it would by default be user-controlled and prompted
if the target did not exist, the default would be to copy from the source to the target
if the target already existed and was newer than the source, the default choice would be not to copy the files, and a choice might not be presented
if the target already existed and was older than the source, the default could be to copy over it, with explicit permission from the user
This would reasonably handle both a migration from native to flatpak and simultaneous usage, and not require users to search for information on configuration files to have a seamless move.