php.ini and my.cnf Config Files Get Overridden upon Upgrade

This is not a duplicate post. Omega8cc asked me to split my original support request issue in to separate issue posts (http://drupal.org/node/1551136#comment-5932720), one for each issue I was dealing with. If you want the whole story, you can find it in http://drupal.org/node/1551136.

My Setup and Background
I'm working on an Ubuntu 10.04 LTS 64bit Linode VPS with 80GB total storage (67 GB used, 13 GB Available, most space used is from site backups), 2 GB RAM.
Here is a link to the
This is not exactly a duplicate post. Omega8cc asked me to split my original support request issue in to separate issue posts (http://drupal.org/node/1551136#comment-5932720), one for each issue I was dealing with. If you want the whole story, you can find it in http://drupal.org/node/1551136.

My Setup and Background
I'm working on an Ubuntu 10.04 LTS 64bit Linode VPS with 80GB total storage (67 GB used, 13 GB Available, most space used is from site backups), 2 GB RAM.
Here is a gist.github.com link to the
BOA files for before upgrading to BOA HEAD as of 3/31/2012
and a gist.github.com link to
BOA files after upgrading to latest version of BOA HEAD as of 4/27/2012
for the following files:

    /var/aegir/config/includes/barracuda_log.txt
    /data/disk/user/log/octopus_log.txt
    /var/aegir/install.log (password removed)
    /root/.barracuda.cnf
    /root/.USER.octopus.cnf

Also here are links to:
Barracuda and Octopus Script Output

Problem: Config Files Get Overridden upon Upgrade
When I run the latest version of BOA HEAD my custom settings in the following files

• /etc/mysql/my.cnf
• /opt/etc/php.ini
• /usr/local/lib/php.ini
• /opt/local/etc/php53.ini

are being overridden by Barracuda even though I have touched the following files to prevent my custom settings from being overridden.

• /etc/mysql/custom.my.cnf
• /opt/etc/custom.php.ini
• /usr/local/lib/custom.php.ini
• /opt/local/etc/custom.php53.ini
• /opt/etc/custom.php53.ini

The Baracuda Changelog.txt file says the following:

  * You can avoid overwriting /etc/mysql/my.cnf with empty
    control file: $ touch /etc/mysql/custom.my.cnf

  * You can avoid overwriting /opt/etc/php.ini on upgrade
    with empty control file: $ touch /opt/etc/custom.php.ini

  * You can avoid overwriting /usr/local/lib/php.ini on upgrade
    with empty control file: $ touch /opt/etc/custom.php.ini

  * You can avoid overwriting /opt/local/etc/php53.ini on upgrade
    with empty control file: $ touch /opt/etc/custom.php53.ini

And this is exactly what I've done. In fact, I added extra touch files in the locations of the actual config files for the php.ini files because just putting them in /opt/etc directory was not working.

Thanks for any and all help in advance. I truly appreciate it!
Steve