docs(phase-04): complete phase execution

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2026-02-11 21:01:50 +08:00
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See: .planning/PROJECT.md (updated 2026-02-11)
**Core value:** Produce a high-confidence, multi-evidence-backed ranked list of under-studied cilia/Usher candidate genes that is fully traceable — every gene's inclusion is explainable by specific evidence, and every gap is documented.
**Current focus:** Phase 4 in progress — Scoring and Integration
**Current focus:** Phase 4 complete — ready for Phase 5
## Current Position
Phase: 4 of 6 (Scoring and Integration)
Plan: 3 of 3 in current phase (complete)
Status: Phase 04 complete — CLI score command and comprehensive test coverage
Last activity: 2026-02-11 — Completed 04-03-PLAN.md
Phase: 4 of 6 (Scoring & Integration)
Plan: 3 of 3 in current phase (phase complete)
Status: Phase 4 complete — verified (14/14 must-haves, 5/5 requirements)
Last activity: 2026-02-11 — Phase 4 verified and complete
Progress: [████████░░] 75.0% (15/20 plans complete across all phases)
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## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 04-03-PLAN.md (CLI score command and comprehensive tests)
Resume file: .planning/phases/04-scoring-integration/04-03-SUMMARY.md
Last session: 2026-02-11 - Phase 4 execution
Stopped at: Phase 4 complete and verified — all 3 plans executed, 14/14 must-haves verified
Resume file: .planning/phases/04-scoring-integration/04-VERIFICATION.md