Taking out what I did for the YourKit plug-in didn't help. Next, I shutdown my Eclipse and then started and stopped Tomcat on the server. The org.eclipse threads were still listed in the thread dump. I recently upgraded B.I.R.T. to version 2.2 on Tomcat and it uses osgi jar files. I'll look to see if there is an issue there or if I need to do something else so Tomcat will shutdown properly.
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