Creating a Java Client WebObjects Application
It can be difficult to debug Java Client WebObjects applications because these applications have a client side and a server side. Each side runs in a totally different process and in a different virtual machine (VM), so you can't debug the one side by running a debugger for the other side.
To debug the server side of a Java Client application use the standard debugging features of Project Builder. Open the launch panel for your application, specify necessary launch options, and start the debugger by clicking the debug button (the spray-can icon) in the launch panel. You can use the Launch panel to perform debugging tasks in all your server side classes.
See the documentation for Project Builder for details on its debugging features.