I want to return to plain *.cpp files. What prerequisites are needed to achieve this on uploading?
Does the "main.cpp" only need to yield a setup() and loop() function or are there other things I need to take into account to upload my "sketch" without any issues?
I'm uploading my sketches via Arduino Makefile, I read that this is one thing I need to take care of?
If you're providing your own main(), then you don't need setup() and loop() at all. Nick Gammon's website, , gammon.com.au, has a page that explains exactly how to write programs with their own main().