I agree, it's a bit confusing how it's written, and I'm not even really sure what using lein would buy you when doing the koans. If anyone is interested in using lein, here's what you need to look at: https://github.com/functional-koans/lein-koan

Specifically:

  git clone git@github.com:functional-koans/clojure-koans.git
  cd clojure-koans
  lein deps
  lein koan run