This ensures that the emptiness cache (used for Repository#empty? and
Repository#has_visible_content?) is flushed after comitting changes
(using the web editor, API or Git) for new repositories. Once a
repository is no longer empty there's no need to explicitly flush the
cache for Repository#empty?. The cache for
Repository#has_visible_content? in turn is already flushed whenever
needed.

Fixes gitlab-org/gitlab-ce#13387