I have the following ear task in my ant build script:

<ear destfile="${product}" appxml="./Source/java/META-INF/application.xml" 
manifest="./Source/java/META-INF/MANIFEST.MF">
		<fileset dir="${deploy.dir}" includes="*.jar">
            		<exclude name="tnrouter-schedulable-1.0.0.jar"/>
		</fileset>
	        <fileset dir="${deploy.dir}" includes="*.war"/>
</ear>

The resulting .ear file does not include the application.xml file in the
META-INF directory (actually not at all). The indicated MANIFEST.MF makes it in
the .ear file just fine.

Running ant -debug produces the following:
ZipFileSet: Setup scanner in dir
C:\PTDT\IntegratedFactory\TNRouter\Source\java\META-INF with patter
nSet{ includes: [application.xml] excludes: [] }
      [ear] Building ear:
C:\PTDT\IntegratedFactory\TNRouter\build\deploy\tnrouter.ear
      [ear] adding directory META-INF/
      [ear] adding entry META-INF/MANIFEST.MF
      [ear] adding entry tnrouter-common-1.0.0.jar
      [ear] adding entry tnrouter-factories-1.0.0.jar
      [ear] adding entry tnrouter-orders-1.0.0.jar
      [ear] adding entry tnrouter-soapservices-1.0.0.jar
      [ear] adding entry tnrouter-gui-webapp-1.0.0.war
      [ear] adding entry tnrouter-soap-webapp-1.0.0.war
      [ear] adding entry tnrouter-webapp-1.0.0.war
      [ear] adding entry META-INF/application.xml

As you can see, ant -debug *says* that it is adding application.xml, however, it
does not appear in my .ear file.