I'm using nginx if that makes any difference.
Below is the output of running the command lines and from phpinfo():
# php --ini
Configuration File (php.ini) Path: /etc/php5/cli
Loaded Configuration File: /etc/php5/cli/php.ini
Scan for additional .ini files in: /etc/php5/cli/conf.d
Additional .ini files parsed: /etc/php5/cli/conf.d/05-opcache.ini,
/etc/php5/cli/conf.d/10-pdo.ini,
/etc/php5/cli/conf.d/20-gd.ini,
/etc/php5/cli/conf.d/20-json.ini,
/etc/php5/cli/conf.d/20-ldap.ini,
/etc/php5/cli/conf.d/20-mcrypt.ini,
/etc/php5/cli/conf.d/20-mysql.ini,
/etc/php5/cli/conf.d/20-mysqli.ini,
/etc/php5/cli/conf.d/20-pdo_mysql.ini,
/etc/php5/cli/conf.d/20-pdo_sqlite.ini,
/etc/php5/cli/conf.d/20-readline.ini,
/etc/php5/cli/conf.d/20-sqlite3.ini,
/etc/php5/cli/conf.d/20-xdebug.ini
# php -v
PHP 5.5.9-1ubuntu4.4 (cli) (built: Sep 4 2014 06:56:34)
Copyright (c) 1997-2014 The PHP Group
Zend Engine v2.5.0, Copyright (c) 1998-2014 Zend Technologies
with Zend OPcache v7.0.3, Copyright (c) 1999-2014, by Zend Technologies
with Xdebug v2.2.3, Copyright (c) 2002-2013, by Derick Rethans
# php -m | grep mcrypt
mcrypt
# ls -al /etc/php5/fpm/conf.d
total 8
drwxr-xr-x 2 root root 4096 Sep 29 13:03 .
drwxr-xr-x 4 root root 4096 Sep 29 13:22 ..
lrwxrwxrwx 1 root root 32 Sep 10 12:19 05-opcache.ini -> ../../mods-available/opcache.ini
lrwxrwxrwx 1 root root 28 Sep 10 12:19 10-pdo.ini -> ../../mods-available/pdo.ini
lrwxrwxrwx 1 root root 27 Sep 20 12:57 20-gd.ini -> ../../mods-available/gd.ini
lrwxrwxrwx 1 root root 29 Sep 10 12:19 20-json.ini -> ../../mods-available/json.ini
lrwxrwxrwx 1 root root 29 Sep 20 12:57 20-ldap.ini -> ../../mods-available/ldap.ini
lrwxrwxrwx 1 root root 31 Sep 29 13:03 20-mcrypt.ini -> ../../mods-available/mcrypt.ini
lrwxrwxrwx 1 root root 31 Sep 10 12:25 20-mysqli.ini -> ../../mods-available/mysqli.ini
lrwxrwxrwx 1 root root 30 Sep 10 12:25 20-mysql.ini -> ../../mods-available/mysql.ini
lrwxrwxrwx 1 root root 34 Sep 10 12:25 20-pdo_mysql.ini -> ../../mods-available/pdo_mysql.ini
lrwxrwxrwx 1 root root 35 Sep 20 12:57 20-pdo_sqlite.ini -> ../../mods-available/pdo_sqlite.ini
lrwxrwxrwx 1 root root 33 Sep 20 12:57 20-readline.ini -> ../../mods-available/readline.ini
lrwxrwxrwx 1 root root 32 Sep 20 12:57 20-sqlite3.ini -> ../../mods-available/sqlite3.ini
lrwxrwxrwx 1 root root 31 Sep 20 12:57 20-xdebug.ini -> ../../mods-available/xdebug.ini
From phpinfo():
PHP Version 5.5.9-1ubuntu4.4
Configuration File (php.ini) Path /etc/php5/fpm
Loaded Configuration File /etc/php5/fpm/php.ini
Scan this dir for additional .ini files /etc/php5/fpm/conf.d
Additional .ini files parsed /etc/php5/fpm/conf.d/05-opcache.ini, /etc/php5/fpm/conf.d/10-pdo.ini, /etc/php5/fpm/conf.d/20-gd.ini, /etc/php5/fpm/conf.d/20-json.ini, /etc/php5/fpm/conf.d/20-ldap.ini, /etc/php5/fpm/conf.d/20-mysql.ini, /etc/php5/fpm/conf.d/20-mysqli.ini, /etc/php5/fpm/conf.d/20-pdo_mysql.ini, /etc/php5/fpm/conf.d/20-pdo_sqlite.ini, /etc/php5/fpm/conf.d/20-readline.ini, /etc/php5/fpm/conf.d/20-sqlite3.ini, /etc/php5/fpm/conf.d/20-xdebug.ini
PHP API 20121113
PHP Extension 20121212
Zend Extension 220121212
This program makes use of the Zend Scripting Language Engine:
Zend Engine v2.5.0, Copyright (c) 1998-2014 Zend Technologies
with DBG v7.0.29, (C) 2000,2014, by Dmitri Dmitrienko
with Zend OPcache v7.0.3, Copyright (c) 1999-2014, by Zend Technologies
with Xdebug v2.2.3, Copyright (c) 2002-2013, by Derick Rethans
Zend Engine v2.5.0, Copyright (c) 1998-2014 Zend Technologies
with DBG v7.0.29, (C) 2000,2014, by Dmitri Dmitrienko
with Zend OPcache v7.0.3, Copyright (c) 1999-2014, by Zend Technologies
with Xdebug v2.2.3, Copyright (c) 2002-2013, by Derick Rethans
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