Trying to update Homebrew with brew update I got the following error
error: The following untracked working tree files would be overwrittenby me
This post helped me after updating to El Capitan. In my case, chown wasn't working ("zsh: command not found: chown"), so step 1 was adding this line to my .zshrc:
export PATH="$PATH:/usr/sbin"
I'd already tried several of the more popular answers above, so I'm pretty sure that git status was coming up clean by the time I pasted in the critical command from the blog post:
sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local