It turns out there is a backdoor way to do what you want. If you modify your project (with JBuilder closed) and add one line to it, you will be able to specify the location of a MANIFEST.MF file which JBuilder will then use when building your EJB jar.

That line looks like (assuming a .jpx project file format)

  <property category="archiving" name="overrideManifestPath" value="src/META-INF/MANIFEST.MF"/>

where the value is a location relative to the EJB Module. The line needs to be specified as a property of your EJB Module so it needs to be inside the existing context, something like:

  <file path="Untitled1.ejbgrpx">
     <property category="archiving" name="overrideManifestPath" value="src/META-INF/MANIFEST.MF"/>
   </file>

Your MANIFEST.MF would look something like:

  Manifest-Version: 1.0

  Name: Test
  Class-Path: My.jar