Code cleanup & documentation for paper

[sweverett]

Now that the paper writing has started in earnest, it's time to clean up a few things and beef up the documentation.

• Update readme
• Check, cleanup, and document class files in balrog
• Check, cleanup, and document scrips in scripts

A few specific coding tasks that need to be taken care of as we come across them:

• Allow either capitalization for uniform sampling to match other choices
• Read xsize and ysize automatically for chip images
• Fully implement FibonacciGrid

We may also want to bring back #7 as well to make the code more generic before releasing, if there is time.