Update behavior for untracked sub-repos

When a directory containing a .git directory (or even just a plain
gitlink) was found, libgit2 was going out of its way to treat it
specially.  This seemed like it was necessary because the diff
code was not originally emulating Git's behavior for untracked
directories correctly (i.e. scanning for ignored vs untracked items
inside).  Now that libgit2 diff mimics Git's untracked directory
behavior, the special handling for contained Git repos is actually
incorrect and this commit rips it out.
Merge pull request #2205 from libgit2/rb/submodule-untracked-vs-ignored

Update behavior for untracked contained repositories