Tweak theorem environment numbering

- Changes the numbering for theorems, etc., to be at the section
  and not the chapter level
- Adds a QED symbol to the end of examples and homework exercises
Remove subsections from TOC
Reorganize regression content
Reorganize statistics content
Add bayesian references
Move R code out of bayesian tex file into R files
Edit material on conjugate priors
Rewrite Bayesian Metropolis-Hastings material

- Rewrite the text as prose instead of an outline
- Remove R code
- Update makefile
fixup f4cf97