I have just done a sync in a direct mode repo:

    git-annex sync sshremote

It has quite a few conflicts (both sides adding the same file with same content). But somehow the merge won't conclude. Here's some log:

    $ git-annex sync sshremote
    commit  ok
    pull sshremote 
    warning: no common commits
    remote: Counting objects: 32162, done.
    remote: Compressing objects: 100% (31192/31192), done.
    remote: Total 32162 (delta 3), reused 32162 (delta 3)
    Receiving objects: 100% (32162/32162), 3.39 MiB | 1.61 MiB/s, done.
    Resolving deltas: 100% (3/3), done.
    From sshremote:/repo
     * [new branch]      annex/direct/master -> sshremote/annex/direct/master
     * [new branch]      git-annex  -> sshremote/git-annex
     * [new branch]      master     -> sshremote/master
     * [new branch]      synced/master -> sshremote/synced/master

    Auto-merging file1
    CONFLICT (add/add): Merge conflict in file1
    Auto-merging file2
    CONFLICT (add/add): Merge conflict in file2
    Auto-merging file3
    CONFLICT (add/add): Merge conflict in file3
    Auto-merging file4
    CONFLICT (add/add): Merge conflict in file4
    Automatic merge failed; fix conflicts and then commit the result.
    file1: needs merge
    file2: needs merge
    file3: needs merge
    file4: needs merge
    ^C

I waited for a few minutes, and checked that both cpu and disk activity is near zero on both server. So I interrupted it, thinking it might be some locking issue. 

But now I cannot sync with the remote anymore because the merge is still in process. How should I resolve the conflicts? I could do it manually if I cannot use annex's auto merge.

    $ git-annex sync sshremote
    commit  ok
    pull sshremote 

    fatal: You have not concluded your merge (MERGE_HEAD exists).
    Please, commit your changes before you can merge.

    fatal: You have not concluded your merge (MERGE_HEAD exists).
    Please, commit your changes before you can merge.
    failed

    $ git merge --abort
    fatal: This operation must be run in a work tree

Update: this is running on OSX with:

    git-annex version: 5.20131221-g00d1673
    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi TDFA CryptoHash
    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
    remote types: git gcrypt S3 bup directory rsync web webdav glacier hook
    local repository version: 3
    default repository version: 3
    supported repository versions: 3 5
    upgrade supported from repository versions: 0 1 2 4