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. 

can you add comments on how this is different that COMDynamicsFullKinematicsPlanner? 
should we only be committing one of them (the winner), or is their value in having both?

also, the COMDynamicsFullKinematics planner should cite the humanoids paper submission in the header documentation.