Got rid of some SecondOrderSystem calls.
PD control.
num_positions, num_velocities in Manipulator.
qd / v difference in Manipulator, RigidBodyManipulator. Copied minimal amount of changes from floatingBase branch.
dofnum/position_num/velocity_num fixes.
getNumDOF fixes.
SecondOrderSystem fix.
num_q --> num_positions.
Updated dynamicsGradients.mat (num_positions/num_velocities in saved AcrobatPlant, copied from floatingBase branch).
Regenerated plants and saved out to .mat files again so that num_positions and num_velocities are set.
Warnings instead of errors in getNumDOF and setNumDOF for now.
Undo changes to CartPole dynamicsGradientsTest.
Got rid of RigidBodyInertialMeasurementUnit sodynamics call.
Comment about dofnum in RigidBody, updated comments for position_num, velocity_num.
fix run serial
Merge pull request #336 from tkoolen/numPositionsNumVelocities

Separate numPositions and numVelocities
proposed resolution to issue #104.  let's see if this breaks everything
fix hybrid trajectories dim
fix merge