Bound Medicago soil activity and metal depletion claims (batch69)

[realmarcin]

Scope

Closes #1588.
Closes #1589.
Closes #1590.
Closes #1591.
Related #1592/#1593 deferred graph research and #1594 non-graph metadata remain OPEN after graph repair merge.

• Retain individual-strain PGP observations with exceptions, not mutualism or in-host trait necessity.; Retain measured host enzyme responses and qualified protective hypothesis.; Retain positive endpoint-specific plant benefits and nodulation, not directly measured fixation flux.
• Retain compartment-specific establishment/sporulation with initial-roster and qualitative-root limits.
• Retain positive isotope-inferred growth and absorb redundant workflow context.; Retain historical precipitation association without isolated selection.; Retain growth association with predicted flagellar capacity, not measured movement.; Retain broad carbon-capacity distribution with site-specific exceptions and flux limits.
• Retain positive element depletion at assay scope without redox, exclusive biosorption or emergent-advantage claims.

Adversarial Review

• Read four whole records, all10 original nodes and2 arrows. Three complete fresh primary main texts/captions and five main tables read; fungal primary abstract and subscription preview only. No separate supplementary files, original figure pixels, raw data or external literature independently audited.
• Medicago retains four distinct strain names despite two shared genus IDs. Individual-strain PGP panels are not mixed-culture mutualism. Table1 and Methods support phosphate/IAA/ACC/biofilm/pectinase assays but biofilm signal declined and N10/N12 lost nitrogen-free growth under metals. Nitrogen-free growth is expressly a first approximation, not direct flux.
• Medicago plant gains are real and treatment-specific. Keep N10-alone comparator, salinity-associated shorter/thicker roots and low heat photosynthesis despite improvement. Keep nodulation and oxidative-stress context; remove misplaced nodulation on isolated traits and unmeasured fixation-process assignment on plant nitrogen. N2 remains a candidate source with a note, not a measured flux.
• Both Medicago arrows remain HYPOTHESIZED with a positive proposed biological route and explicit missing perturbation. Host enzyme induction does not by itself prove ROS clearance or growth mediation. Replace aim-only plant evidence with a plant outcome while preserving original upstream IN_VITRO alias used outside the graph. Host stays external, no invented canonical taxon.
• Fungal root colonization supports broad symbiotic-process context; do not erase it because competition/reciprocal benefit was untested. Six initial species does not establish equal persistence. Spore non-detection is not root extinction, and pooled PCR-TTGE is not quantitative intraradical abundance. Limited host-cover influence is not zero influence. Retain initial canonical roster and exact F.coronatum/F.coronatus distinction without remapping.
• Fungal graph-owned id004/id005 evidence anchors remain valid for untouched environmental aliases. Existing inoculum/protocol discussions remain OPEN and prior Use IN_VIVO evidence for Mediterranean AM fungal mesocosm observations #862/Add direct cultivation evidence to the Mediterranean AM fungal SynCom #863 evidence/cultivation repairs survive. Public publisher page explicitly subscription-preview only; no paywall bypass or claim of full-body review.
• qSIP retains positive DNA-incorporation growth observations, absorbs the redundant active-community-resolution evidence, and preserves the previous four-arrow deletion. Rewetted eight-day laboratory incubations are not in-field trajectories, AFE is not net growth and low activity is not death. Two Bacteria guild entries overlap and are not a resolved species roster.
• qSIP historical rainfall association is not randomized historical selection. Flagellar genomic capacity is not observed movement, and carbon pathway annotation plus organism growth is not substrate flux or sequestration. Preserve broad negative carbon-capacity selection result alongside Angelo/site/taxon exceptions; do not infer niche partitioning. Predicted motility process retained explicitly as potential.
• Missing qSIP labeled-phage/predicted-host activity deserves separate new-structure review, not a workflow edge. Account for prophage labeling and alternative mortality before any lysis-to-necromass arrow. One-record dry run9469chars is not a report. Its reviewed query contains the pre-repair record context; refresh and inspect the dry run before any later paid submission. Research missing qSIP phage-host activity structure before graph extension #1592 remains OPEN and record needs_research.
• A22ED9 preserves Clarify A22ED9 single-metal Fe/Cd/Cr assay labels #1009 single-metal naming and positive92.08/74.15/97.587% averages at initialpH5 after24h. Residual ICP-OES after cell separation does not establish final metal speciation, intracellular uptake or unique biosorption. Chromium atom is element-level reporting, not metallic feed; dichromate challenge is explicit. Do not promote pH8 to a universal endpoint.
• A22ED9 primary source reports cell-free controls while also acknowledging missing abiotic partitioning. Preserve reported little-loss controls and the unresolved pH-matched/live-dead comparison, not a false no-controls claim. SEM-EDX examples are individualSK22/SK18-4, not a uniquely consortium-resolved mechanism. Reported compatibility/stimulation is not higher removal; no field validation claimed.
• Missing KHED9-filtrate stimulation of SK22 is separate from metal depletion. Inspect supplementary FigS2/controls and exact strain assignments before extension; shared genus ID does not merge the two strains. One-record dry run9544chars is not a report. Its reviewed query contains the pre-repair record context; refresh and inspect the dry run before any later paid submission. Research A22ED9 filtrate growth stimulation before causal graph extension #1593 remains OPEN and record needs_research.
• Read complete biological diff; all unchanged top-level raw non-graph blocks,456 other records and920 caches verified. Append-only record events/history, exact graph names/discussion anchors, and19 independently primary-matched excerpts checked. No new nodes/arrows or paid submissions.
• Measure the participant census before updating the exact USERS registry for the fungal and Bacillus records. Counts460/391/123/268/1507/1240 unchanged. All44 network warnings unchanged exactly, no structural defects and no auditor-rule changes. Named initial participants do not prove partner-resolved mechanisms.
• Actual focused schema/strict/terms/references/snippets/history checks, inventory/rank/network, repeat-render and full combined regression outputs retained with hashes. HTML descriptions parsed over456 pages, not browser screenshots; post-commit docs-current is a separate publication gate.
• Dedup879 all-state issue titles/bodies and22 scoped ignored/hidden local matches. Four matching issue bodies (An exact 50/50 majority still grounds, decided by a tie-break rather than evidence #382/Use IN_VIVO evidence for Mediterranean AM fungal mesocosm observations #862/Add direct cultivation evidence to the Mediterranean AM fungal SynCom #863/Clarify A22ED9 single-metal Fe/Cd/Cr assay labels #1009), relevant history and prior A22ED9 review read, not every local match/PR/comment. Bound Medicago SynCom trait and antioxidant mediation claims #1588-Clarify A22ED9 metal depletion endpoint and mechanistic limits #1591 addressed but OPEN pending protected-main merge; Research missing qSIP phage-host activity structure before graph extension #1592/Research A22ED9 filtrate growth stimulation before causal graph extension #1593/Reconcile Medicago qSIP and A22ED9 non-graph source metadata #1594 remain OPEN afterward. Self-review is not independent approval or corpus completion.

