dir: Fix an issue with fetch_remote_ref_sync()

This commit is a follow-up to "Fix implementation of xa.noenumerate
remote option" since that turned out to break
flatpak_installation_fetch_remote_ref_sync() in some cases. I didn't see
it at the time, but flatpak_decomposed_get_collection_id() explains that
the collection ID shouldn't be set on FlatpakDecomposed objects, even
when the remote has a collection ID set, unless they are being used to
enumerate refs from a file:// URI rather than a configured remote. So
this commit changes list_remote_refs() and list_all_remote_refs() to
keep the xa.noenumerate implementation working and to get
fetch_remote_ref_sync() working again (since the latter uses
flatpak_decomposed_new_from_parts() and thus doesn't set a collection ID
on the FlatpakDecomposed object used for comparison).

(cherry picked from commit f3214c59d2f687e47ab5d9a74d8a3ef45f8e0105)