Fixes from trek-e's review on PR #1282:
1. Add missing withProjectRoot() wrapper on output — all other cmdInit*
functions include project_root in JSON, manager was the only one without it.
2. Add getMilestonePhaseFilter() to directory scan — prevents stale phase
directories from prior milestones appearing as phantom dashboard entries.
3. Replace hardcoded .planning/ paths with planningPaths(cwd) — forward
compatibility with workstream scoping (#1268).
4. Add 3 new tests:
- Conflict filter blocks dependent phase execution when dep is active
- Conflict filter allows independent phase execution in parallel
- Output includes project_root field
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
f7031e2f20