corrected in-code occurences of mol/transform.hh, mol::Transform, and...

corrected in-code occurences of mol/transform.hh, mol::Transform, and mol.Transform to geom equivalents

The mol/transform.hh header still exists and typedefs geom.Transform to mol.Transform; however, including it
will give you a deprecation warning; please observe these warning in your code and change your Transforms to
geom::