Bug: Antitraits do not work correctly. This is most prominently seen in agents losing all skill points during a failure (their whole GoodAgent trait line vanishes b/c of the one BadAgent point), but it in fact affects every single antitrait in the game. They are supposed to only cancel an equal number of points from each antitrait not all of the points.
Fix: I managed to work out a fix using only triggers to simulate the way antitraits are supposed to work. It's not a very user-friendly thing to explain, but suffice it to say that I setup triggers to check pretty much all the time to see if a trait and antitrait both have points, and to cancel them from each other if they do. It bloats the file a lot, but doesn't affect game performance in any noticeable way. The link is in my sig for all who are interested.
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