On a linux server I created a (direct) git annex repository:

$ ls -a
.  ..  apps  attic  devel  games  .git  portable  tools

On a Windows client, I want to check it out:

me@client /cygdrive/c/tmp
$ git clone ssh://me@server/srv/data/bin bin
Cloning into 'bin'...

But git annex checks only half of it out :-(

me@client /cygdrive/c/tmp
$ ls -a bin
.  ..  .git  attic  games

Any ideas? Sorry, I am very new to git-annex (and git).