I have a project managed in Maven that has some native dependencies (LWJGL).
Everything works fine in development, but now I want to set up Maven so
Did you try to use maven-assembly-plugin here is an example :
maven-assembly-plugin
your.main.Class
jar-with-dependencies
And for your native dependencies you may want to use Bundle-NativeCode in your manifest file. See http://wiki.osgi.org/wiki/Bundle-NativeCode.
You also may want to have a look at the maven-bundle-plugin : http://felix.apache.org/site/apache-felix-maven-bundle-plugin-bnd.html to generate it with Maven.