metlslime: via tricks with the portals written by the bsp compiler, which means the vis tool has to support them, too. They don't make much, if any, difference to the engine, but they can make a big difference to the vis tool.
qbism: I suspect you're right about func_water and qfbsp. It's the main thing that made me say "most"

I'm pretty certain I got all the openquartz changes.
I haven't had time to check yet as I'm currently doing a forklift course... in Japanese
