Well to be honest i'm not familiar with the Shiro framework. I guess you'll have to disable somehow the jaas authentication and enable yours, so you will probably have to make modifications in web.xml look at the security constraints, roles etc.
For example try to comment them all out to see if security is still required although you'll have to somehow pass the username for the server to make proper retrieval of data i.e. task data, group data etc, i think, not sure though, this happens on the gwt client side by holding the username from the gwt login dialog, then it is using that parameter when requesting stuff from the gwt server by passing it as parameter to the REST API of the gwt server.