Well, my opinion on this is that S.T.A.L.K.E.R. has probarbly just used doom 3, and hamy half life 2, and maybe other games, as examples of work they would like to re-create.
And then if they did, or if they took the game's files and edited them a little bit, and it looks good, why complain about it.
Sure it's cooler and harder to make everything yourself, but why re-make something instead of using what's out there, since you want it to look like that anyway.
Ofcourse this doesn't clear up the fact that the material is not allowed to sell, but I'm pretty confident that they'll have some kind of deal going, if you're posting extracting tools and planning to let modders have a bang at your game you'd be a right idiot to leave in material that's illigal right?
Anyways, wonder what the outcome of this find will be
