repo: Change the pairs of checksums to instead be based on OstreeRepoFiles

We want an OstreeRepoFile to be the way to reference a "filesystem
tree" that's stored in the repo, which is a combination of a DIR_TREE
and a DIR_META. The idea is that once you write an mtree to the repo
using ostree_repo_write_mtree, it becomes serialized and you get an
OstreeRepoFile in return.

Change any APIs that care about DIR_TREE / DIR_META checksums to care
about OstreeRepoFiles instead, which right now is mostly is
ostree_repo_write_commit.

https://bugzilla.gnome.org/show_bug.cgi?id=707727

src/libostree/ostree-repo-private.h

@@ -116,5 +116,10 @@ _ostree_repo_file_new_for_commit (OstreeRepo  *repo,
                                   const char  *commit,
                                   GError     **error);
 
+OstreeRepoFile *
+_ostree_repo_file_new_root (OstreeRepo  *repo,
+                            const char  *contents_checksum,
+                            const char  *metadata_checksum);
+
 G_END_DECLS