StartState convention and treatment for controlled subgroups

[wxmerkt]

We just resolved this with a workaround for @cmower but should look into why it occurs. It occurs when the ControlledJoints are a subset of the ModelJoints. The start state should be able to be set as only a vector of the size of the controlled joints or or a vector of the size of the model joints. However, when first setting the uncontrolled joints and then setting the start state with a vector of only the controlled joints the uncontrolled joints are reset to zero.

We should (a) add a unit test and (b) fix the convention.

It's likely a super quick fix and I'll come back to it after the deadlines.