DRC Drake updates (2nd attempt)

Updated version of #536, with all merge conflicts resolved against the current `RobotLocomtion/master`. I've addressed all of the comments on #536 that pertained to me (@avalenzu). Or at least, I think I've addressed them - we'll see what the build servers say :)

There were a few additional comments on #536 regarding `checkDependency` and cubic spline functions. I'm leaving those to the authors of the relevant changes (@rdeits and/or @kuindersma?)
@avalenzu can you update "collisionDetectmex" to "smoothDistancePenaltymex"?