Notice that in the previous example, git annex sync was used. This lets git-annex know what has changed in the other repositories like the laptop, and so it knows about the files present there and can get them.

Let's look at what the sync command does in more detail:

# cd /media/usb/annex
# git annex sync
nothing to commit (working directory clean)
pull laptop
push laptop

After you run sync, the git repository will be updated with all changes made to its remotes, and any changes in the git repository will be pushed out to its remotes, where a sync will get them. This is especially useful when using git in a distributed fashion, without a central bare repository. See sync for details.

By default git annex sync only syncs the metadata about your files that is stored in git. It does not sync the contents of files, that are managed by git-annex. To do that, you can use git annex sync --content