fix(schema): port the survival-only group_columns exemption from biodata-registry

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

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

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, step 3 (T4): dataset_get_integration_plan wrapper + 0.1.2 re-pin

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

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

Add dataset_filter_to_curated_samples tool and loading plan integration

Add decoupler_load_gdc_star_counts; pivot tcga_paad to Path A / DESeq2

Add covariate to VALID_COLUMN_ROLES; update CLAUDE.md to current state

Add dataset_disclaimer field; assert it in TCGA-PAAD contract test

Phase 4: TCGA-PAAD manifest, integration tests, schema fix

Remove local manifest copies; expand list_available_datasets with full fields

Point dataset registry to biodata-registry package as canonical source

Add YAML manifests for four GEO PDAC microarray datasets

Improve agent accuracy: guardrails, routing rules, and workflow examples

Set limma as preferred DE method for Moffitt with ttest fallback

Complete Moffitt manifest cleanup: all 8 semantic rules applied

Clean Moffitt semantic adapter: semantics only, no observed facts

Improve dataset_count_metadata_values single-column UX

Refactor manifest/metadata to separate semantics from runtime counts

Fix subset_query: non-tumor samples have empty string not 'NA'

Fix schema and tests to match verified GSE71729 manifest

Verify and finalise GSE71729 Moffitt manifest from live data

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