Seems to me there is a bug in how merges are done in direct mode. This is
done in two steps:

1. Merge the remote branch into the local branch, with work tree directed
   to a temp dir.
2. Use the temp dir and the newly merged branch to update the work tree.

If this is interrupted between 1 and 2, by eg the user ctrl-Cing or power
being lost, the result is a repository that thinks the current branch has
been merged, but does not have an updated work tree. The next sync in that
repository will see the files as deleted (or as being an old version), and
commit the current work tree state to the branch. 

Result is files appear to be lost, although `git revert` in an indirect
mode repo can get them back.

To fix this, direct mode merge would need to avoid updating the current
branch when merging the remote branch into it (how?). It should first
update the whole work tree, and only after it's updated should it update
the index and the current branch to reflect the merge.  

This way, if the merge is interrupted, the work tree may have uncommitted
changed -- but it's fine if they get accidentially committed, since when
the merge is re-done, those changes will by the same ones made by the
merge. (I assume this is how `git merge` normally works.) --[[Joey]]

> Implemented that. And then realized that even updating the index
> as part of a merge results in the work tree being out of sync with the
> index. Which will cause the next sync to again delete any files that
> are in the index but not the work tree. Urgh. 
> 
> Seems that a direct mode
> merge also needs to use a different index file to stage its changes?
> (Ugh)
> > done --[[Joey]]

> > > I had to revert the fix on FAT/Windows due to 
> > > a git bug: <http://marc.info/?l=git&m=140262402204212&w=2>
> > > Once that bug's fixed, I can revisit this. --[[Joey]]

[[!meta title="direct mode merge interrupt (fixed for all except FAT, Windows)"]]

## other options

> Or could perhaps use `git-merge-tree`
> and avoid staging the merge in the index until the work-tree is updated.
> 
> Alternatively, could use another strategy.. Add a lock file which is held while 
> the merge is in progress and contains the pre-merge sha.
> If the lock file is present but not held, state is inconsistent.
> `git-annex sync` and the SanityChecker should
> then run mergeDirectCleanup to recover, before any commits can be made
> from the inconsistent state. This approach seems to get complicated
> quickly.. --[[Joey]]