I'm having an issue with 2 repos: one on my laptop, the other on my NAS. Both are in indirect mode, running Arch Linux, and have the latest Git version. Laptop has git-annex 5.20140411-gda795e0, NAS has 5.20140319-g9aa31b7 (from prebuilt tarballs).

The issue is quite simple. When I `git-annex add` new files on my laptop, commit them, and then `git-annex sync` them, they show up as staged for deletion on my NAS.

    laptop $ git annex add some-file
    laptop $ git commit -m "Add some-file"
    laptop $ git annex sync
    commit  ok
    pull ds413j 
    ok
    push ds413j 
    Counting objects: 133, done.
    Delta compression using up to 8 threads.
    Compressing objects: 100% (78/78), done.
    Writing objects: 100% (80/80), 10.64 KiB | 0 bytes/s, done.
    Total 80 (delta 12), reused 0 (delta 0)
    To ssh://**/**
       1dcd188..8ef4249  git-annex -> synced/git-annex
       c0f45a6..21711d6  master -> synced/master
    ok
    laptop $ ssh $NAS
    nas $ git status
    On branch master
    Changes to be committed:
      (use "git reset HEAD <file>..." to unstage)

            deleted:    some-file

    nas $

If I run `git annex sync` on the NAS, it will create a new commit that deletes that file. So I have to play with `git reset`/`git checkout` by hand to make sure that the new file won't be deleted.

I'm not sure when this started, but I think it was after I did some stupid mistake (`git checkout -B master synced/master`, kill a `git annex sync` with Ctrl+C, or something else that even resulted in my non-bare repo to have "bare=true" in .git/config...). And I haven't yet been able to fix this.

Any idea what can have caused this, how to fix it, and how to prevent it from happening again in the future?

.git/config on NAS:

    [core]
            repositoryformatversion = 0
            filemode = true
            logallrefupdates = true
    [annex]
            uuid = d54ae60a-1f59-403c-923f-32ea3bf2d00f
            version = 5
            diskreserve = 1 megabyte
            autoupgrade = ask
            debug = false

.git/config on laptop:

    [core]
            repositoryformatversion = 0
            filemode = true
            bare = false
            logallrefupdates = true
    [branch "master"]
    [annex]
            uuid = f20cb506-945d-4c78-af1a-0aa884bb899b
            version = 5
            diskreserve = 20 gigabytes
            autoupgrade = ask
            debug = false
            expireunused = 7d
            genmetadata = true
    [push]
            default = matching
    [remote "ds413j"]
            url = ssh://**/**
            fetch = +refs/heads/*:refs/remotes/ds413j/*
            annex-uuid = d54ae60a-1f59-403c-923f-32ea3bf2d00f
            annex-sync = true