Some sections jumped from level 2 to level 4, for example.
Also played around with generating book to HTML. I like it, but
it needs some work. The Calico table of content generator cannot
deal with different headers with the same name, for example.
I want to go to HTML so I can use Bokeh to have interactive plots.
But that means no more PDF, because Bokeh will not export to
PDF.
I moved book_format.py to the root directory so that all of the
notebooks do not need to modify the system path to import it. It
modifies the path on import so that all of the code in ./code can
then be accessed.
Altered links to nbviewer to account for no longer using subdirectories.
