Claude also checks your settings.json first, and if it sees a default there it then prefers that over anything in CLAUDE.md. This is particularly nefarious as they ship logic to presume a default if a setting is not there in settings.json, even if there are instructions in CLAUDE.md for exactly that.

For instance, say you added "do not add 'Made with Claude Code' in any issues, pull requests or wiki entries" in your CLAUDE.md. So far, so good.

Well the latest update now looks for something in your settings.json. Since you don't know about it, it is not set. Claude then says "not explicitly set, so now it is true by default". It completely ignores your CLAUDE.md.

Wait, what?

You shouldn't be shipping logic that arbitrarily redefines the behavior of the program, especially if your new logic actually ignores your own configuration or directives.