It seems Leiningen's compile task looks for source packages to start immediately under the /src directory. I use both Java and Clojure in my project, so my /src directory looks like this:
/src/java/myapp
/src/clojure/myapp
Right now Leiningen is looking for /src/myapp and it's failing out during the compile.
Related, I'd like to know how to manually add directories to the classpath for Leiningen's compile and repl tasks. For example, Enlive's deftemplate function will search the classpath for a named template file. Adding /templates to the classpath would be required for my project to build and run properly.