Assignment 1 failed to load into correctly, what to do?

When I loaded Assignment 1 into github and hit the button to work in, I discovered nothing had loaded in, there were no files and it was running bash, not node.js.
After trying multiple times to see if it would reload by logging in and out, the result was the same.
So I downloaded the zip file under a different folder name and everything seemed to be working there.
I have loaded the zip file into the correct folder, but it’s still only running bash and so npm isn’t loaded
Also there are several duplicate files now.
I’m not totally sure what damage I will do if I start deleting stuff.
If I can get it sorted out I can just copy my code over from the other file.
otherwise, is there any help you all can offer on this? I’m losing alot of time trying to figure this one out.
I’m starting to get a little nervous because other than a couple of tweaks, I’m ready to turn it in.
Thanks for help! Peter