GRECLIPSE-1789 Add non default output locations to classpath.

Actually this fix can be applied to org.eclipse.jdt.groovy.core project, but it seems a bit strange to me, that CompilerUtils adds to classpath default output location, but ignores other output locations, so I guess the correct place is here.
Probably the same fix should be applied to other jdt-patch projects, at least for supporting Groovy 2.3 and traits.