I have a git annex repository which I use to store versioned binaries in a regular git repository. We also use submodules in the repository (the sources of the versioned binaries) but the binaries are not in the submodules. This has worked great for us.

Recently, there have been a number of changes (I got a new laptop, moved to fedora 20, renamed the repository, etc...) that happened at once. Now when I checkout a clean working version of the repository and then run git annex get . and then do an unlock and a lock on the file I get the "Locking this file would discard any changes you have made to it. Use 'git annex add' to stage your changes. (Or, use --force to override)" warning.

I have tried to isolate this as much as possible but can't find what caused this. On a co-worker's laptop it seems to work fine so far. A clean repository didn't fix it. An old repository didn't fix it (though I recall it working there previously on this laptop). It did work and just stopped recently.

    $ git annex version
    git-annex version: 5.20140107
    build flags: Assistant Inotify DBus Quvi TDFA
    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
    remote types: git gcrypt bup directory rsync web glacier hook external
    local repository version: 5
    supported repository version: 5
    upgrade supported from repository versions: 0 1 2 4

    $ git annex lock --debug --verbose vendors/unittest-xml-reporting-1.5.0.tar.gz  # (some names changed to protect the innocent)
    [2014-02-05 12:54:45 IST] read: git ["--git-dir=/home/user/loppa_deuce/loppa/.git","--work-tree=/home/user/loppa_deuce/loppa","diff","--name-only","--diff-filter=T","-z","--","vendors/unittest-xml-reporting-1.5.0.tar.gz"]
    [2014-02-05 12:54:45 IST] chat: git ["--git-dir=/home/user/loppa_deuce/loppa/.git","--work-tree=/home/user/loppa_deuce/loppa","cat-file","--batch"]
    [2014-02-05 12:54:45 IST] read: git ["--git-dir=/home/user/loppa_deuce/loppa/.git","--work-tree=/home/user/loppa_deuce/loppa","diff","--name-only","--diff-filter=T","-z","--cached","--","vendors/unittest-xml-reporting-1.5.0.tar.gz"]
    lock vendors/unittest-xml-reporting-1.5.0.tar.gz git-annex: Locking this file would discard any changes you have made to it. Use 'git annex add' to stage your changes. (Or, use --force to override)
