[docs] Set Doxygen extract_all to true and fix Doxygen failures (#3695)

The template argument order for UnscentedTransform was reversed to match
all the other UKF classes. Since UnscentedTransform is intended as a
class for internal use only, this shouldn't cause much breakage.

wpimath/src/main/native/include/frc/controller/LinearQuadraticRegulator.h

@@ -32,6 +32,9 @@ namespace detail {
  *
  * For more on the underlying math, read
  * https://file.tavsys.net/control/controls-engineering-in-frc.pdf.
+ *
+ * @tparam States Number of states.
+ * @tparam Inputs Number of inputs.
  */
 template <int States, int Inputs>
 class LinearQuadraticRegulatorImpl {
@@ -266,6 +269,7 @@ class LinearQuadraticRegulator
   /**
    * Constructs a controller with the given coefficients and plant.
    *
+   * @tparam Outputs The number of outputs.
    * @param plant  The plant being controlled.
    * @param Qelems The maximum desired error tolerance for each state.
    * @param Relems The maximum desired control effort for each input.