To change the configuration for php running as cgi those handy module commands won't work.. The work-around is being able to tell php to start with a custom php.ini file.. configured the way you want.
With multiple custom php.ini files
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/site/ini/1/php.ini
/site/ini/2/php.ini
/site/ini/3/php.ini
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The trick is creating a wrapper script to set the location of the php.ini file that php will use. Then it exec's the php cgi.
shell script /cgi-bin/phpini.cgi
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#!/bin/sh
export PHPRC=/site/ini/1
exec /cgi-bin/php5.cgi
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Now all you have to do is setup Apache to run php files through the wrapper script instead of just executing the php cgi.
In your .htaccess or httpd.conf file
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AddHandler php-cgi .php
Action php-cgi /cgi-bin/phpini.cgi
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So to change the configuration of php you just need to change the PHPRC variable to point to a different directory containing your customized php.ini.. You could also create multiple shell wrapper scripts and create multiple Handler's+Actions in .htaccess..
in your .htaccess
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AddHandler php-cgi1 .php1
Action php-cgi1 /cgi-bin/phpini-1.cgi
AddHandler php-cgi2 .php2
Action php-cgi2 /cgi-bin/phpini-2.cgi
AddHandler php-cgi3 .php3
Action php-cgi3 /cgi-bin/phpini-3.cgi
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The only caveat here is that it seems like you would have to rename the file extensions, but there are ways around that too ->
http://www.askapache.com/php/custom-phpini-tips-and-tricks.html