Writing Plugins
You can create system plugins or audio chain machines by writing Java classes. This is best accomplished using the Netbeans Java IDE from Sun. Presently no other method of development is recommended or supported, however Netbeans uses Ant scripts if you want to work on the project outside of Netbeans.
There are two classes of plugins - system components like the router or composer, and machines. Download (or checkout with SVN) the project source code from SourceForge and then examine the appropriate plugin project for example code. If you have problems or questions feel free to post on the project forum.
At this time the base classes and method signatures for system functions is virtually guaranteed to change dramatically between releases.