How would you correct it in thread-safe manner?  AFAIK, the JVM's notion of 
"current working directory" is a single, global value.  There are other 
subtle issues, as well, e.g., anybody who can connect to your nailgun server 
can cause arbitrary code to be executed in your name.  One of the more 
surprising aspects (to me) is that state defined during one run of 
clojure.main still exists in subsequent runs; e.g.:

$ ng clojure.main -e '(defn speak [] "hello")'
#'user/speak
$ ng clojure.main -e '(speak)'
"hello"

Every time you start a repl with nailgun, your 'user' namespace already 
contains whatever you left in it.

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