Debugging Tomcat webapp

Two years ago I opened http://youtrack.jetbrains.com/issue/IDEA-61791 and http://youtrack.jetbrains.com/issue/IDEA-63362. This issue is occurring here all the time because we're working on a Tomcat webapp in different branches.

IDEA 12.x still opens the wrong files if you click on a exception link in a stacktrace andthe debugger opens the wrong files when a breakpoint is hit.

This happens if you have at least two modules which have the same classes (e.g. a branch and HEAD).

Is there any possibility to get a fix for this in 12.1?

Thanks a lot!

Wallaby