resolved flux or sole-source attribution; the source explicitly permits other exudates. Production is not duplicate exchange. Fluctuating plateaued production in the 42-day replenished culture is not constant high productivity; earlier growth adaptation did not increase production above prior levels. The existing acetate-to-product arrow stays HYPOTHESIZED/PARTIAL and the existing carbon-specificity discussion is preserved verbatim.
• Lichen: sucrose supports R. glutinis but not all tested yeast pairings. Peroxide measurements, catalase rescue and density controls support genuine context-dependent ROS protection, not universal partner dependence. Growth benefit beyond catalase is unresolved. Total fatty acids 54 percent higher in batch is whole-culture, not yeast-specific. Semi-continuous total includes removed culture, not only final biomass. ROS-to-lipid mediation remains hypothetical; no additional factor is invented.
• Periphyton: preserve the source-attributed Sphingomonas EPS attachment role, qualified for the lack of an isolated effect-size or persistence measurement in the reviewed main text. Remove growth-balanced grouping as a niche-partitioning interaction. Early and AB outcomes name only the canonical diatom descriptor, not all phototrophs. Keep attachment/development without intergroup facilitation claims. No workflow arrows are added.
• Periphyton maturity and stress: 26 introduced phototrophs are not a verified final 26-member roster; at least 22 were detected and three introduced species were no longer detected. Aggregate taxonomy and nonaxenic source cultures remain a separate metadata follow-up. Preserve the explicit day-18 high-herbicide PSII exception. Functional redundancy requires further study; stable aggregate PSII does not demonstrate it. Discussion anchors match all retained names.
• Three fresh primary XML extracted main texts were read completely, including abstracts, Methods, embedded captions and tables; displayed equation structure is omitted by extraction. No separate supplements, original image pixels or raw data were certified. Crossref exact DOIs were checked. All 27 graph and three discussion quotations match fresh primary text and unchanged caches under documented normalization. Two discussions are new and one preserved; literal matching is separate from entailment. Cache headers and quote matching are not a whole-cache review.
• Three guarded records and three append-only histories preserve prior history/decisions, 457 other records, 923 caches and raw non-graph blocks. Butanol adds one community-level/mixed record and two taxa to the census denominator, with zero new solely-credited taxa. Two early periphyton nodes narrow to diatoms. Measured census tests were updated; connectivity and share rules are unchanged.
• Four isolated in-memory control/mutation/restored-control probes reject inflated acetate certainty, proven ROS-to-lipid mediation, all-phototroph early attachment and proven functional redundancy. An initial attachment probe duplicated a diatom; that local artifact is retained separately and the corrected probe actually includes diatoms, green algae and cyanobacteria. Canonical hashes are unchanged; probes do not inflate the pytest count.
• Nine focused tests and 1003 combined regressions pass. Three full-record schema/strict/term/reference/local-snippet validations and three history validations pass. All 56 baseline network warnings remain identical, with zero structural defects. Deterministic rendering and exact HTML-description parsing cover 456 pages, 1366 nodes and 536 arrows; not screenshot QA. The informational full-corpus snippet audit includes unrelated preexisting discrepancies, including ligature issue 1863; it is not clean-corpus certification.
• Repairs 1865-1867 await protected-main merge. Non-graph culture issue 1868 and membership issue 1869 remain open. No shared validator/cache changes; DOI-case 1091, bracket 622, ligature 1863, loader 1703 and cache-policy 949/1093 are not certified. macOS reference success is not Linux certification. Denied/unanswered Edison scopes are untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.
• Corpus status is 355 reviewed, 52 pending and 53 needs_research across 460 records. The full goal remains incomplete. Exact-head publication and postcommit docs-current are separate gates, not preasserted here.
• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Verification And Output Records

1003 passed in 467.34s (0:07:47); nine new focused tests and four successful in-memory claim-inflation probes. Three full-record schema, strict, ontology-term, reference and local snippet checks passed; three append-only histories validated. 34 gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Ten of eleven nodes and all three existing directions retained; one assembly-only node removed and three outcome nodes renamed. All 30 graph/discussion quotations match fresh primary text and unchanged caches under documented normalization; literal matching is not entailment. Two discussions are new and one preserved. All 457 other records, 923 caches and raw non-graph blocks remain unchanged. Corpus: 355 reviewed, 52 pending, 53 needs_research. Network: 56 existing warnings and zero structural defects. Community-level census: 409 records, 134 mixed, 1556 taxa, and unchanged 1270 solely-credited taxa; connectivity/share logic unchanged.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 b9209a146bce4345b870374cc07b607d0960607025626e10b669e8970d4461b3. Deterministic rendering and HTML-description checks are not screenshot QA. Three full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 and prior ligature1863 remain outside this batch. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Three primary extracted main texts were read completely, including abstracts, Methods and embedded captions/tables. Displayed equations, separate supplements, original figure pixels and raw datasets were not certified. Non-graph culture metadata #1868 and membership #1869 stay open. The full-corpus snippet audit is informational and includes preexisting discrepancies, not clean-corpus certification. No new topology, Edison spend, access bypass or experimental protocol. This COMMENT is self-review, not independent approval.

