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Issue with creating a new git project, pulling in a past project


I am super desperate for any insight. I have a team project I have been working on for 3 weeks, I recently created a new branch and merged the master to it as my team-mate informed me there were updates. Suddenly my branch started having issues, saying there were random remote branches when I git branch -l. I decided to fork the project but when I did it forked then said I had 5K merge conflicts. I deleted the conflicts and it deleted all branches on our project and also Node off my computer. I reinstalled Node and went to work on a tutorial but when I tried to create a branch on the new tutorial it immediately pulls in files from the team project everytime. Also, I can no longer see what branch I am on, it just says my root but when I try and checkout to a branch it says I am already in it.  

It's almost as if the team project has become the root of my computer, but when I look, it's still in it's own original file?? 

I can't even figure out how to google these issues. I had to update Ruby and install cocoapods which my computer was outdated for both, could this have anything to do with my current issues? Has anyone had anything similar? 

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