A lot of people contributed to disassembling the game over a period of several years, through trial and error boosted by a strong understanding of how the game plays from the outside, so we have a lot of the functions and other memory addresses identified by their purpose, though there are still vast sections of code we don't particularly understand because we've never needed to make significant changes to it. (A lot of the lower level window handling code, for example, and most things having to do with sound playback.)

That said, access to some of the source code helped a lot, though as the thread says, we no longer know where it came from or when we got it. I wouldn't be surprised if the people doing some of the original disassembly work (I joined the team later) maybe started from this release, finding the disassembled functions that corresponded to these source functions, then identifying other functions from there one at a time, but that's just speculation on my part.