[autopatch] TEST BEFORE MERGE ynh_setup_source --full_replace=1

[Salamandar]

This is an automatic PR

This is an automated patch to potentially fix a bug in the upgrade script.

ynh_setup_source doesn't overwrite the destination directory, but rather extracts the source in the existing directory.

This might lead to weird cases where legacy source files aren't deleted.

The command has an argument --full_replace=1 that fixes this behaviour.

BE CAREFUL because this change might lead to data losses! You should check that all the patches calls to ynh_setup_source
do exactly what you expect to do and don't delete user data.

If you want exclude some files from being overwritten/deleted, use the --keep argument, just like that:

ynh_setup_source --dest_dir="$install_dir" --full_replace=1 --keep="config/config.yaml"