fix(scoring): close the six PROGENy per-sample gaps from the GSE205154 eval

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

feat(loveless): ADR-0006 + agent-side sc serving scaffold

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

Remove dead code and standardize MCP tool return schemas

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