Comment made by: stuart.sierra
Currently, clojure.java.classpath handles neither JAR Manifest files nor nested JAR files. As I described in my previous comment, implementing support for this would be difficult and is not likely to be a priority for me any time soon. I would be willing to review a patch to add this capability, but it would have to prove that it protects against recursive cycles.
By my reading of the (link: http://docs.oracle.com/javase/7/docs/technotes/guides/jar/jar.html text: JAR File Specification), the behavior of clojure-maven-plugin could be considered against the spirit of the JAR spec, which decribes the "Class-Path" manifest attribute this way:
"Class-Path: The value of this attribute specifies the relative URLs of the extensions or libraries that this application or extension needs." (emphasis added)
The clojure-maven-plugin is creating a JAR manifest with a "Class-Path" attribute containing absolute URLs to other JAR files which are not embedded in the JAR containing the manifest.
I have always assumed that JAR manifest files with Class-Path attributes are used only when packaging complete applications or JDK extensions, not as a mechanism for specifying the class-path during development. Clearly it is possible, as the current clojure-maven-plugin demonstrates, but it is not a feature I would want to rely on.
In general, the JDK does not support enumerating all files on the classpath, since the classpath can include URLs to remote resources which are downloaded as needed.