Fix skipping content of contained repos

When doing a diff for use in status, we should never show the
content of a git repository contained inside another one.  The
logic to do this was looking for a .git directory and so when a
gitlink plain .git file was used, it was failing to exclude the
directory content.
New tests of status for repo inside repo
Merge pull request #2233 from libgit2/rb/fix-untracked-repo-status

Skip untracked contained repo contents even with gitlink files