Add flags documentation to README.mdown and contrib/make-docflags.sh

Add command flags help to README.mdown. Add contrib/make-docflags.sh to assist in maintaining this.

I updated the README.mdown 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 in the future.

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.