I've been playing with a mixed setup, and I frequentely end up with conflicts which can be ascribed to mixing direct windows repos with indirect linux one(s), and making renames on the indirect ones.
Possibly someone can address what I miss of the git-annex/git interaction.  

#### versions involved ####

linux: git-annex version: 4.20131024
win: git-annex version: 4.20131024-gca7b71e

### Steps to reproduce behaviour ###

###### 1. On linux, i setup bare origin "casa" and client repo "local":
    
    [michele@home ~]$ git init --bare casa
    Initialized empty Git repository in /home/sambahome/michele/casa/
    [michele@home ~]$ cd casa
    [michele@home casa]$ git annex init casa
    init casa ok
    (Recording state in git...)
    [michele@home ~]$ cd ..; git clone casa local
    Cloning into 'local'...
    done.
    warning: remote HEAD refers to nonexistent ref, unable to checkout.
    [michele@home ~]$ cd local; git annex init local
    init local ok
    (Recording state in git...)
    [michele@home local]$ echo lintest > lintest
    [michele@home local]$ git annex add lintest
    add lintest (checksum...) ok
    (Recording state in git...)
    [michele@home local]$ git annex sync
    (merging origin/git-annex into git-annex...)
    (Recording state in git...)
    commit  
    ok
    pull origin 
    ok
    push origin 
    Counting objects: 18, done.
    Delta compression using up to 4 threads.
    Compressing objects: 100% (12/12), done.
    Writing objects: 100% (16/16), 1.48 KiB | 0 bytes/s, done.
    Total 16 (delta 1), reused 0 (delta 0)
    To /home/sambahome/michele/casa
     * [new branch]      git-annex -> synced/git-annex
     * [new branch]      master -> synced/master
    ok
    ```
    
###### 2. On windows I clone origin, and I sync empty

    ```cmd
    M:\>git clone ssh://michele@home/home/michele/casa win
    Cloning into 'win'...
    remote: Counting objects: 20, done.
    remote: Compressing objects: 100% (15/15), done.
    remote: Total 20 (delta 3), reused 0 (delta 0)
    Receiving objects: 100% (20/20), done.
    Resolving deltas: 100% (3/3), done.
    M:\>cd win
    M:\win>git annex status
      Detected a crippled filesystem.
      Enabling direct mode.
      Detected a filesystem without fifo support.
      Disabling ssh connection caching.
    repository mode: direct
    trusted repositories: (merging origin/git-annex origin/synced/git-annex into git-annex...)
    (Recording state in git...)
    0
    semitrusted repositories: 4
            00000000-0000-0000-0000-000000000001 -- web
            598ecfac-087d-49a3-b48d-beafd0d71805 -- origin (casa)
            b2699c17-d0bc-40a0-b447-a64ad109b2a2 -- here (ALICUDI:M:\win)
            bd4166eb-296b-4f0f-a3be-6c25e4c7cbb0 -- local
    untrusted repositories: 0
    transfers in progress: none
    available local disk space: unknown
    local annex keys: 0
    local annex size: 0 bytes
    known annex keys: 1
    known annex size: 8 bytes
    bloom filter size: 16 mebibytes (0% full)
    backend usage:
            SHA256E: 1
    ```
    
###### 3. I copy content from local to win

    ```bash
    [michele@home local]$ git annex copy --to origin lintest
    copy lintest (to origin...) ok
    (Recording state in git...)
    [michele@home local]$ git annex sync
    ...runs ok...
    ```

###### 4. and

    ```cmd
    M:\win>git annex sync
    ...works
    M:\win>git annex get .
    ...works
    M:\win>cat lintest
    lintest
    ```

so far so good.
###### 5. Now the renaming part (performed on linux indirect repo)

    ```bash
    [michele@home local]$ git mv lintest renamed
    [michele@home local]$ git annex list
    here
    |origin
    ||web
    |||
    XX_ renamed
    [michele@home local]$ git annex sync
    ...works
    ```

