In the web case, the problem; as i understand it, is that cvs has some conflicts updating the jboss-web.xml. If you delete it before running xdoclet the security domain specified in the xdoclet-build.xml (the project's xdoclet preferences in the ide) should be ported.
One solution is to set the force attribute to true for the webdoclet subtask. (project>properties>xdoclet> ... webdoclet. double click to force attribute and set to true in the ide)