We are designing a custom board using only nRF9160 as a tracking device. I am connecting Switch and LED to generate various events. Is is possible for me to program nRF9160 module without using any controller in the device. (Programming to control LED) We will be sending a data through LTE whenever any defined events are notified by Switches and LED.
I highly recommend that you use  the samples as a starting point for developing an application.
So then you do not need manually add CMakeLists.txt files etc.
You could go for option 1, but then you have to add those additional files yourself using the other samples as reference.