###### 6.  now, by issuing sync on windows I start getting a "push issue":

    ```
    M:\win>git annex sync
    commit
    ok
    pull origin
    remote: Counting objects: 3, done.
    remote: Total 2 (delta 0), reused 0 (delta 0)
    Unpacking objects: 100% (2/2), done.
    From ssh://home/home/michele/casa
       c3b7a63..a0854bf  master     -> origin/master
       c3b7a63..a0854bf  synced/master -> origin/synced/master
    ok
    push origin
    Counting objects: 9, done.
    Delta compression using up to 2 threads.
    Compressing objects: 100% (4/4), done.
    Writing objects: 100% (5/5), 484 bytes, done.
    Total 5 (delta 1), reused 0 (delta 0)
    To ssh://michele@home/home/michele/casa
       6c18669..8cc74a0  git-annex -> synced/git-annex
     ! [rejected]        master -> synced/master (non-fast-forward)
    error: failed to push some refs to 'ssh://michele@home/home/michele/casa'
    hint: Updates were rejected because a pushed branch tip is behind its remote
    hint: counterpart. Check out this branch and merge the remote changes
    hint: (e.g. 'git pull') before pushing again.
    hint: See the 'Note about fast-forwards' in 'git push --help' for details.
    failed
    git-annex: sync: 1 failed
    
    M:\win>
    ```

at this stage I tried to issue a git annex merge, git annex sync, leading to same result.

somewhere in the forum I read i could try issuing a git pull origin master (this could be the problem).
and the result is as such:

    ```
    M:\win>git pull master
    fatal: 'master' does not appear to be a git repository
    fatal: The remote end hung up unexpectedly
    
    M:\win>git pull origin master
    From ssh://home/home/michele/casa
     * branch            master     -> FETCH_HEAD
    Updating c3b7a63..a0854bf
    error: Your local changes to the following files would be overwritten by merge:
            lintest
    Please, commit your changes or stash them before you can merge.
    Aborting
    
    M:\win>git status
    # On branch master
    # Your branch is behind 'origin/master' by 1 commit, and can be fast-forwarded.
    #
    # Changes not staged for commit:
    #   (use "git add <file>..." to update what will be committed)
    #   (use "git checkout -- <file>..." to discard changes in working directory)
    #
    #       modified:   lintest
    #
    no changes added to commit (use "git add" and/or "git commit -a")
    
    M:\win>cat lintest
    lintest
    ```
    
well, ok it appears modified for some weirdness (crlf?), we can live with it.

    ```
    M:\win>git checkout -->> this replaces files contents with simlink (due to git pull above?)
    ```

at this stage content is lost, and annex has no knowledge about it.

    ```
    M:\win>git annex fsck
    fsck lintest ok
    
    M:\win>cat lintest
    .git/annex/objects/9Z/82/SHA256E-s8--2b721dbe9afe6031cce3004e909dd62e0b4b2f3944438b6a000dffc7ad657715/SHA256E-s8--2b721dbe9afe6031cce3004e90
    M:\win>git annex list
    here
    |origin
    ||web
    |||
    XX_ lintest
    ```

still I cannot sync, but now i can pull origin master:

    ```cmd
    M:\win>git pull origin master                          From ssh://home/home/michele/casa                       * branch            master     -> FETCH_HEAD          Updating c3b7a63..a0854bf                              Fast-forward                                            lintest => renamed | 0                                 1 file changed, 0 insertions(+), 0 deletions(-)        rename lintest => renamed (100%)                      
    ```

this doesnt restore content (annex thinks its already there:

    ```
    M:\win>cat renamed
    .git/annex/objects/9Z/82/SHA256E-s8--2b721dbe9afe6031cce3004e909dd62e0b4b2f3944438b6a000dffc7ad657715/SHA256E-s8--2b721dbe9afe6031cce3004e909dd62e0b4b2f3944438b6a000dffc7ad657715
    ```

I think my mistake is the use of the ```git checkout``` in direct mode. But why is the file detected as modified in the first place ?

note: as long as i didn't drop on origin, i still can recover contents by 'forcing' a content refresh:

    ```
    M:\win>git annex get renamed --from origin
    get renamed (from origin...)
    SHA256E-s8--2b721dbe9afe6031cce3004e909dd62e0b4b2f3944438b6a000dffc7ad657715
               8 100%    7.81kB/s    0:00:00 (xfer#1, to-check=0/1)
    
    sent 30 bytes  received 153 bytes  8.13 bytes/sec
    total size is 8  speedup is 0.04
    ok
    (Recording state in git...)
    
    M:\win>cat renamed
    .git/annex/objects/9Z/82/SHA256E-s8--2b721dbe9afe6031cce3004e909dd62e0b4b2f3944438b6a000dffc7ad657715/SHA256E-s8--2b721dbe9afe6031cce3004e909d
    M:\win>git annex fsck
    fsck renamed (fixing direct mode) (checksum...) ok
    
    M:\win>cat renamed
    lintest
```






