Call 'em "boxes" or "bags" for all I care - the point is the geek word "directory" isn't suitable for non-technical people, I think everyone understand the concept of "putting things in things" because they do it all the time in the real world.
I haven't seen the word "directory" widely used amongst laymen since the move from Windows 3.x to Windows 95, where if my memory serves me (I was 9 at the time) Microsoft made the change to "folder" themselves.