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I am getting an error "Not able to submit breakpoint LineBreakpoint MySource.java : 99, reason: Breakpoint's source file does not belong into the preferred source root ..." The preferred source root belongs to a closed project, and it is not listed in the sources window. How I got there: If I try to set a breakpoint in a class that exists more than once in open projects then it cannot be set at times. I have learned that I must adjust the priority in the debugger sources window so moved up the multiple source roots of the project I am interested in. Finally I got tired of this and closed the conflicting project. I found that adjusting the priority by moving multiple source roots up above the conflicting one is extremely tedious and annoying in a debugging session. Perhaps the process to deal with this conflict could be improved also.
I think I have a different problem. Sorry.