Homebrew - Upgrading software in /usr/bin
Don't replace, modify or rename the system tools in /usr/bin. There are a number of reasons why this is a bad thing, and you can search for the specific reasons, but to be simple, don't edit the system versions.

Homebrew knows this, and that's why it stores the tools in /usr/local/bin. This version is used instead of the system version since Homebrew requests that its directory be before the system path in the $PATH variable.

Run brew doctor and you'll probably get a message like this:


  Warning: /usr/bin occurs before /usr/local/bin This means that system-provided programs will be used instead of those provided by Homebrew. The following tools exist at both paths:

easy_install
easy_install-2.6

  
  Consider amending your PATH so that /usr/local/bin is ahead of /usr/bin in your PATH.


To fix this, either add this to your profile:

export PATH=/usr/local/bin:$PATH


…or add /usr/local/bin to the top of /etc/paths, such as:

/usr/local/bin
/usr/local/sbin
/usr/bin
/bin
/usr/sbin
/sbin