Recently, someone[0] pointed out to me that am-based rebases don't apply
smudge and clean filters on the final checkout.

Reproduction:
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#!/bin/sh -e

mkdir test-repo
cd test-repo
git init
git config filter.test.clean "sed -e 's/smudged/clean/g'"
git config filter.test.smudge "sed -e 's/clean/smudged/g'"

echo a >a.bin
git add a.bin
git commit -m 'Add a.bin'

echo b >b.bin
git add b.bin
git commit -m 'Add b.bin'

git checkout -b test HEAD^

echo '*.txt filter=test' >.gitattributes
git add .gitattributes
git commit -m 'Add .gitattributes'

echo 'This text is smudged.' >a.txt
git add a.txt
git commit -m 'Add a.txt'

git rebase master
grep 'smudged' a.txt
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The correct behavior is to have the script print that the text is
smudged, but with an am-based rebase, the text is clean. If you change
the rebase to use -i or -m, the test succeeds (the filters are applied).
This may also affect things like working-tree encodings or line endings;
I'm not sure.

I'm planning on taking a look at fixing this (unless of course someone
gets to it before me), but I wanted to mention this as in case it rang a
bell for anyone.

I have no reason to think this is version-specific behavior, but I'm
using Git 2.23.0.rc0.142.g4dedae46a2 from Debian experimental, and this
also reproduces on a fairly recent master on macOS.

[0] This was brought to my attention by Erika Ellison.
-- 
brian m. carlson: Houston, Texas, US
OpenPGP: https://keybase.io/bk2204