No, ClickOnce applications cannot be certified. :(
Here is the official word from the team:
ClickOnce deployment manages install / uninstall, slightly different from the traditional installer. For example, the installation location does not go to% ProgramFiles%, as indicated in the requirements for desktop certification, short abbreviations have another extension used by a Windows application, for example. * .lnk etc. As a result, these applications arent correctly detected by the ACK and therefore cannot be certified.
For non-ClickOnce desktop applications, choose compatibility with your desktop application on how to prepare and certify your desktop application. Also look at the sidebar of the left menu (in particular, the Guide to Using the Windows 8 Logo and Windows RT ). This gives you the option to display the "Windows 8 Compatible" logo in the application, as it is certified as compatible.
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