Sneaky Pete. In the Shadows Quake mod
Hopefully I am not the only one here that is interested in this. So far I've only put an hour into it and eventually had to dispense with hiding and rely on guns because I am bad at stealth games so I'll have to work on that. By the way, if you do go in there all guns blazing don't pick up the magical stealth amulet because it makes all guns and their ammo types vanish when you try to grab them. You really have to commit to stealth, there's no turning back. I had a bit of a chuckle the first time that happened to me as I was being chased down by a Hellknight and got to the nailgun when *poof* and then he just opened me up.
The stealth part is bare essentials so it won't be stealing anyone away from Thief but it totally fits Quake. I could totally see Quake being like this back in 1996 if id Software wanted to make a stealth title instead of Doom meets Cthulhu. Two of the maps here are remakes of e1m1 and e1m2 so it's not a stretch. They look fantastic, everything here looks fantastic like those really top shelf mods that you'd stumble upon every few months when Quake was in its prime. Man those were the days.