[x] MatrixNaiveXSubset should save subset as a map. It is inconsistent with how other matrices are defined.
[x] Make sure all "user inputs" are saved as a map. Any derived quantities can be saved internally without a map to maximize shared code between Python and R.
[x] All "user inputs" should have a reference of a copy saved in the Python side.
MatrixNaiveXSubset
should savesubset
as a map. It is inconsistent with how other matrices are defined.