Updates via the same nbgitpuller fail due to conflicts

[camok]

When distributing a nbgitpuller link, the github repository may update from time to time (say on a weekly basis for classes). Reusing the link to update files, however, creates a merging conflict. I haven't been able to recreate the issue but it seemed related to me deleting a file from the git folder on the JupyterHub to see how it would refresh from the GitHub repository.

For now, it doesn't seem to have any issues but I will update the issue if I can recreate it in further detail.

I was able to circumvent the issue by renaming the first cloned copy of the repository. That also raised it's own issue that I will open.

[yuvipanda]

Thanks for trying this out, @camok! If you can reproduce it, that would be very helpful - we'll definitely want to get that fixed.