[codex] curate 50 synthetic communities

[cmungall]

Summary

• Add 50 new synthetic/community model records under kb/communities, with IDs CommunityMech:000079 through CommunityMech:000128.
• Prioritize DOE/BER-adjacent curation areas including rhizosphere, lignocellulose, bioremediation, methane/nitrogen cycling, LBNL/GLBRC/ORNL-style model systems, and plant-microbe SynComs.
• Add the cited PubMed reference-cache files needed to support the new evidence snippets.

Validation

• just validate-all passed for all 128 community YAML files.
• Term validation passed for all 50 new community YAML files.
• Cache-backed evidence audit checked 71 unique PMID snippets from the new records with 0 failures.
• ID audit found 128 unique, gapless IDs from CommunityMech:000001 through CommunityMech:000128.

Test Notes

• just test was run: 90 passed, 10 failed, 7 deselected.
• Failures appear unrelated to this YAML curation: one existing embedding aggregation expectation and nine Anthropic-client tests failing because the anthropic package is unavailable in this environment.