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Environmental hazards: There were plenty environmental hazards in DX that you could simply turn on regen aug or speed enhancement and run right through. More challenges: this would just be an extra camera, NSF, turret, greasel or what have you were it makes sense to do so. Very minor and simple changes that make the related RPG systems that much better. These are always minor changes to give swimming skill and aqualung aug more weight, for example in Everret's fish tank I made getting to the goodies and back harder to navigate, but it's still the same old fish tank. Some AI react to stealing, more AI react to breaking and entering and so on. Half of the AI improvements in GMDX are done via the maps, which is good because some things are situational.
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Primarily to give lockpick skill more weight that it needed. Sometimes in Deus Ex there was an optimal path to take no matter the build. Here's what I've done, in short, with the levels:
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