You can use Sun™ Java System Studio 5 technology for "remote debugging", in order to manually attach the IDE to a remote Web Server started in debug mode.
Using the Sun Java System Web Server Administration interface, restart the server instance in debug mode (Server Manager > JVM General > Debug Enabled).
Note the JPDA port number.
Start the IDE.
Choose Debug > Start.
Select the dt_socket method, and then enter the remote machine name and the JPDA port number.
At that moment, any breakpoint created in the IDE on servlet source code of a deployed application will be active.
For more information about the Sun Java Studio 8 plugin for Sun Java System Web Server, and about using Sun Java Studio, see Using Sun Java Studio.