The .def.xml files are used to AUTO_CONFIGURE modules. When the options that are defined in the xml-file are also present as variables in the form that calls the script, then the module file is automatically loaded in and the module is executed at the given runlevel. The auto-configure option uses the xml.inc.php file for looking up the options in the xml-files. The problem is that this is rather a big class. This means it can downgrade the performance when used with a lot of xml-files and a lot of options. That is why you can turn of the AUTO_CONFIGURE option and use the modules variable/field in the form to load in the specified modules. The file Modules.xsd is the XML-Schema to verify the xml-files for the modules.