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1. Go to the 'Debug' perspective. 2. Place a breakpoint in your main method. 3. Make sure the 'Debug' view is opened. 4. Activate the editor. 5. F11 6. The 'Debug' view is now active but the keyboard focus is still in the editor and the caret can be seen blinking.
The worst part about this bug is that clicking inside the editor doesn't actually activate the editor. So when you think you're "really" in the editor, you're still not and keybindings do not work as you would expect them to.
The same thing happens if you just use Ctrl+F11 to launch an application. The 'Console' activates and you can see stuff being printed out but the keyboard's focus remains in the editor.
This bug is caused by eager context correction code in the EPS's bringToTop(MPart) method.
Fixed in CVS HEAD.