Menu settings does not change menu I have created a new menu called new-menu.  I go to Admin > Structure > Menus > Settings

And I choose "New Menu"  for the "Source for the Main links" option.

However, on my site, it still shows the Main Menu links (instead of New Menu links).

What am I missing?

Note: I am running a custom "Drupal core" from my university, and I've never worked with Vanilla Drupal, so I'm not sure if something is missing that should be there.
You need to change the menu under Structure > Blocks. Find the Main Menu block that is active and click its "Configure" link. The third option is Menu... change this to dropdown to your new-menu.