repo-file: Base OstreeRepoFile on trees instead of commits

repo-file: Base OstreeRepoFile on trees instead of commits

We want an OstreeRepoFile to be the way to represent a filesystem tree
inside an ostree repository. In order to do this, we need to drop the
commit from an OstreeRepoFile, and make that go to callers.

Switch all current users of ostree_repo_file_new_root to
ostree_repo_read_commit, and make the actual constructor private.

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