Hmm, what about checking the darkness while creating an exp file? And about mods - invisibility is quite often used by at least 4 mods, all using the same cvar afair.
About swimming - when fighting, bots don't remember they are out of air...
About doors - as far as I have seen, all classic-type doors recognize(d) it this way, those that move left/right/top do not. But normal door just open in one direction or another... Look at cs_militia.
Shiled is not sufficient, I mean it is good you did that, I pay tribute to you, but lets make PODBot even better
PS. Can't you make waypoints with additional flags make compatible backwards? How are waypoints stored?
EDIT: Bots dont obey waypoints when they are at fight. Then go further from cs_assault's roof and fall too often. And about tactics: an easy way would be covering fire - shooting only to cover and pull other players away. And please reconsider above