Sparse-checkout excluded files show as deleted in git status after some operations

Sparse-checkout excluded files show as deleted in git status after some operations

[Ross Allan]

Hi,

Sometimes when working on a repository with files excluded using the
sparse checkout feature, the skip-worktree flag is incorrectly unset
causing files to show as deleted in git status.

Initially I reported this to git-for-windows at
https://github.com/git-for-windows/git/issues/811 but was recommended
to go here as it is not a windows specific issue (my mistake there).

It has happened a few times when merging and cherry picking. Here is
an example repository which can be used to demonstrate the issue:
https://github.com/nallar/git-issue-sparse-checkout

The following commands run into the issue.

git clone https://github.com/nallar/git-issue-sparse-checkout.git
mcve-sparse-checkout
cd mcve-sparse-checkout
git config core.sparseCheckout true
cp sparse-checkout .git/info/sparse-checkout
git checkout -f master
git reset --hard HEAD
# We now have sparse checkout enabled, so the folder "excluded-folder"
should not be present
ls
# We should have no changes so far
git status
# Cherry-pick top commit from the other branch
git cherry-pick other
# That cherry-pick succeeded with no conflicts. We should have no
unstaged changes
git status
# Oh dear, now it shows 'deleted:    excluded-folder/1.txt'
# Workaround, set skip-worktree which for some reason got unset:
git update-index --skip-worktree excluded-folder/1.txt
# Now it's showing the correct result again
git status
# no changes

Full log demonstrating issue:
https://gist.github.com/anonymous/e1e29f0eb9df25b506fdf555827c73ac

Thanks
Ross Allan