Verification And Output Records

627 passed in 211.69s (0:03:31); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 72 record snippets match selected caches;19 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;19 graph excerpts independently match fresh primary text after whitespace normalization. #1594 metadata and #1592/#1593 research remain OPEN; fungal full text unavailable. Broader #476/#1091/#1095 source limitations persist.

Ten original nodes reviewed;9 retained and1 redundant qSIP workflow node removed. Both Medicago arrows are qualified hypotheses. No new structure or provider spend; two one-record Edison dry runs are not research reports. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural errors;all44 baseline network findings preserved exactly. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure narrowed participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 5bbd1ffb85f27906d74086744df2429d3a3e7f189351134992dd01ff36710a44. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch69. Corpus220 reviewed /216 pending /24 needs_research: unfinished, not independent approval. qSIP and A22ED9 remain needs_research under #1592/#1593; metadata #1594 remains OPEN.

Source Limits

• All10 original nodes and2 arrows reviewed;9 bounded observations remain,1 redundant workflow node removed and2 arrows qualified. No new causal structure; qSIP and A22ED9 remain needs_research under Research missing qSIP phage-host activity structure before graph extension #1592/Research A22ED9 filtrate growth stimulation before causal graph extension #1593.
• Three complete fresh public primary main texts, embedded captions and available main tables read. Fungal source is complete abstract/subscription preview only, not full methods. Separate supplements, original figure pixels, raw data and executable analyses not independently audited.
• Medicago retains positive strain traits and plant benefits with trait exceptions, endpoint specificity and unisolated antioxidant mediation. Tissue nitrogen does not directly measure N2 flux. Broad oxidative-stress and nodulation context retained where supported.
• Fungal initial six-member inoculum is not equal persistence. Root occurrence and spore counts differ; pooled PCR-TTGE is qualitative. Undetectable spores are not extinction. Preserve existing inoculum/protocol gaps and Use IN_VIVO evidence for Mediterranean AM fungal mesocosm observations #862/Add direct cultivation evidence to the Mediterranean AM fungal SynCom #863 fixes.
• qSIP uses rewetted eight-day laboratory soil incubations. DNA incorporation, predicted flagella and genomic carbon capacities are distinct measurements; historical rainfall association is not isolated selection. Missing phage-host structure is explicitly deferred, not forgotten.
• A22ED9 retains positive single-metal depletion and Clarify A22ED9 single-metal Fe/Cd/Cr assay labels #1009 labels, not exclusive biosorption, redox flux or field performance. Source reports cell-free controls while acknowledging missing abiotic partitioning; preserve this tension rather than claiming controls were absent. Missing filtrate stimulation awaits supplement/report review.
• Canonical taxonomy and non-graph raw blocks unchanged, not recertified. Reconcile Medicago qSIP and A22ED9 non-graph source metadata #1594 remains OPEN. Preserve strain identities despite shared IDs, fungal graph-owned evidence anchors and prior qSIP workflow-arrow deletion.
• All920 caches unchanged;19 graph excerpts independently primary-matched after whitespace normalization. This is not historical cache/non-graph provenance certification. Full public sources remain scratch-only.
• Two one-record Edison causal dry runs completed at zero provider submissions/credits; real-run price not quoted and scoped authorization pending. A dry run is not a research report or grounds for adding structure.
• All-state issue titles/bodies and ignored/hidden local files searched before filing; four matching issue bodies and relevant record history/prior A22ED9 review read. Self-review is not independent approval. Repair issues remain OPEN until protected-main merge; research/metadata remain OPEN afterward.

