When installing a site on aegir clean urls were enabled and could not be disabled through the gui or drush.

I ended up inserting ?q= manually to log in and get to the page.

I visited https://drupal.org/comment/reply/5590#comment-form

and was able to disable clean urls using the settings.php method.

$conf['clean_url'] = 0;

Then by using the aegir user I edited the file at /var/aegir/config/server_master/apache/vhost.d/examplesite

I added the following lines

RewriteEngine on
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

Then remove the line from settings.php

Setting the aegir user.

Add

alias agro='sudo su -s /bin/bash - aegir'

to the .bashrc

Then

source ~/.bashrc

The command agro now sets you as aegir