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)
I downgraded my git-annex version, rechecked out the repository and now everything works. $ git annex version git-annex version: 4.20130827 build flags: Assistant Inotify
Recent versions of git-annex have tried to extend the --force option to be needed in any operation that can possibly cause data loss. This includes locking a file, since that throws away any changes.
Note that
git annex lockdoes not check if the file is unmodified. For a few reasons includingIf you are sure you want to throw away any changes, use --force as suggested. If not, use
git annex add $file, and assuming you're using a checksumming backend, it will notice the file has not changed and do what you wantgit annex lock $fileto have done in this case.