Finish Thermodynamics revamp

[trontrytel]

Left to do in follow up PRs:

• Update 2M microphysics to working fluid. Update 2M scheme to working fluid changes #609
• Delete TD.PhasePartition from function signatures in Atmos and then delete the wrappers. Wip on deleting PP from microphysics interface #611
• Change the notation in CloudMicrophysics to q_tot = q_vap + q_liq + q_ice. And q_liq = q_lcl + q_rai, q_ice = q_icl + q_sno
• Update the documentation in CloudMicrophysics to explain the thermodynamics interface
• Following @haakon-e suggestion create internal thermodynamics parameters set