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Say for example we have a program version 1.0 and we want to upgrade it to 2.0

95% of the apps are MSI based installs that have been repackaged

If we import the 2.0 msi into our bundle and up the version to push it out, what happens to the old version of the program, is it uninstalled or somehow upgraded to reflect what is changed by the new MSI install package? or is MSI clever enough to only upgrade the files that need to be changed making the bundle 'upgrade' seamless to users?