Add and update some docs and doc stubs

[charleskawczynski]

This PR:

• Moves the README table to the developer docs (I wrote this when trying to understand the equations)
• Moves the index.md contents to a newly added API.md, where we can have/add doc string links
• Adds Formulation.md, where we can add (perhaps some from the EDMFEquations.md) a story of the EDMF formulation including figures and equations
• Silences the printed statements in ReferenceStates.md

[ilopezgp]

I actually like the prognostic/diagnostic table, I think it is very useful. I would keep it in the README; everything else looks good to me,

[charleskawczynski]

bors r+

[bors]

Build succeeded:

• buildkite/turbulenceconvection-ci
• docbuild
• format