Convert README.txt to markdown file; add waffle.io badge

Since .txt files don't support images, we opted to convert README.txt to README.md so that we could add a waffle.io badge and did some minor formatting.
If you would still like to link to your board but would rather not deal with Markdown, you can add the url http://waffle.io/ged-lab/khmer to the existing README.txt -- won't be able to display the badge image, though.
Thank you for giving us a try!