>I'm not sure the thread Tomcat points out wasn't
>stopped is related to Commons Logging. Could it be
>that you created the thread in your app?

I think that you are correct here although if I post more of the log for you to 
see then maybe we can confirm whether it is a common issue or not

20-Dec-2010 08:52:46 org.apache.catalina.startup.Catalina start
INFO: Server startup in 8843 ms
20-Dec-2010 08:55:09 org.apache.coyote.http11.Http11AprProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8080
20-Dec-2010 08:55:09 org.apache.coyote.ajp.AjpAprProtocol pause
INFO: Pausing Coyote AJP/1.3 on ajp-8009
20-Dec-2010 08:55:10 org.apache.catalina.core.StandardService stop
INFO: Stopping service Catalina
20-Dec-2010 08:55:11 org.apache.catalina.loader.WebappClassLoader 
clearReferencesThreads
SEVERE: A web application appears to have started a thread named [Thread-4] but 
has failed to stop it. This is very likely to create a memory leak.
20-Dec-2010 08:55:11 org.apache.coyote.http11.Http11AprProtocol destroy
INFO: Stopping Coyote HTTP/1.1 on http-8080
20-Dec-2010 08:55:11 org.apache.coyote.ajp.AjpAprProtocol destroy
INFO: Stopping Coyote AJP/1.3 on ajp-8009

>This one? This is about references held by a class
>in the container classloader to a class in the
>webapp classloader, which prevents *all* of the
>webapp classes from being unloaded on undeploy.
>The problem is not related to Tomcat's complaint
>about the thread that wasn't stopped.

The wiki entry I was referring to was this one (I should have included it in 
last post). It has a direct link to the one you provided
http://wiki.apache.org/commons/Logging/FrequentlyAskedQuestions under 
subheading (towards the bottom) "A memory leak occurs when 
undeploying/redeploying a webapp that uses Commons Logging. How do I fix 
this?". This refers to commons-logging-1.0.5.jar, the jar version used within 
the tika parser plugin in my webapp is version 1.1.1, this is why I am unsure 
as to how accurate the code is in this wiki entry (although it was last edited 
on 2010-05-05) actually is. It then goes on to mention that the deployment 
descriptor for the webapp would need to be updated etc... this is what I was 
referring to when I mentioned the can of worms.

In reading about ClassLoader I have come full circle and have ended up running 
back into my friend the Endorsed Standards Override Mechanism. I made Jena 
(which uses its own OWL parser, therefore no need for xerces) available to 
Tomcat in an endorsed folder, this should override the JAXP API's this seemed 
to solve the parser problem. If the error I am getting is not related to 
commons logging, and instead as you mentioned (and as shown in logs) related to 
the WebappClassLoader then I will pursue this route.

Sorry for long post
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