Debug a site inside Eclipse
Create a debug configuration
In order to attach the Eclipse debugger to the running application you need to create a debug configuration.
Go to menu Run > Debug Configurations... and select Remote Java Application from the left Menu. Click the New launch configuration icon in the top left corner of the dialog. Fill in the name of the debug configuration, for instance Debug Myproject Site. On the Connect tab browse to the project you want to debug, for instance myproject-site. This will add the source files from that project to the source path of the debugger so it can show you the sources of the code you are stepping through as you are debugging. To add more source code paths to the debug configuration select the Source tab and choose Add.
You are done. Clicking Debug will attach the Eclipse debugger to the running application. If you now set breakpoints in your code Eclipse will open the debug perspective when your application executes that code.