Dump non-namelist configuration options to yaml file in run directory

[mcgibbon]

We need to be able to look at a run directory and know what configuration was used to make it. The namelist is already stored in input.nml. We should put the other parameters in another file (possibly input.yml or something like fv3config.yml).

[nbren12]

I just ran into this problem. I think fv3run does this but maybe not write_run_directory.