[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/system/Discretization.h

@@ -13,6 +13,7 @@ namespace frc {
 /**
  * Discretizes the given continuous A matrix.
  *
+ * @tparam States Number of states.
  * @param contA Continuous system matrix.
  * @param dt    Discretization timestep.
  * @param discA Storage for discrete system matrix.
@@ -27,6 +28,8 @@ void DiscretizeA(const Eigen::Matrix<double, States, States>& contA,
 /**
  * Discretizes the given continuous A and B matrices.
  *
+ * @tparam States Number of states.
+ * @tparam Inputs Number of inputs.
  * @param contA Continuous system matrix.
  * @param contB Continuous input matrix.
  * @param dt    Discretization timestep.
@@ -54,6 +57,7 @@ void DiscretizeAB(const Eigen::Matrix<double, States, States>& contA,
 /**
  * Discretizes the given continuous A and Q matrices.
  *
+ * @tparam States Number of states.
  * @param contA Continuous system matrix.
  * @param contQ Continuous process noise covariance matrix.
  * @param dt    Discretization timestep.
@@ -105,6 +109,7 @@ void DiscretizeAQ(const Eigen::Matrix<double, States, States>& contA,
  *    using a taylor series to several terms and still be substantially cheaper
  *    than taking the big exponential.
  *
+ * @tparam States Number of states.
  * @param contA Continuous system matrix.
  * @param contQ Continuous process noise covariance matrix.
  * @param dt    Discretization timestep.
@@ -149,6 +154,7 @@ void DiscretizeAQTaylor(const Eigen::Matrix<double, States, States>& contA,
  * Returns a discretized version of the provided continuous measurement noise
  * covariance matrix.
  *
+ * @tparam Outputs Number of outputs.
  * @param R  Continuous measurement noise covariance matrix.
  * @param dt Discretization timestep.
  */

wpimath/src/main/native/include/frc/system/LinearSystem.h

@@ -22,6 +22,10 @@ namespace frc {
  *
  * 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.
+ * @tparam Outputs Number of outputs.
  */
 template <int States, int Inputs, int Outputs>
 class LinearSystem {

wpimath/src/main/native/include/frc/system/LinearSystemLoop.h

@@ -27,6 +27,10 @@ namespace frc {
  *
  * 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.
+ * @tparam Outputs Number of outputs.
  */
 template <int States, int Inputs, int Outputs>
 class LinearSystemLoop {

wpimath/src/main/native/include/frc/system/NumericalJacobian.h

@@ -41,10 +41,11 @@ auto NumericalJacobian(F&& f, const Eigen::Vector<double, Cols>& x) {
  * @tparam States  Number of rows in x.
  * @tparam Inputs  Number of rows in u.
  * @tparam F       Function object type.
- * @tparam Args... Remaining arguments to f(x, u, ...).
+ * @tparam Args... Types of remaining arguments to f(x, u, ...).
  * @param f        Vector-valued function from which to compute Jacobian.
  * @param x        State vector.
  * @param u        Input vector.
+ * @param args     Remaining arguments to f(x, u, ...).
  */
 template <int Rows, int States, int Inputs, typename F, typename... Args>
 auto NumericalJacobianX(F&& f, const Eigen::Vector<double, States>& x,
@@ -62,10 +63,11 @@ auto NumericalJacobianX(F&& f, const Eigen::Vector<double, States>& x,
  * @tparam States  Number of rows in x.
  * @tparam Inputs  Number of rows in u.
  * @tparam F       Function object type.
- * @tparam Args... Remaining arguments to f(x, u, ...).
+ * @tparam Args... Types of remaining arguments to f(x, u, ...).
  * @param f        Vector-valued function from which to compute Jacobian.
  * @param x        State vector.
  * @param u        Input vector.
+ * @param args     Remaining arguments to f(x, u, ...).
  */
 template <int Rows, int States, int Inputs, typename F, typename... Args>
 auto NumericalJacobianU(F&& f, const Eigen::Vector<double, States>& x,