I don't recall ever editing any .ini files.
Can I remove them safely?
$ find /etc/php5/*/conf.d
/etc/php5/apache2/conf.d
/etc/php5/apache2/conf.d/10-pdo.ini
/etc/php5/apache2/conf.d/20-mysqli.ini
/etc/php5/apache2/conf.d/05-opcache.ini
/etc/php5/apache2/conf.d/20-mcrypt.ini
/etc/php5/apache2/conf.d/20-json.ini
/etc/php5/apache2/conf.d/20-mysql.ini
/etc/php5/apache2/conf.d/20-pdo_mysql.ini
/etc/php5/cgi/conf.d
/etc/php5/cgi/conf.d/10-pdo.ini
/etc/php5/cgi/conf.d/20-mysqli.ini
/etc/php5/cgi/conf.d/05-opcache.ini
/etc/php5/cgi/conf.d/20-mcrypt.ini
/etc/php5/cgi/conf.d/20-json.ini
/etc/php5/cgi/conf.d/20-mysql.ini
/etc/php5/cgi/conf.d/20-pdo_mysql.ini
/etc/php5/cli/conf.d
/etc/php5/cli/conf.d/10-pdo.ini
/etc/php5/cli/conf.d/20-mysqli.ini
/etc/php5/cli/conf.d/05-opcache.ini
/etc/php5/cli/conf.d/20-mcrypt.ini
/etc/php5/cli/conf.d/20-json.ini
/etc/php5/cli/conf.d/20-mysql.ini
/etc/php5/cli/conf.d/20-pdo_mysql.ini