Xcode command line tools still offers update after deleting the folder

In addition to the steps above, I had to do the following to get the Command Line Tools update to stop showing up in Software Update.

• If you're still seeing prompts to update Command Line Tools after deleting the folder, some users have reported that disabling and re-enabling SIP can help, but this is a complex and risky procedure.  Only attempt this if you are comfortable working with the Terminal and understand the potential risks.

Boot into Recovery mode (shut down your Mac and then press and hold the power button until you see "Loading startup options." Then, select "Options" and click "Continue," and you'll be in Recovery Mode.).

• • Open Terminal.
  • Run csrutil disable. You'll need to authenticate (be sure to know your actual username, run whoami from Terminal when logged in as admin user) .
  • Reboot into macOS.
  • Open Finder
  • Navigate to /Library/Updates and open any folders to look for packages with CLT in the name, then delete that folder
  • Navigate to /System/Library/AssetsV2 directory and delete anything with CLT in the name
  • Navigate to /Library/Apple/System/Library/Receipts.
  • Remove related receipts: com.apple.pkg.CLTools*.
  • Reboot again, and then re-enable SIP in Recovery using csrutil enable. 

After deleting the folders as previously mentioned, I still saw the updates until I did the above. I hope it helps, and don't forget to go back into Recovery and reenable SIP. It's there for your own good!

With Xcode and its corresponding version of the CommandLine Tools for Xcode moved to the Trash and emptied, then following a reboot, you should be done with future Software Updates offering Command Line Tools again.

I generally keep Xcode and the CommandLine Tools version current on a given macOS version. It would seem the first paragraph should resolve this as there is no version of Xcode present for Software Update to offer a compatible version of the CommandLine Tools.

One approach may be to move the Xcode application to the Trash and empty the Trash. Then press shift+cmd+G (e.g. go to folder) and enter the following:

/Library/Developer

and then drag and drop the CommandLineTools folder to the Trash, emptying it. This will likely challenge you for your admin password before you can do the drag/drop.

Locate Xcode v16.4 and download Xcode 16.4.xip (direct download link).

This may require you to sign in with your Apple ID unless you are already signed into the Apple Support Community in another tab. In your Downloads folder, just double-click the Xcode xip file and wait while it unpacks it in place. Then simply drag and drop Xcode to your /Application folder as before. Then run it to finish its installation.

This entire process should dispense with another 3 GB Commandline tools for Xcode 16.4 appearing in Software Update.