Document input files for common/basic model runs

[khaeru]

@michd-mit, @emonier, @jrscott —can you dump notes here on paths to/contents & purpose of input files, as discussed in the tutorial run by @apsokolov a couple weeks ago?

After that we can decide which to include in the repo, or simply mention in expanded documentation.

[emonier]

@khaeru - I worked on cleaning up the run script and expanded upon the realm file. I need to go back to it and finish it up. I will try to do so next week.