Staged area modified after cross branch checkout

Start by running the provided test_checkout reproducer and inspect the repo.checkout and repo.index behavior across the two branch switches. Compare the staged index after returning to master with the expected empty state, and verify the result against the described git checkout behavior.

I created two branches with commits like this:

Then I call checkout to switch the branch from old_master to master. Somehow, the cached area is updated after checkout:

Here's the code toe reproduce

import pathlib

import pygit2


def test_checkout(tmp_path: pathlib.Path):
    repo_dir = tmp_path

    git_author = pygit2.Signature(name="foo", email="foo@bar.com")
    repo = pygit2.init_repository(str(repo_dir))
    workdir = pathlib.Path(repo.workdir)
    readme = workdir / "README.md"

    readme.write_text("commit0")
    index = repo.index
    index.add(readme.relative_to(workdir).as_posix())
    index.write()
    tree = index.write_tree()
    commit0 = repo.create_commit("HEAD", git_author, git_author, "commit0", tree, [])

    master_branch = repo.branches.local["master"]
    old_master_branch = repo.branches.local.create("old_master", master_branch.peel())

    readme.write_text("commit1")
    index = repo.index
    index.add(readme.relative_to(workdir).as_posix())
    index.write()
    tree = index.write_tree()
    repo.create_commit(repo.head.name, git_author, git_author, "commit1", tree, [commit0])

    repo.checkout(old_master_branch)
    readme.write_text("commit2")
    index = repo.index
    index.add(readme.relative_to(workdir).as_posix())
    index.write()
    tree = index.write_tree()
    repo.create_commit(repo.head.name, git_author, git_author, "commit2", tree, [commit0])

    repo.checkout(master_branch)
    # the staged area should be empty after checkout
    assert not list(repo.index)

I tried it with git checkout master and it works fine without changing the staged area.