The emulator was previously available at http://jsemu.github.io/gba/, and Nintendo’s letter argued that the site gave people “access to unauthorized copies of Nintendo’s copyright-protected video games and videos making use of Nintendo’s copyrighted Pokémon characters and imagery in violation of Nintendo’s exclusive rights.”
Among the titles included in the infringement claim were Advance Wars, Super Mario Advance, Pokemon Emerald, Pokémon Silver and Gold. Nintendo’s request contained links to 32 different emulators that Github was hosting, and a notice that they be removed immediately. Github has complied, as all the links now show 404 errors.
The user who originally posted the files seems to have also deleted his account, possibly out of fear of additional trouble from Nintendo. However, the original code for the Game Boy emulator without any pre-loaded games, is actually open source, and can still be found in a number of places on Github.