filter clean leaves uncommitted file

[shawn wilson <ag4ve.us@gmail.com>]

So, I want a way of sharing parts of a gitconfig organizationally, so
I change and comment out some parts with a filter:

[filter "gitconfig-rmuser"]
  clean = sed -e \"s/^\\( *email =\\).*/\\1 <email address>/\" -e
\"s/^\\( *name =\\).*/\\1 <real name>/\" -e \"s/^\\( *signingkey
=\\).*/\\1 <gpg key>/\"

And then:
$ cat .gitattributes
* filter=ident-line
gitconfig filter=gitconfig-rmuser

Which works. The only problem is that if I change it again after the
commit, I get:
$ git status
# HEAD detached at e872204
# Changes not staged for commit:
#       modified:   gitconfig
#
no changes added to commit
$ git diff gitconfig
$

So the repo remains dirty and I can't do anything with it.