Update README.md with flag commands

I updated the README.md (renamed from README.mdown since .md is more standard) to include docs on all the various commands. I put a script in contrib that will generate most of the text as well. It can be used to help update the README after edits.

I note that shFlags has a FLAGS_HELP variable that can be used with flags_help(). It might be possible to get the various help commands to kick out more info by hooking into that...