When you see XML files on the command line for startup of Jetty, they are always part of the Jetty IoC Configuration mechanism.

Internally, Jetty uses these XML files to build up Jetty with the features that you wan to use.

The module mechanism present in Jetty determines the load order of the XML files. The Jetty Base and Jetty Home resolution logic also applies, which allows you to override a XML file declared by a module with your XML by simply having the same named XML in your ${jetty.base}/etc directory location.