One issue we ran into last semester was providing feedback to students in the middle of assignments. The system we used is that students would either email us or submit an issue, and then we would clone their repo, write down suggestions in the code using comments (all assignments were done in R), and then push these changes back. However, we ran into problems with merging if students continued to work on the assignment and changed code while we provided instructions. This was an introductory class, and we did not want to bog them down with merge conflicts.
Do you have a better way of submitting code feedback or suggestions in the middle of assignments? We would love to hear your suggestions!