Tom Boucher 53b9fba324 fix: stale phase dirs corrupt phase counts; stopped_at overwritten by historical prose (#2459) ...

* fix(sdk): extractCurrentMilestone Backlog leak + state.begin-phase flag parsing

Closes #2422
Closes #2420

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(#2444,#2445): scope stopped_at extraction to Session section; filter stale phase dirs

- buildStateFrontmatter now extracts stopped_at only from the ## Session
  section when one exists, preventing historical prose elsewhere in the
  body (e.g. "Stopped at: Phase 5 complete" in old notes) from overwriting
  the current value in frontmatter (bug #2444)
- buildStateFrontmatter de-duplicates phase dirs by normalized phase number
  before computing plan/phase counts, so stale phase dirs from a prior
  milestone with the same phase numbers as the new milestone don't inflate
  totals (bug #2445)
- cmdInitNewMilestone now filters phase dirs through getMilestonePhaseFilter
  so phase_dir_count excludes stale prior-milestone dirs (bug #2445)
- Tests: 4 tests in state.test.cjs covering both bugs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

2026-04-20 10:08:43 -04:00

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