When Clojure starts, it sets the Var *compile-path* to the value of the Java system property. The default is the directory named "classes".
Whatever value you set for clojure.compile.path, that directory must also be on the Java classpath, set with the -cp command-line option to java.
So, if you want to compile Clojure namespaces rooted at the current directory, you would run:
java -Dclojure.compile.path=. -cp .:clojure.jar clojure.main
-Stuart Sierra