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Do you plan on making this a library?

Also is there a way to remove all viewable sprites in the atlas?  It'll be useful for fighting games that need a lot of sprites for animation.

What do you mean? There is a clean button on the sprites list to remove all sprites from the atlas.

There can be sprites that have a red border around them that are not on the atlas, is there a way to automatically delete all the viewable sprites (ones without the red border)?

(+1)

Not for the moment but I take note about it, I can add it in a future but unfortunately not for next release.

Actually most of the functionality of this tool is directly available in raylib. You can use raylib.