I faced the same issues. I followed the options on this link for migrating from 3.x to 4.x and it worked for me. http://eclipsesource.com/blogs/2012/06/18/migrating-from-eclipse-3-x-to-eclipse-4-e4/ Basically added the following as dependency to my plugin and run configuration.
- org.eclipse.equinox.ds
- org.eclipse.equinox.event
- org.eclipse.equinox.util
- org.eclipse.e4.ui.workbench.addons.swt