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Disclaimer: not the maintainer, just someone who has used the tool.
I think if you have (at any point) installed Xcode through the app store, it installs it as Xcode and tracks that independently. When installing with xcodes it installed with a suffixed name with the version number. The app store will continue to track the Xcode and not the Xcode-NN.N version. I think if you delete the original one and remove it, the warning might go away.
I used Xcodes to update to xcode 16.1. I am still showing in the Mac Settings for Available Updates that 16.1 is an update.
I am not sure Xcodes is supposed to suppress that or whether MacOS is supposed to detect that 16.1 is already on my computer.
I am just looking for an explanation....
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