Bound photosynthetic graph products and electron recipients (batch110)

[realmarcin]

Scope

Closes #1857.
Closes #1858.
Closes #1859.
Research #1860, non-graph #1861-#1862 and validator #1863 remain open.

• Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium scope.; Retain PHB and persistence as a community phenotype, not duplicate exchange or photosynthesis.; Retain alginate intervention effects without colonization typing or proven PHB mediation.
• Retain sucrose carbon support with separate production and DNT assay contexts.; Retain PHA phenotype with correct polymer-family grounding and endpoint comparison.; Retain DNT transformation and PHA outcome without inferring complete mineralization.; Preserve conditional growth partnership without reverse sucrose donation or identified mediator.
• Retain D-lactate supply and anode support without exclusive organic-input claims.; Correct anode recipient and preserve source-proposed CO2 feedback as hypothetical.; Retain abiotic compatibility and duration with distinct replenished-device context.

Adversarial Review

• Whole original targets and all changed graph/discussion diffs reviewed. All ten nodes and six existing directions retained. No renamed, removed or new topology; no Edison job or spend.
• Challenge overcorrection: preserve photosynthetic carbon supply, PHB/PHA accumulation, DNT transformation, cyanobacterial growth benefits, anode current and device-compatibility benefits. Qualification distinguishes observed outcomes from isolated causal mediation, not positive from negative results.
• Halomonas: abstract supports sucrose feeding, PHB up to 31% dry weight, productive persistence over five months and alginate-enhanced export/stability. It does not identify LC1, resolve all organic inputs or isolate encapsulation-to-PHB mediation. Preserve existing identities but mark graph needs_research and retain the mediation arrow as HYPOTHESIZED/PARTIAL. PHB output and alginate intervention are untyped community processes, not duplicate exchange or colonization facilitation.
• Pseudomonas: distinguish cscAB PHA, cscRABY/nitrate-blind and EM173 DNT implementations. Measured medium-chain-length PHA is not PHB homopolymer; 8.8-fold final accumulation is not a rate comparison. DNT disappearance includes adsorption and reductive fates; oxidative intermediates support transformation, not measured complete mineralization. Preserve nitrogen-limited PHA outcome without importing polymer identity from a crotonic-acid assay.
• Pseudomonas feedback: retain conditional carbon-supported partnership and positive cyanobacterial growth. The heterotroph does not gain growth rate over matched externally fed axenic controls. Mixed-cell omics and transporter responses do not establish a donor/recipient mediator or reverse sucrose donation. The unresolved mechanism remains PARTIAL with a discussion, not a new exchange node.
• Shewanella: retain D-lactate contribution using lactate rather than acid grounding, without exclusive organic-carbon attribution. The anode is abiotic, not the cyanobacterium. Source Figure1 proposes CO2 return, so the existing reverse arrow remains explicitly hypothetical; positive cyanobacterial growth is retained separately. Temporal batch, spatial and replenished spatial-temporal devices are distinct. More-than-40-day output is qualified by medium replenishment and LB supplementation; no protocol optimization is added.
• Twenty-four graph and three new discussion quotations match fresh primary text and unchanged caches under documented normalization. Five primary main texts were read in bounded spans and one primary abstract in full; remaining Methods, supplements, figure pixels and raw data were not certified. Halomonas full article was not retrieved in bounded searches, not declared globally unavailable.
• Initial reference failure came from a PDF word join. A replacement excerpt from the same primary paragraph passes CLI validation, with append-only correction history and the failed attempt retained. One remaining local snippet-audit MISMATCH is an exact, independently proven fi-ligature false positive; issue1863 stays open. No shared validator change, cache rewrite or claim that all snippet classifications are clean.
• Three guarded records and four append-only histories preserve all prior history and decision files, 457 other records, all 923 caches and non-graph raw blocks. Shewanella adds one community-level/mixed record and two taxa to the survey denominator, with no new taxa credited solely by the broad rule. Measurement-based census expectations are updated; connectivity and share logic are unchanged.
• Four in-memory control/mutation/restored-control probes reject PHA-to-PHB inflation, complete-mineralization inflation, a cyanobacterial anode recipient and unsupported growth-mediator certainty. Canonical files remain unchanged; probes are not added to the pytest count.
• Seven focused tests and 994 combined regressions pass. Three full-record schema/strict/term/reference validations and four histories pass. Local snippet checks retain the one explicitly documented ligature discrepancy. Network preserves 56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML descriptions cover 456 pages, 1367 nodes and 536 arrows; this is not screenshot QA.
• Repairs1857-1859 await protected-main merge. Research1860, non-graph1861-1862 and validator1863 remain open. Existing loader1703, DOI-case1091 and cache-policy949/1093 are not certified. Denied/unanswered Edison scopes are untouched. Self-review is not independent approval, and no CI/protection bypass or premature branch deletion is allowed.
• Corpus status is 352 reviewed, 55 pending and 53 needs_research. The whole 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

