Feature 43

Removes ApplicationSettings class.

The implementation isn't very nice because everything is so tangled in the GUI but basically I've:

* Taken the handler creation out of the views and now passed them in
* Due to this change the handlers can now take a reference to the PIPEApplicationModel from the view builder
* Moved the pop up code to the handlers out of the views

The whole thing needs a re-architect but I don't have time!