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* If you are trying to have Hudson co-exist with other apps that use JNA in a single container (this includes deploying multiple copies of Hudson on different paths), you can put jna.jar into the container's shared library directory, so that all the webapps will see the same copy.
* Another approach is to run each webapp in its own JVM, then use Apache to aggregate them all under a single HTTP server. See [Running Hudson Jenkins behind Apache] for more details.