994 passed in 335.27s (0:05:35); seven new focused tests and four successful in-memory claim-inflation probes. Three full-record schema, strict, ontology-term and reference checks passed; four append-only histories validated. 35 gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

All ten nodes and six directions retained. All 27 graph/discussion quotations match fresh primary text and unchanged caches under documented normalization; literal matching is not entailment. All 457 other records, 923 caches and raw non-graph blocks remain unchanged. Corpus: 352 reviewed, 55 pending, 53 needs_research. Network: 56 existing warnings and zero structural defects. Community-level census: 408 records, 133 mixed, 1554 taxa, and unchanged 1270 solely-credited taxa; connectivity/share logic unchanged.

Initial reference failure and append-only quote correction are retained. The local snippet auditor still reports one independently proven fi-ligature false positive, explicitly documented under #1863. No claim of a clean snippet audit and no shared validator/cache changes.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 7df6fe24a68b30754527d0817536fb7bb4e559faebcc06300bfb3babb9460137. 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 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Five primary main texts were read in bounded spans and one primary abstract in full; no supplements, figure pixels, remaining Methods or raw datasets certified. Halomonas remains needs_research (#1860); non-graph #1861-#1862 and validator #1863 stay open. No new topology, Edison spend, access bypass or experimental protocol. This COMMENT is self-review, not independent approval.

Source Limits

• Fresh both-root baseline before primary reads:460 records,923 caches,56 existing warnings,zero structural defects. Three full targets and ten nodes/six arrows reviewed. All topology retained; no new nodes/directions or Edison spend.
• Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining Methods, supplementary files, figure pixels and raw datasets not audited.
• Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and needs_research;not silently certified. Existing canonical taxonomy untouched.
• Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not a removal-only assay. No source-cache changes.
• Retain Halomonas feeding,PHB/persistence and alginate intervention;remove duplicate exchange/colonization typing and unsupported organic-input exclusion. Keep alginate mechanism in text without asserting alginic-acid protonation. Existing alginate-to-PHB direction stays HYPOTHESIZED/PARTIAL.
• Pseudomonas preserves separate cscAB,cscRABY/nitrate-blind and EM173 implementations. PHA family not PHB;8.8-fold endpoint not rate;DNT disappearance not complete mineralization. Conditional mutualism retains carbon supply/cyanobacterial benefit,not heterotroph advantage over externally fed controls. Additional molecular exchange unresolved,not reverse sucrose. General PHA term reused from same record.
• Shewanella retains D-lactate contribution,not substrate exclusivity. Anode is abiotic recipient;positive cyanobacterial growth is retained separately from hypothetical CO2-return mediation. Retain existing reverse direction using source Fig1 proposal,not device-separation wording. Device modes and replenishment/LB context qualified. D-lactate CHEBI16004 canonical label checked against EBI acid/base relation and focused term validation. No new engineering/cultivation/protocol instructions.
• Whole reviewed Azotobacter neighboring record and reusable Shewanella MR1 taxon record read as modeling context,not evidence for targets. Reusable record is not linked automatically to the engineered derivative;no gene claims copied. Ignored/hidden kb/taxa search found only that matching reusable taxon. Fresh all-state title/body dedup matched1093,258,1851,1669,1606,1605,837,836,835;all wholebodies and related529 read. Local matching-path index read,not every report;PRs/comments not exhaustive.
• Only ecological_interactions,discussions,curation_history change. Preserve other457records,all923caches,non-graph rawblocks and prior history/decisionfiles. Issues1857-1859 remainopen untilprotectedmainmerge;research1860 and nongraph1861-1862 remainopen afterward. Self-review is not independent approval or full corpus completion. No schema/validator/runtime change. Participantcensus updates must be measurement-based with unchanged connectivity/share rules. Loader1703,DOIcase1091,cachepolicy949/1093 not certified. Denied/unanswered Edison scopes untouched.
• Replace growth-rate excerpt with an exact passage shared by the primary XML and unchanged PDF cache; the initial CLI rejected a PDF word-join artifact. Matched-control growth interpretation and graph topology are unchanged. Issue#1858. Four append-only histories across three records; no prior history rewritten.
• Local snippet auditor reports one exact known MISMATCH for the Pseudomonas discussion because it drops the PDF fi ligature. Primary XML and unchanged cache match under independent NFKD normalization; CLI references pass. Preserve the faithful quote and record the exact classification rather than claiming a clean snippet audit. Shared-auditor follow-up1863 remains open; related257/596 and fresh all-state title/body dedup reviewed. Initial audit assertion failure is retained; no shared validator change.

