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

ADR-0001 Phase 1, steps 5-6 (T5): decoupler_meta_analyze + A->B->refuse wiring

Phase 1: Add decoupler_load_url_counts for flat matrix loading

Revert HTTP tool-call approach; fix rpy2 threading race

Reduce redundant tool calls and pre-warm limma at startup

Eliminate per-call subprocess overhead with persistent HTTP MCP server

Add in-memory dataset cache to eliminate GEO re-downloads

Flatten mcp/ folder and move mcp_server/ into src/