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I have a folder project and it consists of multiple folder and .c and .h files what is the best way to include them all without including the individual folders?

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Assuming you are talking about Atmel Studio 7, which is Visual Studio based, this answer applies: https://stackoverflow.com/questions/392473/how-do-i-add-an-existing-directory-tree-to-a-project-in-visual-studio

You need to put your directory structure in your project directory. And then click "Show All Files" icon in the top of Solution Explorer toolbox. After that, the added directory will be shown up. You will then need to select this directory, right click, and choose "Include in Project."

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