Flush emptiness caches whenever needed
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
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