- SUMMARY.md: CLI orchestration with checkpoint-restart + 10 comprehensive tests - STATE.md: Updated position (Phase 4 complete), progress (75%), velocity, decisions - Duration: 3 minutes, 2 tasks, 4 files (3 created, 1 modified)
- Add SUMMARY for quality control and positive control validation - Update STATE.md: Plan 2 of 3 in Phase 04 complete - Progress: 70% (14/20 plans complete) - Decisions: scipy MAD outlier detection, PERCENT_RANK validation
- Known genes: 38 (10 OMIM Usher + 28 SYSCILIA SCGS v2 core) - ScoringWeights.validate_sum() enforcing weight sum = 1.0 - NULL-preserving weighted average (weighted_sum / available_weight) - Quality flags based on evidence_count thresholds - Per-layer contributions for explainability - 2 tasks, 4 files, 4 min duration
