Change checkpointing to handle new fields at later timesteps

[vidulejs]

setupCheckpointing is called only at the start of the simulation, limiting checkpointing to only the initial fields. However, potentially a new field may be written at a later timestep. Maybe a turbulence model is turned on after initializing with a laminar flow, maybe a function object, etc.

There was a bug associated with a temporary field 'grad(U)' popping up during a step on the 'kOmegaSST' turbulence model calculation, see pull request #344. But this was the opposite case so to say, because a field was present at initialization but not at later timesteps.

I still need to think about the implementation and if this is really needed. Perhaps it's needed if users report problems related to this.