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>

docs/known_limitations.md

@@ -0,0 +1,39 @@
+# Known Limitations
+
+The honest list of what would break this MVP at scale or in a different disease. Useful for the
+next pharma conversation: "yes, we know these are limitations, here's how v2 addresses them."
+Source: PLAN.md §9.
+
+1. **Cell-composition confound in sickle cell expression data.** Whole-blood differential
+   expression partly reflects different blood cell ratios, not disease biology. v1 acknowledges
+   this; v2 should deconvolve cell types.
+
+2. **LINCS L1000 cell-line limitations.** The 978 landmark genes were measured mostly in cancer
+   cell lines (MCF7, A375, PC3, …). Signatures for non-oncology diseases may be noisy. A
+   field-wide limitation, not unique to Reverso.
+
+3. **L-glutamine probably has no LINCS signature.** Amino acids and metabolites weren't LINCS
+   priorities. If true, the ground-truth test effectively rests on hydroxyurea alone, which is
+   weaker. _Status: TBD — record the actual finding here once LINCS is pulled (Week 2)._
+
+4. **Connectivity scoring surfaces broad-effect drugs as false positives.** HDAC inhibitors and
+   broad kinase inhibitors often top connectivity rankings simply because they perturb many
+   genes. The mechanistic prior (Week 3) helps filter, but does not eliminate this.
+
+5. **Hydroxyurea will probably pass the recovery test by construction.** Sickle cell +
+   hydroxyurea is a well-studied pair. Passing is necessary but not sufficient to claim the
+   platform generalizes. The next disease is the real test — do not sell sickle cell results as
+   proving the platform.
+
+6. **No mechanistic validation layer.** Pure ML matching is not sufficient for extrapolation
+   (flagged by multiple experts). The MVP knowingly omits the mechanistic layer; it is a phase-2
+   addition. Position the MVP as "discovery hypothesis generation," not "validated prediction."
+
+7. **Top-ranked novel candidates are not wet-lab validated.** They are computational hypotheses
+   to test, not discoveries. Use careful language in any write-up.
+
+## Drug-specific gaps (fill in during Week 2–3)
+
+| Drug | Issue | Handling |
+|---|---|---|
+| TBD | e.g. no LINCS signature | flagged "not scored, no signature available" |