dir: Make sure all parse_ref_file out params are consistently cleared

parse_ref_file() cleared all its out params to NULL, with the exception
of collection_id_out. Make sure to clear this one as well to avoid
surprises in the future.

Fixes commit ae7d96037 that added collection ID support to flatpakref.
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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