fix(scoring): resolve gene symbols from var; never let a sample filter no-op

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

ADR-0001 Phase 2 Mode A: early integration (T7 + T8 + T9)

fix: load bulk-dataset h5ad/CSV from URLs, not just local paths

Dedup: extract subset_and_require_group shared by activity_stats + microarray

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

Replace rpy2 limma bridge with Rscript subprocess — fixes all conversion errors

Fix run_limma: rename R globals from _lm_ to .lm_ (R names can't start with underscore)

Rewrite run_limma: build design matrix in R to fix non-conformable arrays

Broaden rpy2 converter fallback to catch TypeError in addition to AttributeError

Fix limma: wrap all numpy→R and R→pandas ops in localconverter

Fix limma: replace deprecated rpy2 .activate() API with localconverter

Remove dead code and standardize MCP tool return schemas

Added seperate files, added tests

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