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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.
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Hmmm... Maybe it's the jcaptcha servlet that writes into the outputstream that is doing this behaviour... Like I said I'll look into it.

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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.
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Why have a auto-fetch patch system if you're going to build the all thing? Why not just checkout the project again? Maybe I didn't quite understand you there, though.