Resolve "Notes API for issues no longer returns label additions/removals"

Closes #39461

See merge request gitlab-org/gitlab-ce!15080

(cherry picked from commit f562e69e)

4374a38f fix the commit reference pattern from matching other entities
160324d0 try to fix the failing spec on external refs
71b2cc1d reverting to the simpler approach
869fc05d fix the linting error
9ed91479 add the missing spec
c900c21e add `#with_metadata` scope to remove a N+1 from the notes' API