org.eclipse.jst.j2ee.commonarchivecore.internal.exception.NoModuleFileException:A file does not exist for module element having uri
I assume your application.xml contains one or more module elements. The error message is telling you that a module you have defined in application.xml is not found in your application. That is, the file is not in your .EAR file.
Suppose your application.xml contains these elements:
<module>
<java>MyClient.jar</java>
</module>
<module>
<ejb>MyEjb.jar</ejb>
</module>
<module>
<web>
<web-uri>MyWar.war</web-uri>
<context-root>mywar</context-root>
</web>
</module>
Then your .EAR file should contain these files in the root directory:
MyClient.jar
MyEjb.jar
MyWar.war