When I try and pull from github I get a strange error. Can I bypass this or force it? I have used sudo before which I suspect would work however this caused other problems.
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I had this problem as well. I solved it by changing the ownership of the directories to the user I was trying to git pull with:
I ran that at the root of my git tracked directory to make sure all the files were owned by the correct user.
In my case it was having sublime text open with the git controlled directory added as a folder in the sublime project. After closing sublime I was able to switch branches without a problem.