I just updated my "production" aegir to alpha 5 from alpha 3 and I thought I would put up my notes from it.

I followed the instructions that were linked to from here: http://groups.drupal.org/node/47784#comment-135668

Before i started the whole process I did a an apt-get update and apt-get upgrade to make sure my ubuntu system what up-to-date.

At about line 35 I made these changes (bold are the changes):

...

Shell commands::

export AEGIR_TAG=6.x-0.4-alpha5
export DRUPAL_DIR=/var/aegir/hostmaster-$AEGIR_TAG
export OLD_DRUPAL_DIR=/var/aegir/hostmaster-6.x-0.4-alpha3
export VERSION=6.x-3.0-alpha1
export AEGIR_VERSION=0.4-alpha5

This document also assumes drush is installed properly and we use an
environment variable to simplify the documentation again.
...

After I made those changes everything else went smooth as butter.