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Hey..Cool  Are you running it with jetty or within tomcat with the created WAR?
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Tomcat, last time I test snipit is create a virtual path on my blog site, after startup for a while it throws exception: __Servlet.service() for servlet error threw exception
java.lang.IllegalStateException: getOutputStream() has already been called for this response__ , and then Tomcat terminated.

I think maybe I should have a standard migration process, so I create a vmware machine for this.

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Now about the patches...You're asking how patches should be created right? A simple way is, if you use Eclipse, checkout the version I have on the repository do the patch you want and then go to team -> create patch. Then you could make the patch available for anyone who is interested.
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Not this, I means while building porcess, an ant target can do the patching before compiling and then generate the new and patched jars/war files. 

Maybe those patch file can save at the repository and use a build.properties  file to enable or disable patching process.