Source Limits

• Fresh pre-source both-root baseline:460 records,923 caches,56 existing warnings,zero structural defects. All11 original nodes and three arrows reviewed; retain10 nodes/three directions,remove one assembly-only node,rename three outcome nodes. No new topology or Edison spend.
• Three fresh primary XML main bodies, abstracts, Methods and embedded captions/tables read in full extracted text:butanol lines1-199,lichen1-209,periphyton1-219. Crossref exact DOIs independently checked;all three CCBY. Extraction omits displayed equation structure. No separate supplements,original figure pixels or raw data audited;no exact gene/protocol claims imported.
• All27 graph and three discussion quotations match fresh primary text and unchanged caches. Two discussions are new and the existing butanol carbon-specificity discussion is preserved verbatim. Cache format/header inspection and quotation matching are not whole-cache review;attempt to print lichen DOI cache was truncated and is not claimed complete. Matching is separate from entailment.
• Butanol: retain acetate-supported carbon feeding and measured production;nonexclusive/untraced acetate attribution and fluctuating titers are explicit. Product output is not duplicate exchange. Growth adaptation did not increase product yield in the earlier assays. Existing knowledge gap is reused,not duplicated.
• Lichen: preserve sucrose feeding and conditional mutualism. Peroxide reduction,catalase rescue and high-density controls support context-dependent ROS relief,not obligate dependence or exclusive mediation. Whole-culture fatty-acid yield and harvested semi-continuous material remain distinct from partner-specific output. Existing ROS-to-lipid arrow stays hypothetical;unknown additional growth factor is not invented.
• Periphyton: retain source-attributed Sphingomonas attachment role without an isolated effect size or persistent canonical donor. Remove inoculum grouping as niche partitioning. Preserve measured early and AB attachment/development,scoped to canonical diatom descriptor;three outcome nodes renamed. Mature detection differs from26-member input. Stress-response node keeps generally stable PSII with the reported day18 high-herbicide exception;functional redundancy remains proposed. Staged order does not warrant new workflow arrows.
• Full canonical records and schema interaction/scope definitions read. Ignored/hidden-inclusive kb/taxa search for Synechocystis,taiwanensis,Rhodotorula,elodea,periphyton found no matching reusable record;no whole-repository absence claimed. Full local matching-path index,not all historical reports,read. Fresh all-state issue title/body search matched850,622,1547;wholebodies plus related529/1091 read. PR comments not exhaustively searched.
• Preserve457otherrecords,all923caches,rawnon-graph blocks and prior history/decision files. Only reviewed graph/discussions/curation_history change. Participant census must be measured,not guessed;rules and share guard remain unchanged. No schema/validator/runtime change;DOIcase1091,bracket622,ligature1863,loader1703 and cachepolicy949/1093 not certified. Full-record reference checks on macOS are not Linux certification.
• Repairs1865-1867 remain open until protected-main merge. Lichen culture metadata1868 and periphyton membership1869 remain open afterward. Self-review is not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection bypass or premature branch deletion.

Dependency

Draft depends on #1864. Do not merge into the topic parent. Require actual exact-head checks through protected main; self-review is not independent approval. Root CI blocker #1836 remains separate. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head c38a890; not independent approval.

• Preserve acetate-supported carbon feeding with explicit nonexclusive, untraced attribution.; Retain measurable butanol as a community endpoint with time-course and adaptation bounds.

• Retain strain-bounded sucrose feeding and whole-culture production support.; Preserve demonstrated ROS protection and conditional mutualism without exclusive mediation or obligacy.; Retain mixed-culture fatty-acid and biomass outcomes without duplicate exchange typing.

• Retain source-attributed EPS attachment role without an isolated effect size or persistent donor claim.; Retain early diatom attachment as an untyped, participant-bounded phenotype.; Retain combined AB diatom development without intergroup facilitation typing.; Retain mature community establishment with observed-versus-introduced membership boundaries.; Retain reproducibility and stress phenotypes without niche-partitioning or proven redundancy.