Dependency

Draft depends on #1856. 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 4f41c29; not independent approval.

• Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium scope.; Retain PHB and persistence as a community phenotype, not duplicate exchange or photosynthesis.; Retain alginate intervention effects without colonization typing or proven PHB mediation.

• Retain sucrose carbon support with separate production and DNT assay contexts.; Retain PHA phenotype with correct polymer-family grounding and endpoint comparison.; Retain DNT transformation and PHA outcome without inferring complete mineralization.; Preserve conditional growth partnership without reverse sucrose donation or identified mediator.

• Retain D-lactate supply and anode support without exclusive organic-input claims.; Correct anode recipient and preserve source-proposed CO2 feedback as hypothetical.; Retain abiotic compatibility and duration with distinct replenished-device context.

• Whole original targets and all changed graph/discussion diffs reviewed. All ten nodes and six existing directions retained. No renamed, removed or new topology; no Edison job or spend.

• Challenge overcorrection: preserve photosynthetic carbon supply, PHB/PHA accumulation, DNT transformation, cyanobacterial growth benefits, anode current and device-compatibility benefits. Qualification distinguishes observed outcomes from isolated causal mediation, not positive from negative results.

• Halomonas: abstract supports sucrose feeding, PHB up to 31% dry weight, productive persistence over five months and alginate-enhanced export/stability. It does not identify LC1, resolve all organic inputs or isolate encapsulation-to-PHB mediation. Preserve existing identities but mark graph needs_research and retain the mediation arrow as HYPOTHESIZED/PARTIAL. PHB output and alginate intervention are untyped community processes, not duplicate exchange or colonization facilitation.

• Pseudomonas: distinguish cscAB PHA, cscRABY/nitrate-blind and EM173 DNT implementations. Measured medium-chain-length PHA is not PHB homopolymer; 8.8-fold final accumulation is not a rate comparison. DNT disappearance includes adsorption and reductive fates; oxidative intermediates support transformation, not measured complete mineralization. Preserve nitrogen-limited PHA outcome without importing polymer identity from a crotonic-acid assay.

• Pseudomonas feedback: retain conditional carbon-supported partnership and positive cyanobacterial growth. The heterotroph does not gain growth rate over matched externally fed axenic controls. Mixed-cell omics and transporter responses do not establish a donor/recipient mediator or reverse sucrose donation. The unresolved mechanism remains PARTIAL with a discussion, not a new exchange node.

• Shewanella: retain D-lactate contribution using lactate rather than acid grounding, without exclusive organic-carbon attribution. The anode is abiotic, not the cyanobacterium. Source Figure1 proposes CO2 return, so the existing reverse arrow remains explicitly hypothetical; positive cyanobacterial growth is retained separately. Temporal batch, spatial and replenished spatial-temporal devices are distinct. More-than-40-day output is qualified by medium replenishment and LB supplementation; no protocol optimization is added.

