What’s the best way to manage/edit atlas files? I’m using libGDX and I’ve spent too much time trying to map coordinates and such only to have to change them all again if I decide something in the middle of the map isn’t the right size. I sooooo need an artist. 
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If you’re getting an artist to create and assign atlas coords manually you’re wasting their time. Why would you want them doing that when they could be making your game look more awesome with better art?
Why not generate the atlases automatically? You can do it either at compile-time with a tool or at runtime. Search for bin-packing algorithms if you want to see how it could be done.
What’s wrong with the TexturePacker that comes with libgdx? It packs the textures and provides an atlas completely free
Absolutely nothing… I just starting messing with this yesterday evening and this is what I was looking for; thanks.
Aurelien (the creator of the Libgdx TexturePacker) is an amazing guy. He also made many other tools.
If you want to start using Box2D too, this is your friend: Physics Body Editor
Automated Libgdx Project Setup Tool - Sets up a Project-folder, Desktop-folder, Android-folder and a HTML5-folder. No iOS yet, I’m afraid.
Universal Tween Engine - epic tool to animate, well, ANYTHING. It makes everything SO easy.
Good luck!