In order for native-deps to do the right thing you need to make sure to package your jar properly. Create a folder called native for the native libraries. Also create folder lib for any normal jars that your dependency uses. For example the LWJGL 2.2.2 library was packaged for Leiningen like so:
/lib /lib/*.jar /native/ /native/macosx/x86/*.dynlib /native/macosx/x86_64/*.dynlib /native/windows/x86/*.dll /native/windows/x86_64/*.dll /native/linux/x86/*.so /native/linux/x86_64/*.so /native/solaris/x86/*.so /native/solaris/x86_64/*.so
The naming convention is important.
Platforms: --------------------- Mac OS X -> macosx Windows -> windows Linux -> linux SunOS" -> solaris Architectures -------------------- amd64 -> x86_64 x86_64 -> x86_64 x86 -> x86 i386 -> x86 arm -> arm sparc -> sparc
You should then create your jar with the following command:
jar -cMf foo.jar native lib
Your jar is ready to push to Clojars. You can read more about that process here