update readme

[kkiesling]

I think there have been a fair number of changes in the use for this since the readme was first written, so that should be updated. Also there has been a full additional tool refine_geom.py made since then that needs to be added.

[kkiesling]

I have been getting questions about how to use this tool / asking for help based on the Example Usage in the README. I am not even sure if those are accurate examples at this point, but they should probably be improved to include real example files that people can use to play around with.