A repository does not always have all annexed file contents available. When you need the content of a file, you can use "git annex get" to make it available. We can use this to copy everything in the laptop's annex to the USB drive. # cd /media/usb/annex # git pull laptop # git annex get . get my_cool_big_file (from laptop...) ok get iso/debian.iso (from laptop...) ok Notice that you had to git pull from laptop first, this lets git-annex know what has changed in laptop, and so it knows about the files present there and can get them. The alternate approach is to set up a central bare repository, and always push changes to it after committing them, then in the above, you can just pull from the central repository to get synced up to all repositories.