I'm using IntelliJ Idea 11.1.4 EAP, but I retested the situation on 11.1.3 which has exactly the same behaviour.
We are working with a backend Jetty server which has a war loaded up. This war is built using the Maven-assembly-plugin instead of the regular Maven way.
I set the Jetty server to accept remote debugging, set the remote debug settings up in IntelliJ and connected. At first glace it's all good but then a certain class rather deep within our codebase needed to be debugged. Instead of using the class that is actually on my project IntelliJ chose to use the Maven repository version, which is even in the wrong version. There's another version of that class with a different version name that could be more correct as well. But anyway. I'd much rather like IntelliJ to choose a project class if available.
When I set the setting in Remote Debug "Search sources using the classpath of module" to the module that problematic class is in it works better. But still...
Thanks for reading,