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>

notebooks/02_disease_signature.ipynb

@@ -0,0 +1,50 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 02 \u2014 Disease signature\n",
+    "\n",
+    "Week 1 (PLAN.md \u00a76). Pull Open Targets + a GEO expression study, run differential expression, and build `sickle_cell_signature_v1.json` (Tier A) with full provenance.\n\nSteps: (1) Open Targets associations, (2) choose + download GEO dataset, (3) differential expression, (4) build + persist signature.\n\n**Pitfall to document:** whole-blood expression is partly driven by cell-composition differences, not disease state (PLAN.md \u00a79.1)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.insert(0, '..')  # import the src package from notebooks/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from src import disease\n",
+    "from src.provenance import ConfidenceTier\n",
+    "\n",
+    "# Step 1: Open Targets associations for MONDO:0011382  -> data/raw/open_targets/\n",
+    "# Step 2: choose + download GEO study (GSE53441 / GSE35007 / newer) -> data/raw/geo/\n",
+    "# Step 3: disease.compute_differential_expression(...)\n",
+    "# Step 4: disease.build_signature(...) then disease.persist_signature(...)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}