refactor readme

[X1011]

i think the readme needs some refactoring now. It doesn't make sense anymore to instruct users to edit the variables in the script itself, especially considering how deeply buried those default values have gotten with the recent changes.

i'm thinking we merge the configuration and options sections, and the run section can be simplified, or maybe even mixed somewhere in with the rest, too.

overall, it should be more like a man page now that the script is more like a full-fledged command-line utility.

i hopefully will be able to tackle this in the next couple of days, but you, of course, are welcome to take a shot, too, @matro (or anyone else who happens to be lurking here).

[matro]

I did a quick shuffle of the existing content on my "readme-refactor" branch. Not sure how I feel about it yet.