Separate process outcomes and molecular responses from causal mediation (batch108)

[realmarcin]

Scope

Closes #1843.
Closes #1844.
Closes #1845.
Closes #1846.
Identity #1847 remains open.

• Preserve quantified substrate loss versus the control without reciprocal-benefit or monoculture-synergy claims; qualify its existing outcome contribution.; Preserve community shifts and the PLS-PM hypothesis with bounded statistical provenance, not niche separation or a taxon-specific mediator.; Preserve volatile and sensory outcomes; remove mutualism and misplaced upstream degradation-process annotations.
• Preserve all three quantified removal endpoints and stable 60-day context without inferring cross-feeding or organism-specific flux.; Preserve the positive algal biomass/protein response and explicit BG11 comparator; remove unsupported commensalism and nitrate mediation.; Preserve transcript upregulation with algal participant scope, not measured enzymatic flux or growth-to-expression causation.
• Preserve colonization-associated expression but distinguish inferred movement from direct colonization/facilitation; remove the context-only arrow.; Preserve functional gene enrichment and its qualified existing contribution to host responses; remove mutualism and exclusive inoculant attribution.; Preserve hormone, nutrient and stress transcription without asserting measured stress tolerance; keep the unresolved host/member identity boundary explicit.
• Recast co-selection as the reported tolerance phenotype; remove niche-partitioning typing and unsupported in-vivo assay assignment.; Preserve complementarity/minimal-antagonism context without stable coexistence, directional causation or niche separation.; Preserve plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit or sequestration-flux claims.

Adversarial Review

• Whole original targets and changed graph/discussion diffs reviewed. All 14 original nodes and seven directions have dispositions: retain 12 nodes and three qualified existing directions, remove two workflow nodes and four context/coincidence arrows, rename seven nodes. No new topology or Edison spend.
• Challenge deletion versus evidence loss: preserve measured tobacco substrate loss and sensory outcomes, Chlorella removal/growth/transcript responses, MetG2 microbial/host molecular responses, and Artemisia tolerance/compatibility/carbon-fixation capacity. Positive endpoints and source hypotheses remain.
• Tobacco: the uninoculated comparator does not establish monoculture synergy or reciprocal bacterial fitness. Relative Bacillus abundance is not absolute growth or the beta-diversity path-model variable. Preserve PLS-PM as PARTIAL statistical inference without invented software. Keep the two existing outcome contributions hypothetical; remove degradation-process annotations from the volatile/sensory endpoint.
• Chlorella: construction and 60-day duration are context, not separate biological causal nodes. Preserve all three removal percentages and the BG11-referenced algal response, without inferring exchanged nitrate, neutral bacterial fitness or an isolated bacterial conditioning effect. Transcript upregulation is not enzyme activity or measured flux. Preserve previous October2 edge repairs; give only algal observations canonical identity-only participant scope. Existing unnamed bacterial membership issue183 remains separate.
• MetG2: distinguish inferred colonization from direct tracking, enriched genes from products/transfer, and stress-response transcription from measured stress-challenge performance. Retain one hypothetical functional contribution, remove the context arrow and redundant unverified community-level taxon links. The primary preview names four inoculant strains with a Chiliseed2/Chileseed2 discrepancy; responding native Proteobacteria is not the inoculant. Generic sugarcane does not verify the canonical species. Record remains needs_research under1847.
• Artemisia: retain pair-level tolerance and PGP/carbon-fixation capacity, and the partial complementarity/minimal-antagonism design rationale. None proves niche partitioning, reciprocal fitness or sequestration flux. The abstract does not identify these trait-assay settings, so OTHER replaces unsupported IN_VIVO. Prior removal of screening-order arrows is preserved; no new topology is inferred from other positive plant/soil endpoints.
• Fifteen graph and seven discussion quotations match independently retrieved primary abstracts/indexed publisher previews and unchanged caches. Literal matching is separate from entailment. Whole indexed tobacco/Artemisia abstracts, bounded MetG2 Introduction/section previews and the whole EuropePMC Chlorella abstract were read, not complete papers. Direct publisher403 and public API400 attempts are recorded; two source CC licenses do not imply full-body retrieval. No supplements, figure pixels or raw datasets were certified.
• Four guarded writes produce four append-only histories. All 456 other records, all 923 caches, non-graph raw blocks and prior history/decision files remain byte-identical. No schema, validator, census-threshold or runtime-rule changes. Chlorella identity scopes and removal of redundant MetG2 links leave the global participant census unchanged; canonical MetG2 identities are not certified.
• Three in-memory control/mutation/restored-control probes reject promoting statistical evidence to SUPPORT or restoring the Chlorella and MetG2 coincidence/context arrows at scientific assertions. No canonical files changed; these probes do not inflate the pytest count.
• Eight focused tests and 975 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic rendering and exact HTML parsing cover 456 pages, 1370 node descriptions and 539 arrows, not screenshots.
• Repair issues1843-1846 are addressed but remain open until protected-main merge. Identity1847 and non-graph membership183 stay open. Existing license949, loader1703, DOI-cache case1091 and stub-policy1093 are not certified. Denied and unanswered Edison scopes remain untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.
• Corpus status is 344 reviewed, 64 pending and 52 needs_research, not completion. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.
• Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Verification And Output Records

