The Window Matching Agent is a simple java agent that uses bytecode manipulation to change the value sun.awt.X11.XToolkit assigns to the WM_CLASS property
Make sure you have have ant installed then from the commandline run :
ant jar
the generated agent.jar file will end up in the dist folder
You can download a recent binary from amazon s3
To use it add the following argument to your commandline
-javaagent:agent.jar=YOUR_APPLICATION_IDENTIFIER