Merging in Humanoids 2014 work

We should still move more of our examples out of `solvers/trajectoryOptimization/dev` into `examples/Atlas` (and the one that has been moved - `testRunningPlanner` - should be simplified), but all the functionality works, so I'd like to get this merged in prior to doing that. 

This breaks at least one case: if you call solveTraj without an initial guess, then it tries to call simulate to get an initial x traj.  The manipulator equations still expect the original number of inputs, and so barf.
In fact, I think we should probably make it illegal to call setNumInputs on a RigidBodyManipulator (without updating the actuators, etc).