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 
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
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:

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

.git/config on laptop:

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