"Operation not permitted" for root when trying to ls or chmod -R /Users/user/Desktop "user" can't do it either. Permission of Desktop/ is set to 700 and owned by "user". Here's the sderr output for ls -R command in the home directory:


  ls: Desktop: Operation not permitted 
  ls: AddressBook: Operation not permitted 
  ls: CallHistoryDB: Operation not permitted ls:
  CallHistoryTransactions: Operation not permitted 
  ls: com.apple.TCC:
  Operation not permitted 
  ls: com.apple.sharedfilelist: Operation not
  permitted 
  ls: CloudKit: Operation not permitted ls:
  com.apple.ap.adprivacyd: Operation not permitted 
  ls: Calendars:
  Operation not permitted 
  ls:
  com.apple.CloudDocs.MobileDocumentsFileProvider: Operation not
  permitted 
  ls: com.apple.Home: Operation not permitted 
  ls:
  com.apple.Safari: Operation not permitted 
  ls: com.apple.news:
  Operation not permitted 
  ls: Cookies: Operation not permitted 
  ls:
  HomeKit: Operation not permitted 
  ls: IdentityServices: Operation not
  permitted ls: Mail: Operation not permitted 
  ls: Messages: Operation
  not permitted 
  ls: CoreSpotlight: Operation not permitted 
  ls:
  PersonalizationPortrait: Operation not permitted 
  ls: Safari: Operation
  not permitted 
  ls: Sharing: Operation not permitted 
  ls: Suggestions:
  Operation not permitted
You need to add Terminal to the list of apps that have Full Disk Access in the Privacy pane of System Preferences > Security &amp; Privacy.

Unlock the padlock in the bottom left, and drag the Terminal app icon onto the window.