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/04_connectivity_scoring.ipynb

@@ -0,0 +1,48 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 04 \u2014 Connectivity scoring\n",
+    "\n",
+    "Week 3 (PLAN.md \u00a76). CMap-style connectivity scoring of every drug against the sickle cell signature. Strongly negative connectivity = strong reversal = candidate.\n\nOutputs `data/results/ranked_candidates_v1.csv`. Also build the secondary mechanistically-weighted ranking. Document the gene-overlap count; mark signature-less drugs as 'not scored' rather than dropping them."
+   ]
+  },
+  {
+   "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 scoring\n",
+    "\n",
+    "# Load signature + drug profiles, then:\n",
+    "# ranking = scoring.rank_drugs(up, down, drug_profiles)\n",
+    "# scoring.persist_ranking(ranking) -> data/results/ranked_candidates_v1.csv"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}