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TLDR; erase install if you can’t ignore this and won’t fiddle with the bom.

If you have no directory of command line tools and have restarted, your receipts may be stuck like others have reported. You’ve already done the uninstallation, but the system to track structured package installs thinks all the files are still installed, prompting the update message since you don’t have the updated tools anymore on the drive.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.

TLDR; erase install if you can’t ignore this and won’t fiddle with the bom.

I would try to reinstall the tools and hope that a second attempt to remove them normally clears up the bill of materials tracking that’s your issue.

If that doesn’t work, your receipts may be stuck in an unexpected state like others have reported. You’ve already done the uninstallation, but the system to track structured package installs thinks all the files are still installed, prompting the update message since you don’t have the updated tools anymore on the drive.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

The only other fix is to erase the OS.

Newer OS (including Big Sur) have a sealed system, so erase all contents is quick. Older OS take more time, but in the end, restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.

If you have no directory of command line tools and have restarted, your receipts may be stuck like others have reported. You’ve already done the uninstallation, but the system to track structured package installs thinks all the files are still installed, prompting the update message since you don’t have the updated tools anymore on the drive.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.

TLDR; erase install if you can’t ignore this and won’t fiddle with the bom.

If you have no directory of command line tools and have restarted, your receipts may be stuck like others have reported. You’ve already done the uninstallation, but the system to track structured package installs thinks all the files are still installed, prompting the update message since you don’t have the updated tools anymore on the drive.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.

If you have no directory of command line tools and have restarted, your receipts may be stuck like others have reported.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.

If you have no directory of command line tools and have restarted, your receipts may be stuck like others have reported. You’ve already done the uninstallation, but the system to track structured package installs thinks all the files are still installed, prompting the update message since you don’t have the updated tools anymore on the drive.

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

So I booted into recovery mode, disable SIP, moved all files from that folder that had com.apple.pkg.CLTools in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools.