Editing a note in a stacked note saved cache without the path, so
store.files never received the new SHA and lookups went stale. Pass the
path through, and make addFile dedup by path as well as SHA so an edit
(same path, new SHA) replaces the old entry instead of duplicating it.
Resolves conflict in repo.spec.ts by combining getRepoPermission
tests from main with the getFiles and queryFileContent tests from
the local test pass. Adds getRepoPermission to the userRepo.store
spec mocks so the new permission probe added upstream doesn't break
the store tests.