And I very much do mean "replaced" there. Physics, since you mentioned that, was switched from Havok to the in-house developed Rubikon. And since Havok is a licensed middleware, they couldn't just bolt some new stuff on and call it theirs. That's going to be a full from scratch replacement.
Similarly the "UI module" was fully replaced, from the Flash-based Scaleform to Valve's in-house Panorama which is fairly similar to HTML5/CSS/JS. This module replacement was also "ported" to Source 1, and was implemented in CSGO as well. Which gets back to the lines between game engines "versions" are blurry.