Application.xml over-written when deploying JDeveloper 10.1.3.2

Hi all,
I created a Web Application that contains JSF, EJB, and Toplink. I have a ViewController project, a Model project, and a Deployment project. The ViewController obviously contains my JSPs, etc, the Model my EJBs and server code, and deployment profiles for each. The Deployment project contains a deployment profile for creating the EAR file for the other two projects.
When the EAR is created (or if I deploy to stand-alone OC4J) the application.xml is generated without an module/EJB tag containing my EJB jar. Therefore when the server starts up it does not find any of my EJBs.
If I manually modify the application.xml in a created EAR file and then deploy it manually, everything works great. So, I tried to create an application.xml file in my Deployment project (and I tried in my ViewController project, too), but it ends up getting over-written and changed to still not have the module/EJB tag. Can someone explain to me how to stop JDeveloper from overriding this file or how to get JDeveloper to include this tag set when creating the application.xml?
Thanks,
Mike

JDeveloper 10.1.3.2 supports J2EE 1.4 in which the web.xml does not include the
<taglib> element. Remove the <taglib> element from the web.xml. Specify the http uri in the <%@ taglib prefix='srp' uri='' %>
Add the taglib JAR file to project libraries.

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