If the target is the rofiles-fuse and a file is hardlinked, then
copy will fall back to truncation, which will fail with READONLY.
We work around this sometimes by deleting the destination first
and sometimes by using g_file_set_contents instead.
This way you can e.g. do network i/o in them.
Thats not a recommended way to do it though, as you work around
a lot of the feature in flatpak-builder like the caching and
verification.