AD has some vanilla Quake gun models as placeholders I assume, this "patch" or whatever replaces them, also some sounds, and adjusts the shotgun animation so it's synced up with shell extraction. This uses the models optimized for Spasm, since it's the recommended engine for AD, and the alternative snailgun instead of the Doom chain. The axe isn't replaced. I've only played a little bit so maybe there are other issues, but that fixes the base guns. I haven't touched the nailgun anims because AD guys may still change the spot where the projectiles spawn, as they aren't aligned with the included models. 

Installation: make back ups of "sound" and "progs" folders in quake/ad and extract this archive into it answering yes to all prompts.