• Twenty-four graph and three new discussion quotations match fresh primary text and unchanged caches under documented normalization. Five primary main texts were read in bounded spans and one primary abstract in full; remaining Methods, supplements, figure pixels and raw data were not certified. Halomonas full article was not retrieved in bounded searches, not declared globally unavailable.

• Initial reference failure came from a PDF word join. A replacement excerpt from the same primary paragraph passes CLI validation, with append-only correction history and the failed attempt retained. One remaining local snippet-audit MISMATCH is an exact, independently proven fi-ligature false positive; issue1863 stays open. No shared validator change, cache rewrite or claim that all snippet classifications are clean.

• Three guarded records and four append-only histories preserve all prior history and decision files, 457 other records, all 923 caches and non-graph raw blocks. Shewanella adds one community-level/mixed record and two taxa to the survey denominator, with no new taxa credited solely by the broad rule. Measurement-based census expectations are updated; connectivity and share logic are unchanged.

• Four in-memory control/mutation/restored-control probes reject PHA-to-PHB inflation, complete-mineralization inflation, a cyanobacterial anode recipient and unsupported growth-mediator certainty. Canonical files remain unchanged; probes are not added to the pytest count.

• Seven focused tests and 994 combined regressions pass. Three full-record schema/strict/term/reference validations and four histories pass. Local snippet checks retain the one explicitly documented ligature discrepancy. Network preserves 56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML descriptions cover 456 pages, 1367 nodes and 536 arrows; this is not screenshot QA.

• Repairs1857-1859 await protected-main merge. Research1860, non-graph1861-1862 and validator1863 remain open. Existing loader1703, DOI-case1091 and cache-policy949/1093 are not certified. Denied/unanswered Edison scopes are untouched. Self-review is not independent approval, and no CI/protection bypass or premature branch deletion is allowed.

• Corpus status is 352 reviewed, 55 pending and 53 needs_research. The whole 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.

994 passed in 335.27s (0:05:35); seven new focused tests and four successful in-memory claim-inflation probes. Three full-record schema, strict, ontology-term and reference checks passed; four append-only histories validated. 35 gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

All ten nodes and six directions retained. All 27 graph/discussion quotations match fresh primary text and unchanged caches under documented normalization; literal matching is not entailment. All 457 other records, 923 caches and raw non-graph blocks remain unchanged. Corpus: 352 reviewed, 55 pending, 53 needs_research. Network: 56 existing warnings and zero structural defects. Community-level census: 408 records, 133 mixed, 1554 taxa, and unchanged 1270 solely-credited taxa; connectivity/share logic unchanged.

Initial reference failure and append-only quote correction are retained. The local snippet auditor still reports one independently proven fi-ligature false positive, explicitly documented under #1863. No claim of a clean snippet audit and no shared validator/cache changes.

Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 7df6fe24a68b30754527d0817536fb7bb4e559faebcc06300bfb3babb9460137. 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 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.

Five primary main texts were read in bounded spans and one primary abstract in full; no supplements, figure pixels, remaining Methods or raw datasets certified. Halomonas remains needs_research (#1860); non-graph #1861-#1862 and validator #1863 stay open. 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 0ab36cb after propagating the real CI correction #1899. Not independent approval.

Original head: 4f41c29. Current parent: 1e4ed39. 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 9ecb0ed8656b2a28010d56e20f55a55809670143b3150d0c20ad087c5392e79a).

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 39.66s
Test log SHA256: 740b192b7e98a2bdb0b6dd0cc9abf9c5a9d90070bbec2fefc26c08aaafed4eaf. Fresh docs-current passed with a clean worktree; log SHA256 7df6fe24a68b30754527d0817536fb7bb4e559faebcc06300bfb3babb9460137.

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 cbc4d82889dfc000385981f60f98e10c39ca8cbe.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 9ecb0ed8656b2a28010d56e20f55a55809670143b3150d0c20ad087c5392e79a.
Tree 3bd4e2e6c0251087420c346f030d415a3051f9c2 matches the independently computed clean merge.
Compared with historical tree 8435b0eaf7522f2502d9e56722eaf5e6023cdca3, 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 d61cbc4a4c9ed96b407b70ae12347b6dcafd7852 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.