Dependency

Draft depends on #1587. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head fde6a12; not independent approval.

Repairs #1588-#1591 addressed; #1594/#1592/#1593 unresolved.

• Retain individual-strain PGP observations with exceptions, not mutualism or in-host trait necessity.; Retain measured host enzyme responses and qualified protective hypothesis.; Retain positive endpoint-specific plant benefits and nodulation, not directly measured fixation flux.

• Retain compartment-specific establishment/sporulation with initial-roster and qualitative-root limits.

• Retain positive isotope-inferred growth and absorb redundant workflow context.; Retain historical precipitation association without isolated selection.; Retain growth association with predicted flagellar capacity, not measured movement.; Retain broad carbon-capacity distribution with site-specific exceptions and flux limits.

• Retain positive element depletion at assay scope without redox, exclusive biosorption or emergent-advantage claims.

• Read four whole records, all10 original nodes and2 arrows. Three complete fresh primary main texts/captions and five main tables read; fungal primary abstract and subscription preview only. No separate supplementary files, original figure pixels, raw data or external literature independently audited.

• Medicago retains four distinct strain names despite two shared genus IDs. Individual-strain PGP panels are not mixed-culture mutualism. Table1 and Methods support phosphate/IAA/ACC/biofilm/pectinase assays but biofilm signal declined and N10/N12 lost nitrogen-free growth under metals. Nitrogen-free growth is expressly a first approximation, not direct flux.

• Medicago plant gains are real and treatment-specific. Keep N10-alone comparator, salinity-associated shorter/thicker roots and low heat photosynthesis despite improvement. Keep nodulation and oxidative-stress context; remove misplaced nodulation on isolated traits and unmeasured fixation-process assignment on plant nitrogen. N2 remains a candidate source with a note, not a measured flux.

• Both Medicago arrows remain HYPOTHESIZED with a positive proposed biological route and explicit missing perturbation. Host enzyme induction does not by itself prove ROS clearance or growth mediation. Replace aim-only plant evidence with a plant outcome while preserving original upstream IN_VITRO alias used outside the graph. Host stays external, no invented canonical taxon.

• Fungal root colonization supports broad symbiotic-process context; do not erase it because competition/reciprocal benefit was untested. Six initial species does not establish equal persistence. Spore non-detection is not root extinction, and pooled PCR-TTGE is not quantitative intraradical abundance. Limited host-cover influence is not zero influence. Retain initial canonical roster and exact F.coronatum/F.coronatus distinction without remapping.

• Fungal graph-owned id004/id005 evidence anchors remain valid for untouched environmental aliases. Existing inoculum/protocol discussions remain OPEN and prior #862/#863 evidence/cultivation repairs survive. Public publisher page explicitly subscription-preview only; no paywall bypass or claim of full-body review.

• qSIP retains positive DNA-incorporation growth observations, absorbs the redundant active-community-resolution evidence, and preserves the previous four-arrow deletion. Rewetted eight-day laboratory incubations are not in-field trajectories, AFE is not net growth and low activity is not death. Two Bacteria guild entries overlap and are not a resolved species roster.

• qSIP historical rainfall association is not randomized historical selection. Flagellar genomic capacity is not observed movement, and carbon pathway annotation plus organism growth is not substrate flux or sequestration. Preserve broad negative carbon-capacity selection result alongside Angelo/site/taxon exceptions; do not infer niche partitioning. Predicted motility process retained explicitly as potential.

• Missing qSIP labeled-phage/predicted-host activity deserves separate new-structure review, not a workflow edge. Account for prophage labeling and alternative mortality before any lysis-to-necromass arrow. One-record dry run9469chars is not a report. Its reviewed query contains the pre-repair record context; refresh and inspect the dry run before any later paid submission. #1592 remains OPEN and record needs_research.

