Running git filter manually

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I have a repository that contains a filter (clean and smudge) which replaces tokens with paths (e.g. @ROOT@ with the repository root). However, when doing a fresh clone, the filters are (of course) not set up yet, so after cloning, I need to add the filters to the git config of the repository.

The files, however, still contain the tokens because the smudge filter is not run. The only workaround I found was removing the files and checking them out freshly, this causes the smudge filter to run. Is there another non-hacky way to run the smudge filter?

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