Too many to list honestly; SDL2 implementation for both video and input (both of which have been completely rewritten to take full advantage of it), completely rewritten game-logic in C including a complete base framework for weapons, items and more, separated Launcher/Engine/Game/Menu components, Linux support including a library to deal with all platform-dependent functions, a completely new UI system including support for menu states, a far more versatile particle system with support for textured particles (and lit particles), MD2 and PNG support, a new simple rendering framework with capabilities management and crap with some simple debugging features, various additions to the BSP format, static light references which are used for point-based planar shadows (they're basically affected by both dynamic and static light sources) including blob shadows, log output during runtime, better transparency support for brush models including support for alpha-tested surfaces, brush model rotation support, and about a billion fixes. There's way more but I can't remember off the top of my head, we're looking for more programmers though to help out if you're interested
