In the past, I used the Visual Studio or Innosetup installation project for my programs. I prefer building .msi over exe, so the Visual Studio Setup Project has been my goto for a while. This, however, is sorely lacking in opportunities. In my opinion, the interface is not intuitive. Every time I build the installer, there are a lot of trial and error for installing / uninstalling so that everything is correct. Others pointed to WIX, and I looked at it. It seems very flexible, and since it is open source, we must rely on it in the long run.
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