Ubuntu – File isn’t where locate says it is

The three files you have there are each meant for different uses.

/etc/php/5.6/cli/php.ini is for the CLI PHP program, which you found by running php on the terminal.

/etc/php/5.6/cgi/php.ini is for the php-cgi system which isn't specifically used in this setup.

/etc/php/5.6/apache2/php.ini is for the PHP plugin used by Apache. This is the one you need to edit for changes to be applied for your Apache setup which utilizes the in-built PHP module to Apache.

/etc/php/5.6/fpm/php.ini is for the php5-fpm processor, which is a fastcgi-compatible 'wrapper' for PHP processing (such as to hand off from NGINX to php5-fpm) and runs as a standalone process on the system (unlike the Apache PHP plugin)

For versions of Ubuntu lower than 16.04, /etc/php/5.6/,/etc/php/7.0/,/etc/php/7.1/, and so on, are replaced by /etc/php5/ and so on. Otherwise, these paths remain accurate. Adapt this accordingly for your environment, replacing the 5.6 or number with the actual version folder that exists on your environment.

updatedb only runs once a day, you need to run it with root privileges to find recent files.