This is written from the perspective of CIDER - I assume this still belongs here and not in CIDER

If you call (clojure.main/repl) in nREPL, the reading and printing is not done via nREPL magic anymore but by the implementation of clojure.main/repl.
The stdin reading triggers an outgoing nREPL message with status ("need-input"), which CIDER handles completely different than the normal input prompt in the REPL buffer.

This currently prevents using a break macro (https://gist.github.com/leobm/6061734) in CIDER
and causes clojure-emacs/cider#2017.