I've had this problem too.  I solved in a slightly different way.  I had my 
main function in a clojure file that also defined a component.  I moved my 
main function into a different file and that did the trick.  I didn't need 
a :gen-class directive in each file that had a component.  I didn't need to 
bring my user.clj into my main source tree, I didn't need the 
:clean-non-project-files false directive either...just pulled the main 
function out of the file that also defined a component.  

Each time I did a 

 lein clean; lein deps; lein compile; lein repl


  -or- 
 
lein clean; lein deps; lein compile; lein uberjar



These are the directives I did use in my project.clj:

 
 :main example.core
  :uberjar {:aot :all}
  :aot [example.core]
  :repl-options {:init-ns user}



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