When publishing my first program, I noticed that it put the program in the App folder as opposed to "C:\Program Files\". Is there a way to direct where everything should be stored when you install it on the users computer?



At the time of creating your project define the location of your project in New Project Window. If you check the create Directory for Solution, it automatically creates a folder at the location of your project. the name would be as same as solution name. I which your project should reside.
After creating deployment setup, projects default folder should be the same as you did at the time of creating the project

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