It's just a shortcut through to the MODS folder.
I NEVER extract any mods that I have d/l'd straight into the MODS folder. I always copy+paste after I have checked the file structure & readme
.
As I say, I might be a little lazy.:p
EDIT - I don't know if I'm in the realms of possibility here, however, is there anyway to 'refresh' JSGME's mods list. I have noticed that any additions/deletions within the MODS folder while JSGME is open will not be updated until a restart of JSGME. Just throwing that one 'out there'.