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
You can create another workspace and in that workspace create a new project from the same src code (same files in file system) of the one in your current project in your current workspace. That would let you stop on one breakpoint without the other window stopping their too. Notice that after you make some code modifications in one project you'd have to refresh the other project for those changes to apply in it.
Eclipse switches to the debug perspective for all windows the debug perspective has been opened once (i.e. the little icon on the right top corner is available). If you close that perspective (switch to another perspective is not sufficient), it won't switch to it anymore on that window.
At least, that's the behaviour I observed on Kepler (I know, that question is older but just came across, maybe it still helps someone).
Closing the Debug perspective (righ-click on the little icon on the right top corner) worked for me. I'm using Oxygen and I have the following settings in the Run/Debug Preferences:
This worked for me: In Window->Preferences->Run/Debug->Launching->Launch Configurations enable "Apply window working set(s)"
Personally I find this more efficient than creating two workspaces.
To disable multiple debugging in multiple windows in eclipse, go to Windows > Preferences > Run/Debug and uncheck Activate the debug view when a breakpoint is hit
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.