My server previously did not have the command-line php package installed (php5-cli; debian), only apache2 mod_php; php5-cli was only installed to support Drush.
When php5-cli was installed, it created it's own config file in /etc/php5/cli and that's what it uses when php is run from the shell.
However, apache2 uses it's own config file at /etc/php5/apache2/php.ini
The Drush 'status' command incorrectly lists /etc/php/cli/php.ini as the config file for the site queried.
Fortunately, apache2 does *not* use php5-cli's config file, as it ships (for debian, at least) with magic_quotes_gpc=On
Besides causing confusion, could this cause an actual problem if for instance the ../conf.d/*.ini files differed significantly between the apache2 and php5-cli config files? (specifically mysql/mysqli.ini)
sidebar: could http://drupal.org/node/457416 be related to this?
PHP Version 5.2.6-1+lenny3 System Linux svr-web 2.6.24-1-686 #1 SMP Thu May 8 02:16:39 UTC 2008 i686 Build Date Apr 26 2009 21:57:45 Server API Apache 2.0 Handler Virtual Directory Support disabled Configuration File (php.ini) Path /etc/php5/apache2 Loaded Configuration File /etc/php5/apache2/php.ini Scan this dir for additional .ini files /etc/php5/apache2/conf.d additional .ini files parsed /etc/php5/apache2/conf.d/gd.ini, /etc/php5/apache2/conf.d/mcrypt.ini, /etc/php5/apache2/conf.d/mysql.ini, /etc/php5/apache2/conf.d/mysqli.ini, /etc/php5/apache2/conf.d/pdo.ini, /etc/php5/apache2/conf.d/pdo_mysql.ini
$ 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/gd.ini, /etc/php5/cli/conf.d/mcrypt.ini, /etc/php5/cli/conf.d/mysql.ini, /etc/php5/cli/conf.d/mysqli.ini, /etc/php5/cli/conf.d/pdo.ini, /etc/php5/cli/conf.d/pdo_mysql.ini