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It seems that the debugger process that is started when I'm using the internal debugger doesn't always terminate correctly. Instead it sometimes continues to run in the background and has to be killed manually from the command line. Unfortunately I didn't discover so far under which circumstances the debugger continues to run; it seems that it is always terminated when I manually stop the debugging process. This happens both on MacOS X (10.0.4 with Apple JDK 1.3.0) and on PC (Windows 2000, JDK 1.3.1)
We know about this problem. This happens on Hotspot VM and mainly (only?) when the debugged process is not finished by System.exit() call - e.g. when it is finished by the finish of all threads. It is a problem of JDK and we cannot do anything with it. I do not have much information about JDK on Mac, but on WIN platform it should be fixed in JDK1.3.0_04 and in JDK1.4beta2. You can also try to use Classic VM for debugging - change the Classic Switch property of the Default Debugging (in Project Settings|Debugger Types).
Wontfix -> Closed.