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Best structure for BLE application

I was working my way through the app note nAN-36, where it says you should have a seperate source and header file for each service. However in many of the newer SDK examples the service is included in the source file. This made it a little difficult to follow the app note tutorial since I think the BAS example was in the newer format (service files included in main.c).

What is the best approach in terms of structure when creating a new BLE application?

I've decided to start from scratch and create my own project in order to understand things better.