On top of the previous v1.01 fix:
-Fixed source files not matching what's inside the compiled progs files.
-Fixed duplicate zip file.
-Fixed series of shootable buttons leading to a secret in start.bsp where they were shootable multiple times, nullifying the challenge of finding the secret.
-Fixed possible softlock at the end of tot1.bsp, train doors now open permanently on top of their activator being locked behind counters.
-Railgun now does 95 damage on Deathmatch rather than the whopping 270 in Singleplayer for balancing reasons.
v1.011 fix:
-Added navigation aids for map 3, 4, and 5
-Fixed issues on map 3 and 5 on easy skill where counter-based critical encounters didn't trigger properly, making progress impossible
-Diminished fog amount for the final boss' third phase, making far-away targets easier to see
Download link is the same as before (mediafire link).