repo: Port -refs.c to openat()

I'd like to incrementally convert all of `ostree-repo*.c` to
fd-relative usage, so that we can sanely introduce
`ostree_repo_new_at()` which doesn't involve GFile.

This one is medium risk, but passes the test suite.

src/libostree/ostree-repo-private.h

@@ -50,8 +50,6 @@ struct OstreeRepo {
   int    repo_dir_fd;
   GFile *tmp_dir;
   int    tmp_dir_fd;
-  GFile *local_heads_dir;
-  GFile *remote_heads_dir;
   GFile *objects_dir;
   GFile *state_dir;
   int objects_dir_fd;