Randy Dunlap <rdunlap@infradead.org> writes:

Yup, consider that "git apply" without "--index" is a mere "make goodness invented for Git available outside Git, as a replacement for 'patch'", just like "git diff --no-index" is a mere "make goodness invented for git-diff available outside Git, as a replacement for 'diff'". Their primary value is that they work outside the context of Git without relying on a Git repository, but they have limitations for not relying on a Git repository and data.

There are better alternatives (i.e., "apply" with "--index", or "am"; "diff" without "--no-index") if you are working with Git.