Note that an ear file does not have a Manifest.MF. The war file (containing the servlet) does. So it is really two levels in. What are you trying to accomplish by looking up the Manifest? Maybe there is an easier way.
I think the EAR file also has a META-INF directory containing MENIFEST.MF file.I usually deploy my application ear in OC4J container and the EAR contains few other configuration files along with MENIFEST.MF file.
Even we add some custom entries in the MENIFEST.MF file.