I’ve just had this problem, and I solved it by adding an explicit dependency on the newer version of tools.nrepl to profiles.clj. My ~/.lein/profiles.clj:
{:repl {:plugins [[cider/cider-nrepl "0.9.0-SNAPSHOT"]]
:dependencies [[org.clojure/tools.nrepl "0.2.7"]]}}
No idea whether that’s the best or official way to do it, tho’.