common: Break out the parts of flatpak-utils that deal with FlatpakDir

This breaks the circular dependency between flatpak-utils and flatpak-dir.
There is still a circular dependency between flatpak-dir and
flatpak-dir-utils, but I don't want to make flatpak-dir even larger.

Signed-off-by: Simon McVittie <smcv@collabora.com>
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