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JC was augmented so that chain-eating candy bars would heal his injuries.He has some kind of augmentation that, after allowing the body to take in a set number of calories for the day (calculated considering JC's size and weight and how much he must burn running around killing people), any extraneous calories that JC consumes are used as energy to fuel some rudimentary regeneration and healing capabilities. And the mooks are all augmented with old technology.
JC has a passive adaptive vision augmentation - it adapts to the surroundings, but has its limits (ie pitch black is still pitch black). Perhaps they just don't have the passive vision aug? No word on how this works out in brightly lit labs and complexes, or against augmented mooks. He wears his sunglasses to conceal his augmented eyes, which would be very visible in the dark. Also, if you look at JC's sunglasses closely, you can see two blue dots. One can only wonder how amazing his eyesight would be if he took them off for once.
This HAS to be true, otherwise everything would appear dark and blurry due to his insistence on permanently wearing his sunglasses. The logical solution is that JC has a passive visual augmentation - he sees much more clearly than the NPCs, so an area that appears to moderately dark for him (ie most of the game) is actually much darker through the NPC's eyes. Also, in a oft-quoted line, JC says that "my vision is augmented", yet at that point it's impossible to have any of the vision-related augmentations. JC has passive nightvision.One thing that always bothered me about Deus Ex is how enemies can see you more/less in plain sight, and still not seem to notice you.