Help with documentation what behavior is expected in Github for new users

Hi
I am helping to support the UC Berkeley Datahub - a large Jupyterhub with dozens of classes and 1000s of users. The main way that we deploy curricular materials is to us nbgitpuller to pull in materials.
I do a lot of training new users ( faculty or student staff) to use Nbgitpuller

One chronic issue is that new users will 1) use an Nbgitpuller link once and 2) make a certain type of change in the source repo that 3) breaks the nbgitpuller when the user uses the link again to pull in more materials. 4) sending a particularly ominous and discouraging page of failed gitness

**I would like help to document what is acceptable behavior in Step 2, and what causes problems.**
- many existing classes have safe workflows that iteratively add to the source repo with no problems
- my understanding is that the problems usually come from changing the structure of the repo somehow, but there are multiple reasons something might cause problems

Apologies that I don't have a good example to reproduce these errors, because they are usually particular to an individual user

Outcomes:?
- documentation for new users to understand nbgitpuller safe behaviors - Happy to help with this / not sure where
- potentially changing warnings so that something more helpful and less ominous is communicated to users?

@yuvipanda