marcus.salinas f7031e2f20 fix(manager): address review — withProjectRoot, milestone filter, planningPaths ...

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>

2026-03-21 09:13:32 -05:00

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