More modules / hierarchical code structure

[glwagner]

We may want to consider modularizing our code a bit more; for example we could have a Diagnostics module, an OutputWriters module, etc, with folders that correspond to the module name, and with module functionality split into multiple files.

This may make the source code more navigable and also create some opportunities for a clearer API, since we can selectively export different functionality from Oceananigans than from Oceananigans.Diagnostics (for example). In other words, we could write the API so that using Oceananigans brings only bare-bones diagnostics functionality into scope for users, while using Oceananigans.Diagnostics brings a full-fledged suite of diagnostics functionality into scope if that is desired.