Clean up the sage-code directory

[penguian]

The sage-code directory currently contains a jumble of Sage and Python code, worksheets and PBS jobs. The PBS jobs should be removed or moved to the PBS directory. Some of the Sage code could easily be ported to Python. The Python code used for the NeCTAR dashboard could be moved to a dashboard directory, and much of the remaining Python code could either be moved into boolean_cayley_graphs after addition of doctests, or removed entirely.