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I'm trying to create a template for ArcGIS Pro that users can open that will create or already have our standard file structure, gdb template, some lyr files, etc.

As far as I can tell the Project Template (.aptx) only stores references and when I try and create a Project Package (.ppkx), it keeps my files but changes the folder structure.

For using ArcMap, we just have a zip with the folders and templates and you just need to unzip and rename a few things for each project. I'm trying to replicate, and hopefully improve, this for Pro.

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No, this is not possible via the template package itself, however, you can either add a python toolbox to the template to do this, or, use the Pro SDK to customize the installation. I'd stick with the python route.

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