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You can have your own J2EE web application sit alongside the Enunciate-generated Web service application. The only issue is that you have to "merge" the web.xml file that Enunciate generates with your own web.xml file. (Of course, you won't even have to do that with the J2EE 5 support for the webapp fragment.)

Fortunately, Enunciate provides a way to automatically merge your web.xml file into the Enunciate-generated one:

Element Order

By default during a merge, Enunciate puts the elements if your web.xml file before the elements that are generated by Enunciate. But sometimes order is significant (e.g. listeners, servlets, filters, etc.). 

As of Enunciate 1.29, you can tell Enunciate to put the elements after the generated elements, you can add a custom attribute to the web.xml element, e.g.:

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