cmdPhasesClear hard-deleted committed phase directories (rmSync) with no
archive, so browsable phase history was silently lost at a milestone switch.
The #1447 dirty-tree guard was a no-op for the common committed case (a clean
tree passes the guard, then rmSync destroyed the dirs, leaving orphaned
uncommitted deletions and no archive).
Archive-then-remove: move each non-999 phase dir to
milestones/<version>-phases/ (version from getMilestoneInfo; timestamp
fallback; collision-safe) using retryRenameSync — mirroring the existing
archivePhases path in cmdMilestoneComplete. The #1447 uncommitted-changes
guard is retained as a secondary backstop.
Tests in tests/new-milestone-clear-phases.test.cjs updated: phase content is
asserted to SURVIVE in milestones/*-phases/ (archived), not be destroyed —
including the committed-dirs case that previously codified the no-op.
Closes#1871
