I recently installed a bunch of dotfiles on my Mac along with some other applications (I changed to iTerm instead of Terminal, and Sublime as my default text editor) but eve
I had a broken virtual env due to a Homebrew reinstall of python (thereby broken symlinks) and also a few "sudo pip install"s I had done earlier. Weizhong's tips were very helpful in fixing the issues without having to reinstall packages. I also had to do the following for the mixed permissions problem.
sudo chown -R my_username lib/python2.7/site-packages