git: re-checkout files after creating smudge filter

Situation: I've just cloned a git repo, and then I configure the smudge filter for the repo. There are .gitattributes files scattered around the repo that specify the filter that should be used on the files at checkout. But since I setup the filter after the checkout (clone), none of the files were processed.

How can I tell git to go through the repo, find all the .gitattributes files, and update (re-checkout, apply filter, whatever) all the files which have a smudge filter on them?

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.

Alexander Amelkin comments below:

I have created an alias 'reattr' to perform all those steps and now I am happy.

reattr = !sh -c "\"git stash save; rm .git/index; git checkout HEAD -- \\\"$(git rev-parse --show-toplevel)\\\"; git stash pop\""

(multi-line for readability)

reattr = !sh -c "\"git stash save; \
                   rm .git/index; \
                   git checkout HEAD -- \\\"$(git rev-parse --show-toplevel)\\\"; \
                   git stash pop\""

You can remove the Git index and let Git rescan it to aware the changes. Then you can checkout all the files which have a smudge filter on them.

# remove Git index
rm .git/index

# rescan index
git reset HEAD -- .

# checkout all the files which have a smudge filter on them
git ls-files --modified | grep -v .gitattributes | awk '{print "git checkout HEAD -- \""$1"\""}' | bash

Note: Save your uncommitted changes before the re-checkout, otherwise, all your modifications on those smudge-filter-applied files will be overridden.