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See attachment.
Created attachment 81069 [details] Thread dump
Sorry, now I see it wasn't a deadlock. The IDE continues to run, just the UI was frozen for a long time.
I'll change MetadataModel.runReadAction() to MetadataModel.runReadActionWhenReady() in projectClosed(). This change should fix the problem with blocking AWT thread. We had a similar issue in Maven projects: Two many threads were waiting in the Default request processor. I've created single-purpose request processor there for the task checking the web services annotations. I'll do the same for Ant projects. Hopefully this will also help. See the issue 162052.
Fixed. Details: http://hg.netbeans.org/main/rev/43c2a5a5d075
Integrated into 'main-golden', will be available in build *200904290201* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main-golden/rev/43c2a5a5d075 User: mkuchtiak@netbeans.org Log: #163900: fixed AWT thread blockage