This is one annoying footgun. It would be great if git could ignore some special .bisect directory during the entire process. This way the script doesn’t need a load of ../..

Create a .bisect directory and stick a gitignore inside it that ignores the folder. Or, add .bisect/ to a global gitignore file.

You can checkout the bisect script commit in another directoy. Or use $git bisect run $(git show ...).