Tweak footnote source to make line-wrap work better
Reorganize code (big!)

This commit is a massive code reorganization. There are several reasons
for it:
- R 3.0x came out and my old packages weren't valid any more
- The pgfSweave package is obsolete, and so I've unbundled
  the sweave files that were using it.
- It seemed like an opportunistic time to make a few other
  changes.
Try to resolve problems in pdf fonts
Increase number and detail of simulations
Change NAMESPACE formatting for better git
Change LaTeX package loading for better git
Add recursive-window simulations

This commit adds recursive window simulations; they are plotted
in the appendix.tex file. Additionally, the package functions
and the simulation code have been modified.
Remove pgfSweave from makefile
Add to ignore list
Merge branch 'wins' into math-rewrite

Conflicts:
	macros.tex
	paper.tex