For git-annex version 6 with 'thin'. [I want 1) not store date twice 2) to be able to have self-sufficient repository at different machines (i.e. not special remotes, which don't contain the git tree)].

Say I've two machines A and B and the server S.

I setup a local repository on A:

git init
git-annex init $HOSTNAME --version=6
git config annex.thin true
git add .

on S:

mkdir test
cd test
git init
git-annex init $HOSTNAME --version=6
git config annex.thin true

on A:

git remote add S:~/test.git
git-annex sync --content

on B:

git clone S:~/test.git
cd test
git-annex init $HOSTNAME --version=6
git config annex.thin true
git-annex sync

(the reply)

...
merge: refs/remotes/origin/master - not something we can merge

failed
push origin 
Counting objects: 6, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (6/6), 714 bytes | 0 bytes/s, done.
Total 6 (delta 1), reused 1 (delta 0)
remote: git-annex: unknown command post-receive
...

and the file contains only '/annex/objects/SHA256E-s0--e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'.

Another time with another repo which I tried to sync from S at B, I got

$ git-annex sync --content
Initial commit

Untracked files: 

(all my files untracked)

merge: refs/remotes/origin/master - not something we can merge

error: Untracked working tree file 'applications/algorithms/file.pdf' would be overwritten by merge.
fatal: read-tree failed
failed
git-annex: sync: 1 failed

On walkthrough it's written how to sync with USB. How should one initialize remote repositories and use them e.g. as central repositories (though they should work probably not depending on 'central' or not they are)?

I've read a lot of manuals on git-annex and the forum; the questions here remain unanswered:

http://git-annex.branchable.com/forum/git-annex_SSH_server_+_cloud_remote/

http://git-annex.branchable.com/forum/Synchronize_two_latops_with_a_ssh_remote/

I hope this is a basic and popular usage of git-annex and that one can write a howto for that or at least answer this question.