Staged area modified after cross branch checkout

[fangpenlin]

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.