The PDE files that are available in that project are simply text files. You can either use them in your code directly, or better yet, try to understand what they're doing and adapt the code to your own purposes.
But to answer your question, you don't include PDE files in a Java project. You included the Processing library jars on your classpath, which give you access to things like the PApplet class. Then you can include a PApplet (which is just like a Processing sketch, in fact a Processing sketch is a PApplet) in your Java application and pass it whatever information you want.
More info here: http://processing.org/tutorials/eclipse/