* Replace Matrix<> with Vector<> where vectors are explicitly intended.
I found these via `rg "Eigen::Matrix<double, \w+, 1>"`.
* Pass all Eigen matrices by const reference. I found these via `rg
"\(Eigen"` on main (the initializer list constructors make more false
positives).
* Replace MakeMatrix() and operator<< usage with initializer list
constructors. I found these via `rg MakeMatrix` and `rg "<<"`
respectively.
* Deprecate MakeMatrix()
This address some problems with the LinearSystemLoop class that were discovered through testing.
The initial state estimate of the observer was set to the provided initial state rather than zero as previously, a non zero initial state passed into reset() would lead to a discrepancy between the current state estimate and the actual system state.
