Clean up legacy constructors

[ali-ramadhan]

I think we need a PR focused on cleaning up some of the legacy constructors out there before the code gets used by others.

In particular I'd like to work on #413 (currently on the grid-xyz branch) which involves refactoring the RegularCartesianGrid constructor and I'd rather not leave behind three legacy constructors.

Also, I'm not a fan of the BasicModel constructor. I understand it was introduced to avoid refactoring all the Model constructors, but would be nice to get rid of it.

[ali-ramadhan]

I'd also like to introduce a single time_step! function

time_step!(model; Δt, Nt=1)

and get rid of the "legacy" time_step! functions.