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Structured List of Quake Engines
Quake Essentials. Better than what a licencee of id would get in 1996. For even more goodness to base your game off of, see https://github.com/VeraVisions/nuclide
Quake 1 & 2 .pak tools for creating and extracting pak files
Single Player Deathmatch mod incorporating the incredible work of Jan Paul van Waveren (creator of the bots for Quake III)