More re-organization

I moved around a few of the sections you wrote and re-worded a few things in an attempt to organize things a little more linearly. Most of what you've written is left intact, though moved around a bit. 

Let me know what you think about this re-org. I've tried to make things more linear. The big change I made shows up in what is now section V. I've created sub-sections for each of the major MDAO problem primatives I think we need to cover. 

Give this a careful re-read to see if you like it before merging it in with your stuff.