Situation: I've just cloned a git repo, and then I configure the smudge filter for the repo. There are
Simply re-checkout everything.
cd /path/to/your/repo git stash save rm .git/index git checkout HEAD -- "$(git rev-parse --show-toplevel)" git stash pop
The smudge filter will be applied at that new checkout.
Note, as seen in this answer, you need to remove the index in order to force the filter to run again.