Simplify README

The list of the commands is starting to make less and less sense to me. With all the logic we've introduced, the list does not really work. I created wiki pages for the each of the commands, which is basically an HTML version of the man page. I'm hoping that once the wiki pages are good, this PR can go through.
Do we need to document the particulars of the output? I don't think it adds much to the understanding of it here on the top-level page. I would either scrap this part, or move it into a dedicated page that is linked to from here.