git checkout -m <filename>
This will remove it from the index, and revert back to a “conflicted” file that has all of the markers required to then do a merge.
From the git help checkout man page:
-m, --merge
When switching branches, if you have local modifications to
one or more files that are different between the current
branch and the branch to which you are switching, the command
refuses to switch branches in order to preserve your
modifications in context. However, with this option, a
three-way merge between the current branch, your working tree
contents, and the new branch is done, and you will be on the
new branch.
When a merge conflict happens, the index entries for
conflicting paths are left unmerged, and you need to resolve
the conflicts and mark the resolved paths with git add (or git
rm if the merge should result in deletion of the path).
When checking out paths from the index, this option lets you
recreate the conflicted merge in the specified paths.
(The last sentence is the most important one).
Here is a blog post that describes why it was added and how it is not possible with older versions of git: http://gitster.livejournal.com/43665.html