Currenlty config files from older stl versions do not get any updates automatically, so you either have to delete them so they will be re-created with all current default settings or you have to add new configurations manually.
The implementation will work like this:
On every stl call all main config files (currently, global.conf, default_template.conf and the game config of the started game) will be compared against all of their up2date available config entries - every entry missing will be added automatically to the config with the default value (usually disabled). Already existing entries will remain untouched, so 3rd party variables survive this.
The update function will be generic and therefore be used for all config files, the list of available entries will be cut direcly out of the code, so it will be always up2date in the future.
There's also no option currently to change a specific config entry for all game config files at once.
The implenentation will have a commandline option with following arguments:
stl set ENTRY (SteamAppID or "all") "VALUE"
"ENTRY" will be compared with all valid entries, if the string is not an option it will quit
if the config file for SteamAppID does not exist it will quit
there's no validity check on "VALUE"
Examples:
stl set PROTON_DEBUG_DIR_FILE 1232570 /random/path/
will set PROTON_DEBUG_DIR for the game 1232570 to "/random/path/" if the game has a config file in $STLGAMEDIR
stl set RUN_REPLAY all 1
will enable RUN_REPLAY in all game config files found in $STLGAMEDIR
edit: ping #16 (comment)