The shell scripts that are used to run the server and client support remote debugging. If you pass the appropriate flags to the script you will be able to connect to the processes with a remote Java debugger.
To debug a wave server use the --debug flag (the same approach also works for the console client).
The server will print its debug port number, by default 10876, and then run as usual.
To debug the process connect a Java debugger to this port. In Eclipse you can connect by doing the following:
Eclipse will connect to the server and you'll be able to debug it as a standard Java application.
If you want the program to not start running before a debugger is connected, for instance if you're debugging an issue that occurs during startup, add the --suspend option.
If you want to use a different debug port you can specify one explicitly using --debug_port=<port>