Remove prototype functions

#1082 
Removed prototype functions from:
AxisAlignedBoundingBox, BoundingRectangle, BoundingSphere, Plane, Ray, Spherical

I left in `AxisAlignedBoundingBox.prototype.intersect`, `BoundingRectangle.prototype.intersect` and `BoundingSphere.prototype.intersect` because one of the `CullingVolume` tests made it look like it was necessary.