Mms proposed updates

These are my proposed updates, mostly reflecting the things that I've been doing without documenting them. Feel free to tear them apart. I'll annotate changes that I think need explanation.
This is something that I believe Brendan and Jim had decided on when I came on. I've been trying to be consistent about the two lines, so I updated the rest of the doc to reflect it too. Personally, I think it's useful because logical sections of methods are split by 1 line. To further differentiate between methods, I think 2 is helpful.