Only Sven can do that. Now I understand your position, you would like JogAmp to use the same signature for all JARs including JogAmp so that you don't have to sign them by yourself and only a single window asks the user whether he accepts these JARs. In my humble opinion, mixing signed and unsigned JARs is a dead end and you might have to sign JInput by yourself to avoid some problems. What is wrong with signing JInput?
You cannot always rely such a solution. For example, in my case, I use some APIs that cannot be used without being signed from different "providers". I cannot ask them to use the same (non free of charge) certificate, I cannot ask them to sign all their JARs. If you don't want any warning (except the very first time but it's blue, not really scary), buy your own certificate and sign all JARs including those of JInput, GlueGen and JOGL with it.
In my humble opinion, you should not overestimate the impact of the "scary" warning. More than 1300 persons have tried my ugly first person shooter despite this thing.