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I'd like to get into modding and I was wondering if anyone had suggestions for a first game to get my feet wet. I have a good amount of programming experience and am proficient in C++, Java, and Python. Most of what I have found has pointed toward the Unreal Tournament series or Half Life 2 due to the plethora or documentation, tutorials, developers tools, ect. However, I haven't been able to find a thread that's newer than like 2009 so maybe there's something newer that would be better. If it helps, I'm not very interested in changing skins/graphics, I'd rather write code to alter gameplay mechanics and behavior of items/weapons. Thanks for your input.
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Though I think that it might be a little different from what you are actually asking.
I'd start there, or with Minecraft, and move up to UDK.
The downside with Minecraft is, at any moment, they could release their modding API and basically completely set everything back to square 1 as far as modding goes.
They also reobfuscate all their code with each update making modding a nightmare.
Also you have to mod directly to the metal.
Minecraft would be a great choice once the API is available, but right now it's all working with obfuscated code and that's just no fun from my perspective. You can do quite a lot with the Bukkit API, but it's on its way out now that its developers were hired to produce the official MC API.
Skyrim is a good choice for the actual "modder" because it's basically a big modding toolkit, but if you're interested in programming there's not a lot there aside from the scripting engine. Skyrim modding is basically working with its "Creation Kit," which is a full suite of game editing tools; map editor, quest/dialog/item editor, etc.
I'm going to throw out another suggestion because you specifically talk about your programming experience: Torque.
It's technically based on the engine from Tribes 2, but it's been upgraded over the years to be graphically in-line with modern engines, have PhysX support, etc. It's also completely open source, which means instead of just some modding API you can work with the entire code library, from physics engine integration all the way down to deep rendering code and networking. This suggestion is less for the aspiring modder (most mods are level design, scripting, art assets, etc.) and more for the aspiring game developer, because you'll get exposed to the serious parts of a game engine (the parts most engines make you pay big $$$ to even look at). It also has a pretty powerful scripting engine on top of all the code and has good world editing tools built into the engine, so you get exposure to the whole game development chain.
Here's the GitHub page for Torque: https://github.com/GarageGames/Torque3D
A lot of people prefer Unity, and it's probably a more robust tool if you're actually making a game, but if you want to get your hands straight into some serious engine code Torque is a better choice since you can get access to that engine code without having to pay (and as far as I know Unity never upgrades to full engine code, it just has an SDK like Source). Torque might be a bit overwhelming to jump straight into so it really depends on what you want out of this.