Fix repository safety, test, documentation, and CI contracts

[realmarcin]

Summary

• make just clean remove only disposable outputs and guard against tracked-file deletion
• restore normal import and out-of-root subprocess behavior for the provider changes
• make provider CI deterministic with pinned uv tooling, frozen installs, path coverage, and Python 3.13 compatibility testing
• rebuild README commands, links, and YAML examples from executable repository behavior
• rewrite CLAUDE.md as a stable operational guide with contract tests

Validation

• full suite before the final rebase: 2,563 passed, 89 skipped, 8 deselected
• affected contracts after rebasing onto the current Fix Edison sidecar provenance, drop malformed citation sidecar, KNOWN_BLOCKED provider #662 head: 243 passed, 6 skipped
• Black, Ruff, mypy, and git diff --check pass

Stacking

This PR is stacked on #662 so it contains only the remediation commits. #668 remains open for the human packaging/runtime decision; the documentation describes the current checkout-dependent behavior without selecting the long-term architecture.

Closes #663
Closes #664
Closes #665
Closes #666
Closes #667
Refs #668
Refs #669

[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, 55 warning across 27 records with findings
Only error-severity findings fail the build.

ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia
--------------------------------------------------------------------------------
  [warning] NAME_MISMATCH: Source 'ANME-1' matches no taxonomy entry by name; resolved to 'ANME-1 (anaerobic methanotrophic archaea, clade 1)' by source_id NCBITaxon:588814
  [warning] NAME_MISMATCH: Target 'Desulfofervidus' matches no taxonomy entry by name; resolved to 'Desulfofervidus (sulfate-reducing bacterial partner of ANME-1)' by target_id NCBITaxon:1902583
  [warning] NAME_MISMATCH: Source 'ANME-2a' matches no taxonomy entry by name; resolved to 'ANME-2a (anaerobic methanotrophic archaea, clade 2a)' by source_id NCBITaxon:588816
  [warning] NAME_MISMATCH: Target 'Seep-SRB1' matches no taxonomy entry by name; resolved to 'Seep-SRB1 (sulfate-reducing bacterial partner of ANME-2a)' by target_id NCBITaxon:213119
  [warning] NAME_MISMATCH: Source 'ANME-2c' matches no taxonomy entry by name; resolved to 'ANME-2c (anaerobic methanotrophic archaea, clade 2c)' by source_id NCBITaxon:3386252
  [warning] NAME_MISMATCH: Target 'Seep-SRB2' matches no taxonomy entry by name; resolved to 'Seep-SRB2 (additional sulfate-reducing bacterial partner)' by target_id NCBITaxon:213118

Total: 6 issues (0 error, 6 warning)

Aalborg_East_Full_Scale_EBPR_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacteroidetes flanking community members' has no interactions
  [warning] DISCONNECTED: Taxon 'Tetrasphaera-related actinobacterial PAOs' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Desulfovibrio piger comparator' has no interactions

Total: 1 issues (0 error, 1 warning)

BioModels_MODEL2204300001_Kefir_Community_Model
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Lactobacillus kefiri' has no interactions
  [warning] DISCONNECTED: Taxon 'Lactococcus lactis' has no interactions

Total: 2 issues (0 error, 2 warning)

BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacteroides ovatus' has no interactions
  [warning] DISCONNECTED: Taxon 'Bacteroides vulgatus' has no interactions
  [warning] DISCONNECTED: Taxon 'Bifidobacterium bifidum' has no interactions
  [warning] DISCONNECTED: Taxon 'Bifidobacterium breve' has no interactions
  [warning] DISCONNECTED: Taxon 'Blautia producta' has no interactions
  [warning] DISCONNECTED: Taxon 'Enterococcus faecalis' has no interactions
  [warning] DISCONNECTED: Taxon 'Escherichia coli K-12' has no interactions
  [warning] DISCONNECTED: Taxon 'Lacticaseibacillus rhamnosus' has no interactions
  [warning] DISCONNECTED: Taxon 'Ruminococcus gnavus' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus thermophilus' has no interactions

Total: 10 issues (0 error, 10 warning)

Crucian_Carp_Gut_Disease_Resistance_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Aeromonas hydrophila' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Drosophila five-species bacterial microbiota' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'core floodplain bacteria' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_SOURCE: Source taxon 'East River floodplain bacteria' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Chryseobacterium sp. MF1' has no interactions

Total: 1 issues (0 error, 1 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Olsenella (Actinobacteriota)' not found in taxonomy section (community-level scope)
  [warning] NAME_MISMATCH: Target 'Clostridium (Firmicutes)' matches no taxonomy entry by name; resolved to 'Clostridium_B sp. (MAG CLOS1)' by target_id NCBITaxon:1485

Total: 2 issues (0 error, 2 warning)

Hanford_300_Area_Unconfined_Aquifer_Community
--------------------------------------------------------------------------------
  [warning] NAME_MISMATCH: Source 'intrusion-associated Actinobacteria' matches no taxonomy entry by name; resolved to 'Actinobacteria/Actinomycetota aquifer bacteria' by source_id NCBITaxon:201174
  [warning] UNKNOWN_TARGET: Target taxon 'Hanford groundwater bacteria' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_SOURCE: Source taxon 'aquifer redox guild bacteria and archaea' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

High_Solids_Switchgrass_Methanogenic_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Bacilli' has no interactions

Total: 1 issues (0 error, 1 warning)

KB1_Chlorinated_Ethene_Dechlorinating_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Sporomusa spp. in KB-1' has no interactions

Total: 1 issues (0 error, 1 warning)

Legume_Rhizobia_Mars_Simulant_Symbiosis
--------------------------------------------------------------------------------
  [warning] NAME_MISMATCH: Source 'Sinorhizobium spp. (rhizobial symbionts)' matches no taxonomy entry by name; resolved to 'Sinorhizobium meliloti' by source_id NCBITaxon:382
  [warning] UNKNOWN_TARGET: Target taxon 'Medicago truncatula (host legume)' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Lunar_Martian_Simulant_PGPB_Lettuce_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Lactuca sativa (lettuce host)' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Lactuca sativa (lettuce host)' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Nicotiana benthamiana' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'model lignocellulose consortium members' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'model lignocellulose consortium members' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Moss_Microbe_Complex_Regolith_Biofertilizer
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Hypnum plumaeforme (moss host)' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Hordeum vulgare (barley model crop)' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'three-species model community' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'other groundwater bacteria' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

PET_Artificial_FourSpecies_Degradation_Consortium
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'engineered PETase/MHETase and TPA-utilization members' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

PMI_Variovorax_Thermotolerance_Collection
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Variovorax' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Arabidopsis thaliana' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Rice_Duckweed_Bacillus_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Bacillus SynCom' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Rhizoctonia solani' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Saanich_Inlet_OMZ_Redox_Gradient_Community
--------------------------------------------------------------------------------
  [warning] UNKNOWN_SOURCE: Source taxon 'Saanich Inlet redox-gradient microorganisms' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'anode-associated biofilm community' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'anode' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Sulfide_Spring_Autotrophic_CPR_Biofilm
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Beggiatoa' has no interactions

Total: 1 issues (0 error, 1 warning)

Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Pseudomonas aeruginosa' not found in taxonomy section (community-level scope)

Total: 1 issues (0 error, 1 warning)

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