How to re-merge a file in the git?

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