See my post about How the IDE organizes things.
Also see my page about how to avoid the quirks of the IDE sketch file pre-preprocessing.
You can certainly manage without .ino files. As Edgar Bonet says, they are really C++ files with certain pre-processing (see link above).
but what about these loop() and setup() functions
Effectively, the Arduino IDE supplies a main function that looks like this:
int main ()
{
init (); // initialize hardware, including timers and timer interrupts
setup (); // user setup
while (true)
loop (); // stuff to be done repeatedly
return 0; // this will never be executed
}
(It's slightly more complex, to allow for USB where applicable, but that is the idea).
But still I did not found the step by step guide how to do it.
I'm pretty sure there are a lot of example "make" files around which show the idea.
I have an example here.