Make sure git will recognize *.git as repositories, even empty ones, after restore
On restore we were initializing refs/ and objects/ for repositories obtained from backuped refs set, but this approach does not cover empty repositories - e.g. repositories without any ref at all. A frequent case for this is *.wiki.git in gitlab, and if we restore only files for such repo, without empty refs/ and objects/ it would look like restored ok, but any git-related operation on such repo will fail. Fix it via making sure to create refs/ and objects/ the first time we see a *.git while restoring files. /cc @kazuhiko
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