Fixes
- fix: restore module-level extension discovery —
_discover_extensions()was accidentally moved insidemain()in the recent lean-out refactor (eb78378), which meant it ran after@hydra.mainhad already composed configs. All extension search paths (omics popgen, singlecell, dogma) were silently invisible to Hydra. Moved back to module level.
Tests
- 16-test integration suite (
tests/test_extension_discovery.py) — entry-point contract, plugin registration, idempotency, error tolerance, AST-based guards that verify the call stays at module level, omics-specific checks, and core plugin coexistence.