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 master # git annex get . get my_cool_big_file (copying from laptop...) ok get iso/debian.iso (copying 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.