I haven't worked with Cocoon so I don't know how soemthing built with Coccon is deployed, but maybe this will help.
Deploy your app as an exploded set of files within directories, rather than packaged up within war and ear files. For example, assume you have xxx.ear which contains aaa.war and bbb.war. Under the deploy directory, create a directory named xxx.ear. In that directory create two more directories aaa.war and bbb.war. Into those directories place the contents of the two war files. Also, in the xxx.ear directory place the rest of the contents that would have been in the ear file, such as the META-INF/application.xml file.
Now, for example, you can easily add deploy/xxx.ear/bbb.war/some-new-file.html or edit deploy/xxx.ear/bbb.war/some-file.jsp.
Perfect! This is exactly what I was looking for. Thank you very much, Peter. :)