phases clear now checks for phase dirs before deleting. If any exist and
--confirm is absent, the command exits non-zero with a message showing the
count and how to proceed. Empty phases dir (nothing to delete) succeeds
without --confirm unchanged.
Updates new-milestone.md workflow to pass --confirm (intentional programmatic
caller). Updates existing new-milestone-clear-phases tests to match new API.
Closes#1826
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>