Pursuant to the earlier discussion,
I have copied the OSGi preferences API (3 types) into the runtime plugin
and deleted the runtime requirement on org.eclipse.osgi.services. As
such, the services bundle has been removed from the osgi.bundles list in
config.ini and the osgi.bundles value in eclipse.properties. These
changes have been released in HEAD.
PDE should update their default launch
configuration to not include services.