This part has been troubling me too. As I don't 'alter' the base program or Geometries folder(s), I do rearrange the figure/prop/materials folders to keep things separated for ease of finding them as my minagerie grows: does this constitue "modified" or is the notice refering to 'app specific files'? (rearranging/reinstalling the libraries can take a lot of time and one never knows what was updated or changed when you go to put it all back again)