Added atomic check before calling extends_protocol.
Moved the example project and the Prolog perspective from pdt to pdt.common. The console and contextview plug-in extend the perspective. This allows having the perspective without the contextview plug-in.
Restored "in clause starting at line" label part for Logtalk reference matches.
Improved handling entity reference search. Only consider From::Functor/Arity and From:Functor/Arity references and also check that From is not a variable.