Depricate `ShapeModel` classes public facing `setHasIntersection` function

Anyone directly using the `ShapeModel` class in ISIS should not be able set whether there is a surface intersection on the model.

Any `ShapeModel` in ISIS should determine whether an intersection is present internally and not expose that determination to outside programs modifying the state of the `ShapeModel`.

Locate the ShapeModel classes and every declaration or use of the public setHasIntersection function. Read how each ShapeModel determines surface intersections internally, then verify that external callers can no longer change that state while existing intersection behavior remains intact.

Written by the indexing model from the issue text.