Comment 3 for bug 1007018

You're right András, the only way I could uninstall was to delete files manually. And it does affect php5-apc as well. Based on a quick search of which quantal packages are installing config files in the new /etc/php5/mods-available/ location, it currently affects:
libpuzzle-php
php-apc
php5-gdcm
php5-rrd
php5-suhosin
php5-vtkgdcm
php5-xcache
php5-xdebug
And will affect any other packages that upgrade to the new config file layout and don't depend on php (>= 5.4).
The weird thing is that they appear to be ok upstream on Debian, but whoever is repackaging them for Ubuntu is lowering the dependency version.