one-jar's [http://sourceforge.net/projects/one-jar] jar-in-jar doesn't work w/ Jogamp. It shall work similar as w/ Eclipse's jar-in-jar, see Bug 522 Comment 7.
One-Jar lacks support of a URL handler for it's jar-in-jar files and hence we would need to extract the jar-in-jar resources w/ our TempJarCache from one one-jar file .. too bad. Looks like it's incomplete. i.e. we cannot access the jar-in-jar gluegen-rt.jar resources of jar:file://home/sven/projects/JOGL/gluegen/test/TestOneJar_InJar/jogamp01/build/jogamp01.jar!/lib/gluegen-rt.jar!/com/jogamp/common/os/Platform.class jar:file://home/sven/projects/JOGL/gluegen/test/TestOneJar_InJar/jogamp01/build/jogamp01.jar!/lib/gluegen-rt-natives-linux-amd64.jar!/ Note the jogamp01.jar notation as a file within jar, i.e. 'file:/</home/sven/.../jogamp01.jar!>/..', where /home/ denotes the authoritative section. Since One-Jar does not register the URL handler .. we would need to extract all jar-in-jar files and map them ..