How to move an app into the Applications root folder from an Applications Subfolder?

For whatever reason my Applications folder has a subfolder "Utilities". The Utilities folder contains apps from the App Store as well as system apps like Disk Utility etc.

• If I drag an app from the subfolder into the root, I just wind up creating an alias.
• If I try using chmod in Terminal, I get "operation not permitted". (sudo chmod 777 followed by a space and then dragging a subfolder app into Terminal)
• If I "Get Info" on the Utilities subfolder or any app within it and try to unlock it, it fails saying that I don't have the necessary permission.

I'm of course trying these things while using my admin user account. How can I fix this mess or should I just learn to live with it? It seems like it should be simple and I haven't found anyone else with a similar problem which is a bit disconcerting.