Help with managing project

I’m using github repo as an intemediary for developing a website.
I have the website being hosted from a RPi and am working on the website from my computer.

What I am trying to achieve is origin (my PC) > remote > destination (the RPi), I can make changes on my PC fine and push it to github, but when I try to pull it from github on to the RPi I get:
fatal: refusing to merge unrelated histories
So I tried:
git pull destination master --allow-unrelated-histories
And all I get are merge conflicts.

I just want the github version to flat overwrite the destination version?