joey@darkstar:~/tmp/bench/me>git init ../other
Initialized empty Git repository in /home/joey/tmp/bench/other/.git/
joey@darkstar:~/tmp/bench/me>git remote add other ../other
joey@darkstar:~/tmp/bench/me>date > foo
joey@darkstar:~/tmp/bench/me>git-annex add foo

With this setup, git-annex sync --content does not send foo to other the first time run. However, on the second run it, does.

If the other repo had git-annex init ran in it first, it would sync content to it on the first run.

Auto-init only happens once the git-annex branch gets pushed to the remote and git-annex enumerates that remote. So after the first sync in this situation, the remote has a synced/git-annex branch, but no uuid yet. The second sync then auto-inits.

To fix this, sync could re-enumerate remotes after pushing, I suppose. But re-enumerating remotes is some work so it would need to do it only for ones that have no uuid.

Saw this happening in yann's talk. --Joey