Actually replace sources.

scripts/upgrade

@@ -36,7 +36,7 @@ then
 	ynh_script_progression --message="Upgrading source files..." --weight=1
 
 	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$install_dir" --keep=".env"
+	ynh_setup_source --dest_dir="$install_dir" --full_replace=1
 fi
 
 chmod -R o-rwx "$install_dir"