975 passed in 301.81s (0:05:01); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 41 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Twelve nodes and three qualified existing directions remain, with seven renames. Two workflow nodes and four context/coincidence arrows are removed. All 22 reviewed graph/discussion quotations match fresh primary abstract/preview text and unchanged caches; literal matching is not entailment. All 456 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 344 reviewed, 64 pending, 52 needs_research. Network: 56 existing warnings, zero structural defects. Participant census and thresholds are unchanged.

Three in-memory control/mutation/restored-control probes reject promoting modeled mediation to SUPPORT and restoring Chlorella/MetG2 coincidence or context arrows. Canonical files remain unchanged; these probes are not added to the pytest count.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 3e1bd273401d0fece7010a1ff4385fb5fee6042e2a126b89942e81afeed15df4. Deterministic rendering and HTML parser checks are not screenshots. Four 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.

Review is bounded to independently retrieved primary abstracts and indexed publisher previews, not full papers, supplements, figure pixels or raw data. Direct publisher403 and two public API400 responses are recorded; CC license metadata does not prove full-body access. No new topology, Edison spend or experimental protocols. MetG2 identity #1847 remains unresolved and its record stays needs_research; existing Chlorella membership #183 also remains open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

Source Limits

• Fresh both-root baseline precedes source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Whole four records and all 14 original nodes/seven directions reviewed. Retain 12 nodes/three qualified existing directions; remove two workflow nodes/four context or coincidence arrows; rename seven nodes. No new topology or Edison spend.
• Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live.
• Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation.
• Tobacco: preserve measured substrate loss, community shifts and volatile/sensory outcomes. Remove mutualism and niche partitioning, qualify the existing directions and preserve PLS-PM mediation as a statistical hypothesis. No invented software/version, taxon-specific mediator or monoculture-synergy claim. Endpoint process annotations are removed because they describe upstream degradation, not volatile/sensory measurement.
• Chlorella: preserve 60-day removal, algal biomass/protein versus BG11 and transcript responses. Remove construction/duration nodes and three remaining noncausal arrows while preserving prior October2 repairs. No demonstrated cross-feeding, neutral bacterial fitness, isolated medium effect or measured metabolic flux. Only the algal observations gain canonical identity-only participant scope; unnamed bacterial membership remains existing issue183.
• MetG2: preserve microbial and host molecular responses and one qualified source-proposed functional contribution. Remove the context-only arrow, unestablished interaction types and redundant community-level source/target links. The indexed source names four inoculant strains and has a Chiliseed2/Chileseed2 spelling discrepancy; broad native rhizosphere Proteobacteria is not a resolved inoculant identity. Generic sugarcane is not verified as the canonical species. Record remains needs_research under1847; no new identifiers or canonical-taxonomy edits.
• Artemisia: preserve the pair-level tolerance, complementarity and PGP/carbon-fixation capacity. Remove niche partitioning and mutualism; source assay setting is not specified in the reviewed abstract, so OTHER replaces unsupported IN_VIVO assignment on these trait/design items. Preserve previous removal of screening-order arrows. Positive whole-abstract plant/soil outcomes are not rejected, but no new graph mechanism or sequestration-flux claim is introduced.
• Repair issues1843-1846 await protected-main merge; identity1847 and existing membership183 remain open. Fresh all-state issue titles/bodies and ignored/hidden local search matched1093,1091,184,183; all four bodies read. The122 local matching paths were inspected as an index, not all read; focused prior access/missing-PDF/author-request leads were inspected without contacting anyone. No reusable taxon match found in ignored/hidden-inclusive kb/taxa searches for the target names/IDs. PRs/comments not exhaustively searched.
• Only existing graphs, focused discussions and curation events change. All456 other records,923 caches, non-graph raw blocks and prior histories/decisions preserved. No schema, validator, runtime, census threshold or configuration changes. Non-graph membership, abundance, growth and role claims are not recertified. Loader1703, DOI-case1091 and stub-policy1093 remain separate. Self-review is not independent approval or corpus completion. Denied AM_AB000444 and unanswered Edison scopes untouched; validation/publication not preasserted.

