style: apply ruff lint --fix + ruff format across the tree

Dedup: extract subset_and_require_group shared by activity_stats + microarray

Lint cleanup: remove unused imports, empty f-strings, split import lines

HF wheel registry, pinned deps, apt probe, security scan, API-key fallback

Refactor manifest/metadata to separate semantics from runtime counts

Added seperate files, added tests

Add PDAC dataset adapter, workflow, semantic, and analysis layers