dir: Remove unused non-_decomposed() helpers

This removes flatpak_dir_list_remote_refs() and
flatpak_dir_list_all_remote_refs() which have no more users, as everything
migrated to the _decomposed() versions.
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Internal Server Error - Gitea: Git with a cup of tea
500 Internal Server Error

Gitea Version: 1.28.0+dev-477-g8b6ad49a5f