Dependency

Draft depends on #1842. Do not merge into the topic parent. Require 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 5c3a892; not independent approval.

• Preserve quantified substrate loss versus the control without reciprocal-benefit or monoculture-synergy claims; qualify its existing outcome contribution.; Preserve community shifts and the PLS-PM hypothesis with bounded statistical provenance, not niche separation or a taxon-specific mediator.; Preserve volatile and sensory outcomes; remove mutualism and misplaced upstream degradation-process annotations.

• Preserve all three quantified removal endpoints and stable 60-day context without inferring cross-feeding or organism-specific flux.; Preserve the positive algal biomass/protein response and explicit BG11 comparator; remove unsupported commensalism and nitrate mediation.; Preserve transcript upregulation with algal participant scope, not measured enzymatic flux or growth-to-expression causation.

• Preserve colonization-associated expression but distinguish inferred movement from direct colonization/facilitation; remove the context-only arrow.; Preserve functional gene enrichment and its qualified existing contribution to host responses; remove mutualism and exclusive inoculant attribution.; Preserve hormone, nutrient and stress transcription without asserting measured stress tolerance; keep the unresolved host/member identity boundary explicit.

• Recast co-selection as the reported tolerance phenotype; remove niche-partitioning typing and unsupported in-vivo assay assignment.; Preserve complementarity/minimal-antagonism context without stable coexistence, directional causation or niche separation.; Preserve plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit or sequestration-flux claims.

• Whole original targets and changed graph/discussion diffs reviewed. All 14 original nodes and seven directions have dispositions: retain 12 nodes and three qualified existing directions, remove two workflow nodes and four context/coincidence arrows, rename seven nodes. No new topology or Edison spend.

• Challenge deletion versus evidence loss: preserve measured tobacco substrate loss and sensory outcomes, Chlorella removal/growth/transcript responses, MetG2 microbial/host molecular responses, and Artemisia tolerance/compatibility/carbon-fixation capacity. Positive endpoints and source hypotheses remain.

• Tobacco: the uninoculated comparator does not establish monoculture synergy or reciprocal bacterial fitness. Relative Bacillus abundance is not absolute growth or the beta-diversity path-model variable. Preserve PLS-PM as PARTIAL statistical inference without invented software. Keep the two existing outcome contributions hypothetical; remove degradation-process annotations from the volatile/sensory endpoint.

• Chlorella: construction and 60-day duration are context, not separate biological causal nodes. Preserve all three removal percentages and the BG11-referenced algal response, without inferring exchanged nitrate, neutral bacterial fitness or an isolated bacterial conditioning effect. Transcript upregulation is not enzyme activity or measured flux. Preserve previous October2 edge repairs; give only algal observations canonical identity-only participant scope. Existing unnamed bacterial membership issue183 remains separate.

• MetG2: distinguish inferred colonization from direct tracking, enriched genes from products/transfer, and stress-response transcription from measured stress-challenge performance. Retain one hypothetical functional contribution, remove the context arrow and redundant unverified community-level taxon links. The primary preview names four inoculant strains with a Chiliseed2/Chileseed2 discrepancy; responding native Proteobacteria is not the inoculant. Generic sugarcane does not verify the canonical species. Record remains needs_research under1847.

