In the past, when a new php version was stabilized, I'd get a prompt to run etc-update to merge the configuration files. For the 5.4 stabilization, this didn't happen; the 5.4 php.ini seems to have gotten installed to a separate directory from the 5.3 one. This had me running into errors on one of the web apps I manage because the configuration was setup wrong.
Ping! Any response?
In this particular case, the php ebuild tells you where it installs its configuration file in the ebuild log. Also you have to actively change the active php slot for each sapi, so it is not like the upgrade happens without you noticing. At some point I need to redo the php documentation in full, but it is not a high priority.
This is still happening with php5-4 -> php5-5, and it still sucks. IMO the /etc/php/apache2-php5.5/php.ini should be installed from the 5.4 php.ini, such that I can use etc-update to merge both. If that is too hard, documenting such a process in the PHP upgrade guide seems like the least you can do.
To wit: $ sudo mv /etc/php/apache2-php5.5/{,._cfg0000_}php.ini $ sudo mv /etc/php/apache2-php5.4/php.ini /etc/php/apache2-php5.5/php.ini $ sudo etc-update
Documentation is in the wiki now.