The Ximix codebase is made up of six modules. Three of these modules, common, client, and node, provide the core functionality of Ximix. The other three, demo, console, and test, provide some demo clients, additional test code, and a console client which can be used with a Ximix network.
If you are trying to write code which talks to Ximix the client package is where you want to look.
If you want to introduce new algorithms, or different shuffling techniques, the node package is probably going to be of most interest.
Javadoc for core functionality can be found at API Javadoc
The source code itself is available at GitHub Ximix Repository