What is the best-practice for managing Aegir sites in Git?
Here's the recommended way for Barracuda/Aegir by Omega8:


  The recommended (and also more advanced) way to manage your Sites code
  is to use Makefiles (and then Drush Make) to build your Platforms,
  apply patches to contrib or custom modules etc, then using Profiler
  module to create your custom Installation Profile and manage in your
  Git repo just your Makefiles, your Installation Profiles and only your
  custom modules and patches – in a separate repo per module and per
  theme.


Source: http://omega8.cc/managing-your-code-in-the-aegir-style-110.