Use Homebrew recommended installation command and run brew doctor

This command also takes care of setting the permissions on the /usr/local/
folder so that we don't have to care about this. During initial clenaup,
remove contents of /usr/local without removing the folder (may not be
permitted).
Do not allow BREW_DIR to be overriden

Since using the default Homebrew installation command, we don't have the
choice of the installation directory anymore.