When a new bundled skill's name collided with a pre-existing user skill
(from hub, custom, or leftover), sync_skills() recorded the bundled hash
in the manifest even though the on-disk copy was unrelated to bundled.
On the next sync, user_hash != origin_hash (bundled_hash) marked the
skill as "user-modified" permanently, blocking all bundled updates for
that skill until the user ran `hermes skills reset`.
Fix: only baseline the manifest entry when the user's on-disk copy is
byte-identical to bundled (safe to track — this is the reset re-sync or
coincidentally-identical install case). Otherwise skip the manifest
write entirely: the on-disk skill is unrelated to bundled and shouldn't
be tracked as if it were.
This preserves reset_bundled_skill()'s re-baseline flow (its post-delete
sync still writes to the manifest when user copy matches bundled) while
fixing the poisoning scenario for genuinely unrelated collisions.
Adds two tests following the existing test_failed_copy_does_not_poison_manifest
pattern: one verifying the manifest stays clean after a collision with
differing content, one verifying no false user_modified flag on resync.
3a97fb3d47