dir: Don't prune refs immediately after calling flatpak_dir_remove_ref
dir: Don't prune refs immediately after calling flatpak_dir_remove_ref

It might be more efficient to perform this operation at the end of
removing a batch of refs, so perform it there instead.

Closes: #1034
Approved by: alexlarsson

handsome-feng/flatpak,flatpak/flatpak,flatpak/flatpak,matthiasclasen/flatpak,handsome-feng/flatpak,matthiasclasen/flatpak,matthiasclasen/flatpak,handsome-feng/flatpak,flatpak/flatpak,matthiasclasen/flatpak,flatpak/flatpak,handsome-feng/flatpak,matthiasclasen/flatpak,flatpak/flatpak,handsome-feng/flatpak