Check-manifest in pre-commit hooks includes untracked files

[lauraporta]

Describe the bug
Untracked files in a repository are considered in the evaluation of check-manifest during the pre-commit hooks.

To Reproduce
In a repo using the last cookie-cutter, have a tracked file staged for commit and an untracked file with an extension you are not managing in the MANIFEST file. You will see that pre-commit will fail at least at the check-manifest stage.

Expected behaviour
Untracked files should be ignored, what the pre-commit hooks should check should be the staged file.