I ran into a problem where git cherry-pick incorrectly alters a patch that should apply cleanly, and leaves the working tree dirty despite claiming to finish successfully. I minimized the problem to the reproduction recipe below. Bisecting git.git shows the problem was introduced by 49b8133a9ece199a17db8bb2545202c6eac67485 (v2.25.0-rc0~144^2~1) “merge-recursive: fix merging a subdirectory into the root directory”, and it remains a problem in v2.32.0.

To reproduce:

git init
echo foo >foo
echo bar >bar
echo baz >baz
git add foo bar baz
git commit -m 'Initial commit'
mkdir dir
git mv foo dir/foo
git commit -am 'Move foo'
git mv bar dir/bar
echo baz >>baz
git commit -am 'Move bar'
git tag move-bar
git reset --hard move-bar~2
git cherry-pick move-bar

The rename part of the patch has been unexpectedly lost, and ‘bar’ has been unexpectedly deleted from the working tree:

$ git show
commit f06592b45db70540983a6c3e8bcf62712c694257
Author: Anders Kaseorg [off-list ref]
Date:   Sat Jun 12 00:20:13 2021 -0700

    Move bar

diff --git a/baz b/baz
index 7601807..1f55335 100644
--- a/baz
+++ b/baz

@@ -1 +1,2 @@
 baz
+baz

$ git status
On branch master
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        deleted:    bar

no changes added to commit (use "git add" and/or "git commit -a")

Before 49b8133a9e, the results are as expected:

$ git show
commit b7a2a3505dae3589203ca4469cb49e8a8e2727c3
Author: Anders Kaseorg [off-list ref]
Date:   Sat Jun 12 00:23:07 2021 -0700

    Move bar

diff --git a/baz b/baz
index 7601807..1f55335 100644
--- a/baz
+++ b/baz

@@ -1 +1,2 @@
 baz
+baz

diff --git a/bar b/dir/bar
similarity index 100%
rename from bar
rename to dir/bar

$ git status
On branch master
nothing to commit, working tree clean

Anders