Update behavior for untracked contained repositories

When a directory inside a repository that itself contained a `.git` entry was found, libgit2 was going out of its way to treat it specially.  This seemed like it was necessary only 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.