Right the directory structure in the FAQ is no longer 100% correct but it did not change that much. navnodeedit was removed, Nexuiz.app added and a pk3 file was also added to data.. Should be corrected for the next version though.
I do not find the content of the Nexuiz dir confusing. All you need are those two .sh scripts of linux and they even have nexuiz-linux in their name. The nexuiz.exe and nexuiz-sdl.exe should be clearly named too.
Well you NEED to be in the Nexuiz main directory when starting Nexuiz but that could be solved via script files for windows/linux (not sure about mac) when one wanted to create subdirectores Nexuiz/windows Nexuiz/linux und Nexuiz/mac.
Hmm the .app directories should be displayed as a executable on a mac so i guess you just can't see it normaly but others should know more about it.
I think on a mac ~/.nexuiz is used but i'm not sure were that is sorry
