Attempt at fixing referencing issue when deep copying the various pykat objects. It was an issue because they create dynamic properties for classes on the fly depending on which components are added, e.g. so that you can do kat.m1. However on copying the class definitions also need to be deep-copied by creating a new class and copying over the properties.

Changing documentation, adding printExtraLines methods to see what commands haven't been parsed into pykat objects. Adding more squeezing to numpy arrays