I'm also having this problem. I just started playing with Clojure, Lein and 
Clooj and am working with the Halloway Programming Clojure book next to me. 
I'm was just trying to do some file reading using 
clojure-contrib.duck-streams and is working in Lein but somehow not in 
Clooj. I can see the correct jars will get picked up on the classpath in 
Lein, and from what you say that means should definitely be picked up into 
Clooj REPL also - is there a means of checking the Clooj classpath directly?

Anyhow only just started, but does all look very promising - Clojure, Lein 
and Clooj

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