Ok so the solution is reasonably simple.
sudo git stash
sudo git pull
sudo git stash pop
stash stashes (hides) the changed files. You can now do a pull to merge in the changes made. The stash pop brings the changed files back into the working directory structure.
I suggest you offer your change as a PR on GitHub or @emrys might be able to look at it else you will have to do this every time!