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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)