Don't generate app bundle anymore.

The assembly generates an app bundle that requires Java 6.  This is no
longer valid as Protege 5.0 beta requires Java 7.  See this issue in
GitHub for a more detailed discussion:
https://github.com/protegeproject/protege/issues/29.  When we have time
to work on generating an app bundle that can use Java 7 or later, we
could uncomment/modify these lines in the assembler.