Switch to literate-style coding for bootstrap

This commit switches the code to be embedded in the LaTeX source
and then extracts it with knitr.
Add files generated for bootstrap to repo

Not sure that this is the best way to go, but this commit embeds
the figures and macros for the bootstrap in the repository.  This
should make it easier for people unfamiliar with R and the linux
command line to contribute to the rest of the book.
Add citations for R and knitr
Update documentation
Merge branch 'literate-knitr'

Conflicts:
	asymptotics/bootstrap_fig1.R
	asymptotics/bootstrap_fig2.R
Update clean and burn targets

Since there are some generated files in the repo, I've
taken them out of 'make clean' and 'make burn'.