docs(todo): mark ADR-0001 T7/T8/T9 (Mode A) done; T11 unblocked

Built on branch adr-0001-phase-2-mode-a (a7a8caa); not deployed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

TODO.md

@@ -74,11 +74,18 @@ refuse, driven by registry metadata. ADR + plan + per-task spin-off prompts in
   4-case gradio_client eval on dev: refuse ✅ / early→late-fallback no-fabrication ✅
   / late no-pooling ✅ / `decoupler_meta_analyze` positive path ✅ (paca_au_rnaseq +
   paca_au_array). Q/I² reporting polish (`c54b550`). registry re-pinned 0.1.3.
-- **Med — T7: `src/workflows/integration.py`** concat + batch AnnData (Mode A core).
-- **Med — T8: `batch_column` on DE** — DESeq2 `~batch+condition` + `run_limma` design-matrix refactor.
-- **Med — T9: `decoupler_integrate_datasets`** behind confound guard (needs T7/T8/T4).
+- **Done — T7: `src/workflows/integration.py`** combined-AnnData builder (gene-symbol
+  intersect + `batch` obs key = dataset_id); pure `combine_anndatas` + loader
+  `build_combined_anndata`. Branch `adr-0001-phase-2-mode-a` (`a7a8caa`), NOT deployed.
+- **Done — T8: `batch_column` on the DE tool** — DESeq2 `~batch + factor`; new
+  `run_limma_covariate` (`~batch + group`) in microarray.py; ttest+batch refused (no
+  silent covariate drop). Back-compat default off. (`a7a8caa`.)
+- **Done — T9: `decoupler_integrate_datasets`** (3rd integration_mcp tool, server
+  52→53) — pools + one batch-aware DE only on plan mode=="early"; refuses/reroutes for
+  late/concordance/refuse; auto-picks deseq2 (raw counts) / limma. (`a7a8caa`.) v1
+  limits: gene-symbol axis only (no probe collapse/ortholog); ComBat (T11-opt) deferred.
 - **Low — T10: orchestrator routing + capability + reporting rules** (pdac-analysis-orchestrator).
-- **Low — T11: cross-dataset evals** (pool/fallback/refuse; needs T5/T9).
+- **Low — T11: cross-dataset evals** (pool/fallback/refuse; needs T5/T9) — now unblocked (T9 done).
 
 ### ADR housekeeping (reconciled 2026-06-24)