> what do you do when English grammar calls for a question mark to be inside your quotation mark at the end of a sentence, but you’re literally quoting something that should not include the question mark?

AP style (at least, according to the cheatsheets I've found online; I don't have access to the current edition of the full guide) only puts periods and commas inside quotation marks-- question marks, exclamation points, semicolons, and other punctuation only go inside quotation marks if they belong to the quoted matter.

So, that makes "Shouldn’t the title be 'Redesigning the GitHub Repository Page'?" correct, according to them, at least. (This is a matter of style more than a matter of grammar, though.)