Git is a little peculiar about tracking file renames - in short, it doesn't.
This sort of makes sense, because git doesn't actually track changes at all - every commit is a snapshot of the entire repository. So although there's a "git mv" command, there isn't actually anywhere to record that you used it - all git records is the result, which is exactly the same as if you deleted the original file, and retyped the new one from memory.
What makes this a bit confusing is that git occasionally pretends to know what moving or copying files means. It does this by guessing when it looks at a diff that a creation and a deletion actually go together. It can do that guessing at any time, and some commands have options to make it not guess, or try harder to guess, when displaying things.
So "git apply" did exactly the right thing: it created a state of the repository equivalent to moving the file. Commit that state, and the file will show as renamed or not in all the same places as if you'd run "git mv".