Hello
I had this issue on one machine, and I cannot explain why this one and not the others. It seems that git files were updated but git does not remember about it.
Anyway, ./scripts/github-remove -d is the first step as you already found. And then you can move the last 3 files to /tmp:
config/hashing.php
config/logging.php
config/tinker.php
after this, ./daily.sh should do his magic 
Bye