Is this maybe a mistaken abstraction?

What if the 'settings' being described here aren't 'project settings' they're 'personal settings for the project'.

I imagine we're following dev ecosystem conventions where everybody puts their tool settings in the project folder so they know where to find it and can share it; but are agent directives like this closer to a 'tool', or closer to a 'contributor'?

If the latter, I wouldn't expect to see "Joe's personal list of naughty and nice commands" in my project files either, certainly not under 'settings'. So just don't put them there.