Upgrade skills_sync manifest to v2 format (name:origin_hash). The origin
hash records the MD5 of the bundled skill at the time it was last synced.
On update, the user's copy is compared against the origin hash:
- User copy == origin hash → unmodified → safe to update from bundled
- User copy != origin hash → user customized → skip (preserve changes)
v1 manifests (plain names) are auto-migrated: the user's current hash
becomes the baseline, so future syncs can detect modifications.
Output now shows user-modified skills:
~ whisper (user-modified, skipping)
27 tests covering all scenarios including v1→v2 migration, user
modification detection, update after migration, and origin hash tracking.
2009 tests pass.
4f56e31dc7