Well, as far as the launcher goes, for a game I'm making myself I'll be using a launcher written in C++/Qt. The idea was that it will be user friendly as they can just double-click on the icon to run the thing; the launcher is then to hide its window, start the JVM process and game jar with whatever arguments are defined, wait until JVM finishes. The reason I'm doing it this way is because Qt is crossplatform, so I can easily recompile it for Windows/Linux/Mac.
For a linux version, having just a .tar.gz with an obvious launcher will be plenty. I think most linux users know what an archive is and how to extract it, and running the launcher themselves shouldn't be too hard. To be honest, I find extracting a .tar* to be much easier than installing an .rpm or God forbid .deb on an .rpm-based system, or the other way around.
I've not had any security warnings running your game btw. I understand the concerns you have in your post, and would encourage you to make Jiun download based instead of browser-based.
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