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I left the IDE running over the weekend and when I came back on monday it was hung. This has happened a few times before and this time I happened to be able to get a thread dump. So I thought I'd report it.
Created attachment 9334 [details] Thread Dump
JDK issue. I searched bugs in bugparade and found http://developer.java.sun.com/developer/bugParade/bugs/4809173.html which is duplicate of http://developer.java.sun.com/developer/bugParade/bugs/4789067.html.
Marek is right - it's JDK bug - verifying, closing.