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I got a thread lock between, assumingly, the "Building Workspace" thread and the "Initializing Java Tooling" thread. This is what I did. The night before I deleted all .class files and backup my workspace to CD. When I started up again today, I ran "Clean" to rebuild all my class files everywhere. The compile operation never finished. It normally only takes a minute, two max. I opened the task progress view and saw two tasks running, the Building Workspace and Initializing Java Tooling. I went to get coffee and after fifteen minutes no progress on either task. I tried to cancel the tasks but they still didn't die. So, the obvious workaround is don't try to clean your workspace until initialization is complete, but thought you should know anyway.
Can you provide build ID? If you can easily reproduce this lock then please make a VM thread dump in the console (start eclipse with -consoleLog option and hit Ctrl+Pause in the Dos cmd window) and attach output to this bug, thanks
Closing as REMIND. Reopen when information requested in comment 1 is available.
As of now 'LATER' and 'REMIND' resolutions are no longer supported. Please reopen this bug if it is still valid for you.