Two bugs in sync_skills():
1. Failed copytree poisons manifest: when shutil.copytree fails (disk
full, permission error), the skill is still recorded in the manifest.
On the next sync, the skill appears as "in manifest but not on disk"
which is interpreted as "user deliberately deleted it" — the skill
is never retried. Fix: only write to manifest on successful copy.
2. Failed update destroys user copy: rmtree deletes the existing skill
directory before copytree runs. If copytree then fails, the user's
skill is gone with no way to recover. Fix: move to .bak before
copying, restore from backup if copytree fails.
Both bugs are proven by new regression tests that fail on the old code
and pass on the fix.
211b55815e