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When the Source engine was being developed (and still is being updated, with current versions having great technical potential - hence Dear Esther and several amazing Source mods) they started out with the GoldSrc code, and eventually replaced all the existing code for a particular component as a new one was being developed.
So, have you seen Source source code? Or are you Valve employee? How do you explain that bugs from original Quake (eg. bunnyhopping) still exist?
A lot of these bugs are common for the type of renderer that Source uses and happens across multiple different engines that use the same sort of renderer. Also, there are things that still exist from the Quake days because the engine isn't entirely rebuilt - only most of the major components have been recreated.
I think there was an article detailing the engine's development process from 2006, but I'm not having luck finding it.