The PDF was not setting the Preface as a unnumbered chapter.
I think there is more work to get it's subsections unnumbered.
Added empty Particl filter chapter. Had to renumber the chapters
to make it fit in.
I finally learned that the raw cells let you put latex directly
into the output. So now I have the appendix being created without
the [1] %%latex showing up in the output. Also wrote code to parse
the .tex file to make the Preface a chapter without numbering, so it
is now a proper preface, and not "chapter 0".
I have not touched the Windows generation tools, so PDF generation
in Windows is now broken. I don't think I care.
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.
