I usually run a dual-monitor setup, so I have two Eclipse windows open for the same workspace, displaying different files. When I\'m debugging and a breakpoint is hit, Eclipse s
Maybe you select the sources for Debugging by "File System Directory" instead of by "Java Project". To change this go to Run=>Debug Configuration=>Add Sources=Button: ADD...=>Java Project and select your Projects.
Make sure, that the added sources are found first by moving them to the top.