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. 

I've moved all of the examples except for `testRunningPlanner` into dev so that cleaning them up doesn't delay merging of the changes that add the new functionality. I'd suggest that, after this pull-request is merged, we create issues for that clean-up and assign them to me or @hongkai-dai