An introduction on how this can be done is given in class.egw_include_mgr.inc.php.
This file/class may lateron be extended to minifiy, compress and cache groups of js files - currently only the 'debug-mode' is implemented, which sends all javascript files as individual files, making it easy to debug the java-script files in the browser.
The new method should work with all old code, especially including java-script files as part of an ajax-response, if something is broken, please report that!