v2.1.0

2.1.0

New Commands

• bactopia-sysinfo - auto-detect host resources and emit Nextflow --max_memory/--max_cpus overrides for local profiles
• bactopia-docs - validate reference documentation for deprecated patterns (D0xx) and ground-truth assertions (D1xx)

New Lint Modules

• bactopia/lint/citations.py - cross-repository citation validation: orphan detection, missing workflow @citation keys, provenance-only filtering
• bactopia/lint/docs.py - documentation staleness checker: deprecated pattern detection, count/version/reference assertions, skill inventory sync

Enhancements

• bactopia-citations gains --validate flag for citation integrity checking with Rich table output and --json for CI
• bactopia-catalog expanded output to better support Claude Code skills on the Bactopia side
• bactopia-merge-schemas minor fix for schema merging
• Updated GroovyDoc parser in nf.py to handle Nextflow 25.04.6+ syntax (record(), stage: block, balanced-paren inputs)
• Module lint rule M018 updated for both legacy and current meta initialization patterns

New Dependencies

• psutil >=5.9.0 (used by bactopia-sysinfo)

Tests

• 19 tests for bactopia-sysinfo (eligibility, profile gating, flag parsing)
• 25 tests for citation linting (orphan detection, provenance filtering, potential homes)
• 60+ tests for docs linting (D0xx/D1xx rules, inline ignores, CLI integration)