On my Linux box, it's the folder that shows up as KOBOeReader; it has a visible folder called "Desktop Installers", and several hidden folders: .adobe-digital-editions, .kobo, and .Trash-1000 - those are not marked as hidden when I connect to my Windows laptop. All my books show up beside the "Desktop Installers" folder, as I don't usually "Show Hidden Files".
This is how it shows up to mount:
/dev/sdc on /media/KOBOeReader type vfat (rw, nosuid, nodev, uhelper=udisks, uid=1000, gid=1000, shortname=mixed, dmask=0077, utf8=1, flush) -- (spaces added to allow wrapping)
|