I don't think it's the working directory. AFAIK, ls-files will only list files that are known to Git (i.e., files that have been `git add`). ls-files won't list

I don't think it's the working directory. AFAIK, ls-files will only list files that are known to Git (i.e., files that have been `git add`). ls-files won't list files that are not known to Git, even if they're present in the working directory.