• Artemisia: retain pair-level tolerance and PGP/carbon-fixation capacity, and the partial complementarity/minimal-antagonism design rationale. None proves niche partitioning, reciprocal fitness or sequestration flux. The abstract does not identify these trait-assay settings, so OTHER replaces unsupported IN_VIVO. Prior removal of screening-order arrows is preserved; no new topology is inferred from other positive plant/soil endpoints.

• Fifteen graph and seven discussion quotations match independently retrieved primary abstracts/indexed publisher previews and unchanged caches. Literal matching is separate from entailment. Whole indexed tobacco/Artemisia abstracts, bounded MetG2 Introduction/section previews and the whole EuropePMC Chlorella abstract were read, not complete papers. Direct publisher403 and public API400 attempts are recorded; two source CC licenses do not imply full-body retrieval. No supplements, figure pixels or raw datasets were certified.

• Four guarded writes produce four append-only histories. All 456 other records, all 923 caches, non-graph raw blocks and prior history/decision files remain byte-identical. No schema, validator, census-threshold or runtime-rule changes. Chlorella identity scopes and removal of redundant MetG2 links leave the global participant census unchanged; canonical MetG2 identities are not certified.

• Three in-memory control/mutation/restored-control probes reject promoting statistical evidence to SUPPORT or restoring the Chlorella and MetG2 coincidence/context arrows at scientific assertions. No canonical files changed; these probes do not inflate the pytest count.

• Eight focused tests and 975 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic rendering and exact HTML parsing cover 456 pages, 1370 node descriptions and 539 arrows, not screenshots.

• Repair issues1843-1846 are addressed but remain open until protected-main merge. Identity1847 and non-graph membership183 stay open. Existing license949, loader1703, DOI-cache case1091 and stub-policy1093 are not certified. Denied and unanswered Edison scopes remain untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch deletion.

• Corpus status is 344 reviewed, 64 pending and 52 needs_research, not completion. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.

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

975 passed in 301.81s (0:05:01); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 41 recorded gate outputs/digests. Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.

Twelve nodes and three qualified existing directions remain, with seven renames. Two workflow nodes and four context/coincidence arrows are removed. All 22 reviewed graph/discussion quotations match fresh primary abstract/preview text and unchanged caches; literal matching is not entailment. All 456 other records, all 923 caches and non-graph raw blocks are unchanged. Corpus: 344 reviewed, 64 pending, 52 needs_research. Network: 56 existing warnings, zero structural defects. Participant census and thresholds are unchanged.

Three in-memory control/mutation/restored-control probes reject promoting modeled mediation to SUPPORT and restoring Chlorella/MetG2 coincidence or context arrows. Canonical files remain unchanged; these probes are not added to the pytest count.

Decisions, cache provenance, validation and self-adversarial review are committed under reports/causal_graph_review. Postcommit docs-current passed clean, SHA256 3e1bd273401d0fece7010a1ff4385fb5fee6042e2a126b89942e81afeed15df4. Deterministic rendering and HTML parser checks are not screenshots. Four 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.

Review is bounded to independently retrieved primary abstracts and indexed publisher previews, not full papers, supplements, figure pixels or raw data. Direct publisher403 and two public API400 responses are recorded; CC license metadata does not prove full-body access. No new topology, Edison spend or experimental protocols. MetG2 identity #1847 remains unresolved and its record stays needs_research; existing Chlorella membership #183 also remains open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.

[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]

Exact-head self-adversarial restack review at 17d603f6d3a32039b8dae44447d23bdee548cb6c.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 5776a3db3d0f3925063e212dd8fcc1260820717aa33e615570e6542c5eeb8ad3.
Tree 27dbf6240a40469e836b474bd4b3cd7b3b386774 matches the independently computed clean merge.
Compared with historical tree 31d1cdf9d46733907a0efd6a06f7a4f9bc210609, 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 6a6e6344fd601c2f963bca28d5460599cb8794c8 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.