• Whole original targets and complete graph/discussion diffs reviewed. All 11 original nodes and three directions have dispositions. Ten nodes and all three directions remain; one assembly-only node is removed and three outcome nodes are renamed. No new topology or Edison job/spend.

• Challenge overcorrection: retain acetate-supported feeding and butanol production, sucrose feeding, conditional lichen mutualism, measured peroxide relief, catalase rescue, whole-culture fatty-acid increase, periphyton attachment, mature establishment and stress responses. Positive outcomes do not establish exclusive carbon attribution, obligate dependence or isolated mediation.

• Butanol: lower extracellular acetate supports consumption, not isotope-resolved flux or sole-source attribution; the source explicitly permits other exudates. Production is not duplicate exchange. Fluctuating plateaued production in the 42-day replenished culture is not constant high productivity; earlier growth adaptation did not increase production above prior levels. The existing acetate-to-product arrow stays HYPOTHESIZED/PARTIAL and the existing carbon-specificity discussion is preserved verbatim.

• Lichen: sucrose supports R. glutinis but not all tested yeast pairings. Peroxide measurements, catalase rescue and density controls support genuine context-dependent ROS protection, not universal partner dependence. Growth benefit beyond catalase is unresolved. Total fatty acids 54 percent higher in batch is whole-culture, not yeast-specific. Semi-continuous total includes removed culture, not only final biomass. ROS-to-lipid mediation remains hypothetical; no additional factor is invented.

• Periphyton: preserve the source-attributed Sphingomonas EPS attachment role, qualified for the lack of an isolated effect-size or persistence measurement in the reviewed main text. Remove growth-balanced grouping as a niche-partitioning interaction. Early and AB outcomes name only the canonical diatom descriptor, not all phototrophs. Keep attachment/development without intergroup facilitation claims. No workflow arrows are added.

• Periphyton maturity and stress: 26 introduced phototrophs are not a verified final 26-member roster; at least 22 were detected and three introduced species were no longer detected. Aggregate taxonomy and nonaxenic source cultures remain a separate metadata follow-up. Preserve the explicit day-18 high-herbicide PSII exception. Functional redundancy requires further study; stable aggregate PSII does not demonstrate it. Discussion anchors match all retained names.

• Three fresh primary XML extracted main texts were read completely, including abstracts, Methods, embedded captions and tables; displayed equation structure is omitted by extraction. No separate supplements, original image pixels or raw data were certified. Crossref exact DOIs were checked. All 27 graph and three discussion quotations match fresh primary text and unchanged caches under documented normalization. Two discussions are new and one preserved; literal matching is separate from entailment. Cache headers and quote matching are not a whole-cache review.

• Three guarded records and three append-only histories preserve prior history/decisions, 457 other records, 923 caches and raw non-graph blocks. Butanol adds one community-level/mixed record and two taxa to the census denominator, with zero new solely-credited taxa. Two early periphyton nodes narrow to diatoms. Measured census tests were updated; connectivity and share rules are unchanged.

• Four isolated in-memory control/mutation/restored-control probes reject inflated acetate certainty, proven ROS-to-lipid mediation, all-phototroph early attachment and proven functional redundancy. An initial attachment probe duplicated a diatom; that local artifact is retained separately and the corrected probe actually includes diatoms, green algae and cyanobacteria. Canonical hashes are unchanged; probes do not inflate the pytest count.

• Nine focused tests and 1003 combined regressions pass. Three full-record schema/strict/term/reference/local-snippet validations and three history validations pass. All 56 baseline network warnings remain identical, with zero structural defects. Deterministic rendering and exact HTML-description parsing cover 456 pages, 1366 nodes and 536 arrows; not screenshot QA. The informational full-corpus snippet audit includes unrelated preexisting discrepancies, including ligature issue 1863; it is not clean-corpus certification.

• Repairs 1865-1867 await protected-main merge. Non-graph culture issue 1868 and membership issue 1869 remain open. No shared validator/cache changes; DOI-case 1091, bracket 622, ligature 1863, loader 1703 and cache-policy 949/1093 are not certified. macOS reference success is not Linux certification. Denied/unanswered Edison scopes are untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.

• Corpus status is 355 reviewed, 52 pending and 53 needs_research across 460 records. The full goal remains incomplete. Exact-head publication and postcommit docs-current are separate gates, not preasserted here.

• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

1003 passed in 467.34s (0:07:47); nine new focused tests and four successful in-memory claim-inflation probes. Three full-record schema, strict, ontology-term, reference and local snippet checks passed; three append-only histories validated. 34 gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Ten of eleven nodes and all three existing directions retained; one assembly-only node removed and three outcome nodes renamed. All 30 graph/discussion quotations match fresh primary text and unchanged caches under documented normalization; literal matching is not entailment. Two discussions are new and one preserved. All 457 other records, 923 caches and raw non-graph blocks remain unchanged. Corpus: 355 reviewed, 52 pending, 53 needs_research. Network: 56 existing warnings and zero structural defects. Community-level census: 409 records, 134 mixed, 1556 taxa, and unchanged 1270 solely-credited taxa; connectivity/share logic unchanged.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 b9209a146bce4345b870374cc07b607d0960607025626e10b669e8970d4461b3. Deterministic rendering and HTML-description checks are not screenshot QA. Three full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 and prior ligature1863 remain outside this batch. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Three primary extracted main texts were read completely, including abstracts, Methods and embedded captions/tables. Displayed equations, separate supplements, original figure pixels and raw datasets were not certified. Non-graph culture metadata #1868 and membership #1869 stay open. The full-corpus snippet audit is informational and includes preexisting discrepancies, not clean-corpus certification. No new topology, Edison spend, access bypass or experimental protocol. This COMMENT is self-review, not independent approval.

[github-actions]

Network integrity findings

Warnings 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.

Network Integrity Audit Report
================================================================================

0 error, 56 warning across 20 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

KBase_Models_for_Zahmeeth_Original_PLOS
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Klebsiella' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas fluorescens' has no interactions

Total: 2 issues (0 error, 2 warning)

Lake_Washington_Methane_Oxygen_Methylotroph_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylosarcina' has no interactions

Total: 1 issues (0 error, 1 warning)

Lotus_LjSC3
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Burkholderiaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule210' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule215' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule218' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Oxalobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Phyllobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonadaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobiaceae bacterium' has no interactions

Total: 9 issues (0 error, 9 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Panzhihua_Vanadium_Titanium_Tailings
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Polaromonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium pisi' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobium selenitireducens' has no interactions

Total: 3 issues (0 error, 3 warning)

Phormidium_Alkaline_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacteroidota members' has no interactions

Total: 1 issues (0 error, 1 warning)

Polaromonas_Vanadium_Reduction_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Desulfitobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Desulfovibrio species' has no interactions
  [warning] DISCONNECTED: Taxon 'Geobacter species' has no interactions

Total: 3 issues (0 error, 3 warning)

Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa MDR6-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa NfxB-CAZ' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa OrfN' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa PA14' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas aeruginosa mexZ' has no interactions

Total: 5 issues (0 error, 5 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial review refreshed at exact head f97306e after propagating the real CI correction #1899. Not independent approval.

Original head: c38a890. Current parent: 0ab36cb. Only tests/test_datamodel.py changes in the tree for batches109-114; batch115's whole tree is unchanged. Scientific records, prior histories/decisions, caches, renderings and all other files are byte-identical to the respective reviewed trees. Each batch-owned patch excluding this test is byte-identical (SHA256 b374ba6e9d2b6f03de55b056d09a77054e651ad794f6561a51b78a01230c6023).

The stale smoke test now requires the reviewed source and target names, resolving target, canonical pairwise taxa, qualified sucrose mediation and both SUPPORT/PARTIAL evidence. No graph was reverted or test skipped. The batch115 CI artifact records the original failed strict run, reproduction, 24 related test passes and seven rejecting counterfactual probes.

Fresh tests at this head: ............. [100%]
13 passed in 20.76s
Test log SHA256: 6f24186a70a0794ccec0fd5d72d99ccd7115d56a934cc8792668ff37a5e60b65. Fresh docs-current passed with a clean worktree; log SHA256 b9209a146bce4345b870374cc07b607d0960607025626e10b669e8970d4461b3.

The propagation-pending entries in batch115's immutable publication report describe the earlier publication state; this exact-head review records the subsequent propagation. Focused tests are not a new full-suite pass. Real exact-head protected CI remains required; #1836 independently blocks the upstream root PR. #1899 remains open until protected-main integration. No artificial CI, protection bypass, merge or branch deletion was performed.

[realmarcin]

Exact-head self-adversarial restack review at af3b5317abfd3667539e19bfdba10fc8b27d09bb.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 b374ba6e9d2b6f03de55b056d09a77054e651ad794f6561a51b78a01230c6023.
Tree d71736d520c9c4ad4c3cf31f453a7a301a89aded matches the independently computed clean merge.
Compared with historical tree cdf02a9ffbf84aa6681665c99ccfaa0045bd544c, 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.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head 10ddc0d351c462236f4e4d76e2649791eae345d5 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

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.