git-rebase + git-mergetool results in broken state

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I'm experiencing an annoying issue which leaves the repository in a
weird, broken state. I am attempting a rather vanilla rebase, rebasing
the commits from a feature branch on top of the newest commits on
master.

So, I run a typical series of commands:
1. git checkout feature-branch
2. git rebase master (conflicts ensue)
3. git mergetool

The conflicts are expected, but when using mergetool to resolve them,
I encounter many "no such file or directory" errors.

mv: cannot stat
‘app/components/mediaManager/kbImageEditor.directive.coffee’: No such
file or directory
cp: cannot stat
‘./app/components/mediaManager/kbImageEditor.directive_BACKUP_13615.coffee’:
No such file or directory
mv: cannot move ‘.merge_file_ogGjXX’ to
‘./app/components/mediaManager/kbImageEditor.directive_BASE_13615.coffee’:
No such file or directory
/usr/lib/git-core/git-mergetool: 229: /usr/lib/git-core/git-mergetool:
cannot create ./app/components/mediaManager/kbImageEditor.directive_LOCAL_13615.coffee:
Directory nonexistent
/usr/lib/git-core/git-mergetool: 229: /usr/lib/git-core/git-mergetool:
cannot create ./app/components/mediaManager/kbImageEditor.directive_REMOTE_13615.coffee:
Directory nonexistent

This leaves weird dangling files like '.merge_file_ogGjXX' in the
repo, and I assume I should not proceed with the merge since it
couldn't even create the files to compare.

Is this a known issue? Is there any workaround? Is it safe to proceed
with the merge?

Thanks,
Joe Einertson
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