I decided to throw away the repo and the project and start from zero. The next project I created was done exclusively with Builder and I did not use the Coder. Everything went well. I think the cause of the problem was the fact that PsychoPy couldn’t sync with the head of the master after I had set the upstream with git.
So I guess this thread is solved but some part of the documentation could be used to describe the git integration of the sync function. Then users of git could attempt to reattach the head / get remote updated via git, or to not accidentally get them out of sync.