Make several cosmetic changes to the document

- Reverts fonts to Computer Modern (default): the tufte-latex
  serif/unserif/mono combinations are horrible together.  I'd
  like to have something better than CM, but don't want to spend
  a lot of time thinking about it now.  This issue has bothered
  me more now that there's a fair bit of embedded R code.

- Removes "list of figures" etc.  They can go back in later, but
  they too need some more thought.

- Change back to the tufte-handout class to save some paper and
  have a more natural pdf reading experience.

- Remove the 'literate' style typesetting of R code.  It's pretty,
  but it will probably just confuse students and potential
  contributors.