repo.status() appears to be broken?

I'm running repo.status().items() in a pre-commit hook using the -a flag (git commit -a -m "Test"), and I get a result that looks like this:

[('config/git_hooks/pre-commit', 256), ('bin/run_flake8', 256)]

If I run git status in that same process, I get:

On branch ops_1331_fix
Your branch is ahead of 'origin/ops_1331_fix' by 2 commits.
  (use "git push" to publish your local commits)
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    modified:   bin/run_flake8
    modified:   config/git_hooks/pre-commit

In other words, pygit2 is reporting those files as not being staged, and git is reporting them as being staged. Why the discrepancy?

Empieza reproduciendo la discrepancia con repo.status().items() en el pre-commit hook al usar git commit -a; después, compara su resultado con git status para los dos archivos indicados. Lee la pygit2 status API y el comportamiento relacionado de libgit2; el trabajo estará terminado cuando expliques por qué los archivos preparados reciben el estado 256 y corrijas la discrepancia si se trata de un error.