TEIIDDES-2156: Eliminate use of CoreModelerPlugin.toRuntimeException

* The function CoreModelerPlugin.toRuntimeException, by throwing a runtime
  exception, has the potential to drastically upset Eclipse's normal
  operations, eg. stopping build dead.

* Removes uses of toRuntimeException and replace with appropriately handled
  normal exceptions either properly thrown or caught and conveyed to the
  display (logged or shown in a dialog).