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!
I was trying to capture the fact that needs and contributions of the community ideally drive extensions to Cyclus. I wonder how we can capture that in a way that makes sense. Also, I can't pull this change. We can't be adding bold notes at this point in the editing process. We need to be polishing at this point. Not adding placeholders (or else something like this could happen : https://twitter.com/davidjayharris/status/531927801037729792/photo/1)