So yesterday I started playing The Challenger Deep 2, and, as always, I go through the mod's readme text file for anything important. I found out that the author (DocRock) used Valve Hammer Editor 3.5.2 as the mapping tool. Wait. What?
Turns out that VHE 3.5.2 is an unofficial update based on the latest 3.5 beta released by Valve way back in... 2003? Not sure anymore, but this update has some neat new features. Go here to see the changes.
Vluzcans hacks are included but are not applied yet. Just run the executables and follow the instructions to apply the Hammer floating point patch and the Hammer grid hack patch.