Yeah, that is pretty much where I'm coming from. I started with pncconf's generated HAL file. However, that does not bind the physical pin with the net for things like homing, etc. (interestingly, a lot of the fields in pncconf were grey'd out too, so I couldn't enter things I wanted to). My next step was to take the boss control sample because it is one of the few that seems to use analog and index pulses for homing. I'm not sure this was the right decision because it looks like the Boss control has a fair amount of PLC stuff too (loads something called 'boss_plc' which, unfortunately, I didn't see in my quick check of files.

. That is where I am now. I didn't do the a 'man motion'. That is a good idea.
I did read the homing ini documentation that you referenced. It does a good job of introducing the capabilities. Where it fell apart for me, however, was in the actual implementation. Everything described is for the INI file but one still needs to somehow bind a physical pin so that the boiler plate can work. Or maybe I'm over complicating all of this.