One of the aspects emphasized in TFA is being able to simulate gates of any dimension/number of qubits (like a 3-qubit Toffoli or a 5-qubit Molmer-Sorensen), instead of just 1- and 2-qubit gates. Have you thought about extending your simulator to support gates of greater than two qubits?
I guess back when I wrote it I didn't see the need given that single qubit gates along with CNOT are universal and they're implemented. I think airing on the side of 'as few features as is educational' was my mentality on this.
See e.g. equations (5) and (6) from [1], where any qubit subset of a system might undergo the action of the M–S gate. But definitely the usual presentation of the physics of M–S is on a two qubit system.
