If I capture an exe with a shortcut where the exe has an internal manifest file, the packaging tool adds the allowElevation capability into the appxmanifest file automatically.
If I capture an exe with a shortcut where the exe has no internal manifest file but does have an external manifest file (foo.exe.manifest) containing the "requireAdministrator" trust setting, the capability is not added, and the package will fail to launch.
I believe this should be added automatically in the external manifest case for the same reason as per the internal manifest case.
