Split classes into separate files.

Moved classes from __init__.py into their own files.
- hierarchy_classes.py :: For the Project, Model, etc. classes.
- calc_classes.py :: For the DataForCalc, DataFromCalc, etc. classes.

Edited __init__.py to read in the contents of these files.  Motivation is to
make things better organized and encapsulated in terms of what file they are
in.