System constraints

Replaces stateConstraint method logic with a list of constraint objects for each DrakeSystem.  These can handled more elegantly (preserving the structure of the constraints, and avoiding function handles) by the optimization classes.  

Taking another crack at finishing and merging this (just had a rough time bringing it back in line w/ master).  

In the `RigidBodyManipulator`, will `setJointLimits` also change the joint limits in the C++ object?