Aoskim

More reorg:
- in "simulation assistance" section (does this need to be renamed?), put cycamore first. 
- melded (squashed?) the framework structure section with the ABM section because it initially came from the intro and thus served as a great intro to the section with no rewording

Added a more accurate intro section to methods and implementation (please edit brutally!)

Skimmed otherwise. Fixed figure captions, stuff like that.

STILL CANNOT FIGURE OUT SUBSUBSECTION LABELING PROBLEM!!!!! HELP!
Maybe "Modular Software Architecture?"