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Git filter clean not working when staging files


I've got a question or maybe bug about Git clean filter.
According to documentation[1] clean should be run when staging files.
When I'm staging file I see my script was run (I'm logging execution
into /tmp), but file content is unmodified.
My script is reading stdin and writing to stdout.
Nothing breaks in the script, from logs I see the source and modified
content are proper and I'm returning 0 return code.

Is this behavior intended? What should I do to modify the content?

Smudge works as intended.
But I've also noticed that git status runs clean filter but does not
modify contents.
Is that also intended?

Maybe I'm missing something?

If this is not going to work,
is there other way to modify file content on commit? (so the fixed
content goes to local repo)
Any other options ?

[1] https://git-scm.com/book/en/v2/Customizing-Git-Git-Attributes#filters_b

Thanks for help,