Change wpilibmath Javadocs to use "reference" instead of "setpoint"

[KennanHunter]

(closes #6749)

The WPILibMath module uses the setpoint terminology instead of reference in the implementation and public APIs as well as the documentation. Before this gets merged we should discuss if it makes sense to fragment our terminology between javadocs and API. I only changed the javadocs where it seemed uncontroversial.