PROBLEM extra menu item in menu manager

[Tania]

Well pages won't show orphans , so if you restore the parent it will show up so you can change its parent or edit it manually of course

That makes sense, and I really appreciate your quick help. But I'm still wondering about pages.xml. In what folder does it belong? What happens if it's deleted?

I'm just trying to understand. I've tried reading through the code, but got lost