feat(uploads): ADR-0011 manual-upload safety gate (Now slice)

Merge feat/configurable-log-sink: always-on audit log sink (ADR-0008 + ADR-0009)

fix(rna_sc): harden load/visualize UMAP against missing embedding/leiden (#1)

feat(logging): implement S3 log sink (ADR-0009 Phase 1)

feat(loveless): Role-2 signature consumable — resolve private signature URLs

Add configurable, always-on execution-trace log sink (local|hf|s3)

feat(loveless): integrate biodata-registry 0.1.8 sc datasets (Path P by modality)

feat(loveless): sc loaders resolve hosted/private h5ad URLs (ADR-0006)

feat(loveless): ADR-0006 #6 — h5ad source type + Path P loading plan

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

perf(mcp): HTTP transport core — add_mcp_http on agent/tool_manager + adata cache + instrumentation

perf(mcp): wire persistent HTTP MCP server + in-memory adata cache + step timing

fix(loader): authenticate h5ad loads in dataset metadata tools

feat(integration): ComBat per-sample scoring tool decoupler_pool_cohorts (ADR-0001 item 10)

refactor(loader): centralize authenticated URL->local resolution

fix(loader): authenticate huggingface.co downloads via HF_TOKEN

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

feat(concordance): same-cohort normalization concordance routine (decoupler_normalization_concordance)

fix(loaders): accept http(s)/ftp URLs in bulk dataset loaders

feat(sanity): ADR-0002 Phase 2 — auto-fire tissue-identity contamination + PROGENy/Hallmark parity

feat(sanity): ADR-0002 Layer-2 result-aware sanity layer (Phase 1 + S1)

fix: resolve CollecTRI TF symbols + restore igraph network plot

Surface per-dataset preprocessing + re-pin biodata-registry 0.1.5

feat: hide microarray from advertised inventory + plain-language Approach in solutions

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

ADR-0001 Phase 1, step 3 (T4): dataset_get_integration_plan wrapper + 0.1.2 re-pin

ADR-0001 Phase 1, step 4: meta-analysis engine (Mode B late integration)

ADR-0001 Phase 1, step 1: declare Mode-B combine conformance on rna tools

ADR-0001 Phase 0: cross-dataset integration contract + specs

UI exports: fix angle-bracket content loss; embed plots in downloads

UI: save a full-run PDF to the results repo alongside md/json

Fix: raise on MCP tool errors instead of returning error text as a string

Split bulk_rnaseq.py (1073) into a package preserving the public API

Split dataset_tools.py (1709) into a package preserving the public API

Security: replace pickle GPL cache with JSON; document accepted exec risk

Dedup: extract subset_and_require_group shared by activity_stats + microarray

Suppress star-import lint noise in rna package (file-level noqa)

Split rna.py (1847 lines) into an rna/ package preserving the public API

Mark planned survival-stub params as intentionally unused (vulture)

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

Extract _resolve_env_vars from MCPManager.add_mcp (CC 31->26, out of E)

Refactor decoupler_join_clinical_metadata: extract helpers (CC 36->15)

Refactor dataset_count_metadata_values: extract helpers (CC 38->14)

Refactor DatasetManifest.validate into per-concern helpers (CC 34->1)

Code-quality fixes: dead assignments, redundant imports, MD5 intent, type hints

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

Stage: pinned deps, API-key fallback, apt probe, security scan

Make decoupleR method-limitations text deterministic

Add probe-collapse precompute Phase 2 (collapsed_url support)

Fix 4 GPL-annotation fallback edge cases + 2 integration test bugs