* 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 helps reduce compilation overhead. I tried slimming down includes
of <Eigen/QR>, but the householderQr() function we use from there
requires including dependency headers from Eigen that don't fit with
lexographic ordering. It didn't seem worth the effort to work around.
This won't affect user code at all since all the Eigen feature usage
here is internal only; users generally only need <Eigen/Core>.
