Scaffold Reverso MVP pipeline structure

Set up the project skeleton per PLAN.md §4:
- src/ package: identifiers, disease, drugs, scoring, provenance
  with pydantic schemas and confidence-tier logic (working);
  data-pull/compute functions stubbed per their build week
- 5 starter notebooks (01-05) with PLAN-referenced steps
- tests/test_scoring.py: tier-assignment tests pass; scoring
  reference test xfail until Week 3
- docs/: recovery_test_report, data_sources, known_limitations skeletons
- pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README
- data/ tree preserved via .gitkeep; raw/processed/results gitignored

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

README.md

@@ -1 +1,48 @@
-# Reverso
+# Reverso MVP — Sickle Cell Repurposing Pipeline
+
+A minimum viable drug repurposing pipeline for **sickle cell disease**: build a disease
+signature from public transcriptomic data, build drug profiles for ~300 small molecules,
+and rank them by CMap-style connectivity scoring. Validated by a recovery test — do the two
+known sickle cell drugs (hydroxyurea, L-glutamine) rank near the top?
+
+See [`PLAN.md`](PLAN.md) for the full specification, locked decisions, and week-by-week build plan.
+
+## Quickstart
+
+```bash
+# Requires Python >=3.11,<3.13 (see note below)
+pip install -e .            # or: pip install -e ".[dev]" for test/lint tooling
+pytest                      # run unit tests
+```
+
+> **Python version note:** use Python 3.11–3.13 (`python3.13 -m venv .venv`). Python 3.14 is
+> not yet supported by all pipeline dependencies (`pydeseq2`, `cmapPy`).
+
+## Project layout
+
+```
+data/         raw (downloaded, never edited) / processed / results — gitignored
+notebooks/    01..05, run end-to-end in order
+src/          identifiers, disease, drugs, scoring, provenance
+tests/        scoring unit tests
+docs/         recovery_test_report.md, data_sources.md, known_limitations.md
+```
+
+## The deliverable
+
+When complete, the artifact to share is three files:
+1. `docs/recovery_test_report.md` — the 2-page write-up
+2. `data/results/ranked_candidates_v1.csv` — the ranked drug list
+3. The signature + drug profile files with provenance
+
+## Pipeline
+
+| Notebook | Stage | Output |
+|---|---|---|
+| `01_setup_identifiers.ipynb` | Pin disease/gene IDs | `data/processed/identifiers.json` |
+| `02_disease_signature.ipynb` | GEO + differential expression | `sickle_cell_signature_v1.json` |
+| `03_drug_profiles.ipynb` | ChEMBL + LINCS | `drug_profiles_v1.parquet` |
+| `04_connectivity_scoring.ipynb` | CMap scoring | `ranked_candidates_v1.csv` |
+| `05_recovery_test.ipynb` | Validation | `docs/recovery_test_report.md` |
+
+Every persisted artifact carries a **confidence tier** (A/B/C) and provenance. See `PLAN.md` §3.