I have some knowledge of C++ as well as experience in modding and such for a bunch of other games. I don't know the first thing about modding for JK2 or JA, though.

I want to make some simple server modifications. I want to fix it so people get 100 life and shield when they engage in a duel in FFA, and I want to be able to make people spawn with certain extra weapons and items. If possible, I'd also like to be able to make new cvars to turn some of those extra items on/off.

It'll be very simple compared to most mods. All I need is some quick info on where to find what I need to add to, like a server script that it runs when people spawn or something like that. Can anyone tell me how to get started?

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Download the JK2 Edit Tools v.2 from Jedi Knight II Files (http://www.jediknightii.net/files/index.php?link=file&id=951)
Take a look at some of the source code for other server mods made available freely by the author (look around and you'll find some)
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Those should be plenty to get you started thinking about modding for JKA.