(defproject ordered-set "0.2.0"
  :description "A Clojure set that maintains the insertion order of items"
  :dependencies [[clojure "1.2.0"]]
  :source-path "src/clj/"
  :java-source-path "src/jvm/"
  :library-path "lib/"
  :javac-options {:destdir "classes/"}
  :aot [clojure.lang.PersistentOrderedSet]
  )

Project structure:

./LICENSE
./README.md
./project.clj
./src
./src/clj
./src/clj/ordered_set.clj
./src/jvm
./src/jvm/clojure
./src/jvm/clojure/lang
./src/jvm/clojure/lang/PersistentOrderedSet.java
./test
./test/test_ordered_set.clj
./classes
./classes/clojure
./classes/clojure/lang
./classes/clojure/lang/PersistentOrderedSet$TransientOrderedSet.class
./classes/clojure/lang/PersistentOrderedSet.class

The error:

[:-)] % lein compile
Compiling 1 source file to /home/horn/repos/clj/ordered-set/classes
Compiling clojure.lang.PersistentOrderedSet
Exception in thread "main" java.io.FileNotFoundException: Could not locate clojure/lang/PersistentOrderedSet__init.class or clojure/lang/PersistentOrderedSet.clj on classpath:  (NO_SOURCE_FILE:1)
	at clojure.lang.Compiler.eval(Compiler.java:5440)
	at clojure.lang.Compiler.eval(Compiler.java:5415)
	at clojure.lang.Compiler.eval(Compiler.java:5391)
	at clojure.core$eval.invoke(core.clj:2382)
	at clojure.main$eval_opt.invoke(main.clj:235)
	at clojure.main$initialize.invoke(main.clj:254)
	at clojure.main$null_opt.invoke(main.clj:279)
	at clojure.main$main.doInvoke(main.clj:354)
	at clojure.lang.RestFn.invoke(RestFn.java:422)
	at clojure.lang.Var.invoke(Var.java:369)
	at clojure.lang.AFn.applyToHelper(AFn.java:165)
	at clojure.lang.Var.applyTo(Var.java:482)
	at clojure.main.main(main.java:37)
Caused by: java.io.FileNotFoundException: Could not locate clojure/lang/PersistentOrderedSet__init.class or clojure/lang/PersistentOrderedSet.clj on classpath:
	at clojure.lang.RT.load(RT.java:412)
	at clojure.lang.RT.load(RT.java:381)
	at clojure.core$load$fn__4511.invoke(core.clj:4905)
	at clojure.core$load.doInvoke(core.clj:4904)
	at clojure.lang.RestFn.invoke(RestFn.java:409)
	at clojure.core$load_one.invoke(core.clj:4729)
	at clojure.core$compile$fn__4516.invoke(core.clj:4916)
	at clojure.core$compile.invoke(core.clj:4915)
	at user$eval7.invoke(NO_SOURCE_FILE:1)
	at clojure.lang.Compiler.eval(Compiler.java:5424)
	... 12 more