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If debugging an event handler e.g PopupMenuListener the whole KDE is blocked. This works with Java 5 System: Suse Linux 10.1 (64 bit), KDE (3.5.1). Java 6 (32 bit). Netbeans 5.5
This is unfortunately not solvable AFAIK. The problem is, that the debugged application acquired focus and is suspended by the debugger. So other applications (including the debugger) can not gain the focus. You need two independent terminals to debug code like this.
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This is a duplicate of issue #93076 - JDK bug 6517045. *** This issue has been marked as a duplicate of 93076 ***
Verified ... and Closing all issues resolved into NetBeans 6.7 and earlier.