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SDK structure and project structure

I am looking at the NRF52832 for some projects and so downloaded the SDK and opened an example project in Segger Embedded Studio (SES).  I was shocked to find that the directory structure in SES did not match anything in the SDK and vise verse.  

Is there any logic to the SDK directory structure? If so why is not reflected in the project?  I imagine it is a royal pain in the butt when a new SDK comes out and you have to try and update your project with the changes to the SDK. 

I also see it is a pain to pick and choose which files you need to check in with your project, so how do people handle this? 

Thanks

Trampas

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