• A22ED9 preserves #1009 single-metal naming and positive92.08/74.15/97.587% averages at initialpH5 after24h. Residual ICP-OES after cell separation does not establish final metal speciation, intracellular uptake or unique biosorption. Chromium atom is element-level reporting, not metallic feed; dichromate challenge is explicit. Do not promote pH8 to a universal endpoint.

• A22ED9 primary source reports cell-free controls while also acknowledging missing abiotic partitioning. Preserve reported little-loss controls and the unresolved pH-matched/live-dead comparison, not a false no-controls claim. SEM-EDX examples are individualSK22/SK18-4, not a uniquely consortium-resolved mechanism. Reported compatibility/stimulation is not higher removal; no field validation claimed.

• Missing KHED9-filtrate stimulation of SK22 is separate from metal depletion. Inspect supplementary FigS2/controls and exact strain assignments before extension; shared genus ID does not merge the two strains. One-record dry run9544chars is not a report. Its reviewed query contains the pre-repair record context; refresh and inspect the dry run before any later paid submission. #1593 remains OPEN and record needs_research.

• Read complete biological diff; all unchanged top-level raw non-graph blocks,456 other records and920 caches verified. Append-only record events/history, exact graph names/discussion anchors, and19 independently primary-matched excerpts checked. No new nodes/arrows or paid submissions.

• Measure the participant census before updating the exact USERS registry for the fungal and Bacillus records. Counts460/391/123/268/1507/1240 unchanged. All44 network warnings unchanged exactly, no structural defects and no auditor-rule changes. Named initial participants do not prove partner-resolved mechanisms.

• Actual focused schema/strict/terms/references/snippets/history checks, inventory/rank/network, repeat-render and full combined regression outputs retained with hashes. HTML descriptions parsed over456 pages, not browser screenshots; post-commit docs-current is a separate publication gate.

• Dedup879 all-state issue titles/bodies and22 scoped ignored/hidden local matches. Four matching issue bodies (#382/#862/#863/#1009), relevant history and prior A22ED9 review read, not every local match/PR/comment. #1588-#1591 addressed but OPEN pending protected-main merge; #1592/#1593/#1594 remain OPEN afterward. Self-review is not independent approval or corpus completion.

627 passed in 211.69s (0:03:31); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 72 record snippets match selected caches;19 graph excerpts independently match fresh primary text with whitespace-only normalization.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. Cache MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;19 graph excerpts independently match fresh primary text after whitespace normalization. #1594 metadata and #1592/#1593 research remain OPEN; fungal full text unavailable. Broader #476/#1091/#1095 source limitations persist.

Ten original nodes reviewed;9 retained and1 redundant qSIP workflow node removed. Both Medicago arrows are qualified hypotheses. No new structure or provider spend; two one-record Edison dry runs are not research reports. Canonical taxonomy and raw non-graph blocks preserved, not recertified.456 other records unchanged. Zero structural errors;all44 baseline network findings preserved exactly. Coarse scope census remains460 records,391 with community-level nodes,123 mixed,268 community-only,1507 taxa and1240 solely-rule count; no taxonomy or auditor-rule change. This census does not measure narrowed participant credit.

Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 5bbd1ffb85f27906d74086744df2429d3a3e7f189351134992dd01ff36710a44. Every-node/every-arrow decisions,39 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch69. Corpus220 reviewed /216 pending /24 needs_research: unfinished, not independent approval. qSIP and A22ED9 remain needs_research under #1592/#1593; metadata #1594 remains OPEN.

Protected-main merge pending.

[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, 44 warning across 16 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)

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 integration review at exact head c19c57957cd9818886c84556bea31b163d758f2a. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head fde6a128ac49c8740b7f3827811cc07998f30725, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 5799b33b6b0b10e3eccbb028e653ac5d6df105e542972321d8354c85b2bb4051). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head ec79f2eed34d442a39133adb6043091c819e7ce0
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b87041f7e77cd94f42ffcf34a89e8d27b1be3a5c.
The batch-owned binary patch is byte-identical
(SHA-256 5799b33b6b0b10e3eccbb028e653ac5d6df105e542972321d8354c85b2bb4051); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial governance integration review at exact head 307c5eb3cc09f654863aaacedf8fe2099ccb3b25. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head ec79f2eed34d442a39133adb6043091c819e7ce0, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 5799b33b6b0b10e3eccbb028e653ac5d6df105e542972321d8354c85b2bb4051). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at fed573d4aab957f225f546cf88e35c1aed7e7920.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 5799b33b6b0b10e3eccbb028e653ac5d6df105e542972321d8354c85b2bb4051.
Tree 1e7b3b36d31fe70cba7009f099ce83458a769d25 matches the independently computed clean merge.
Compared with historical tree d35c2b1fa0df9335d67af72d11b15d4ce27203d7, 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 4e55aee42b39702fc696f049690eb43d14f769d3 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.