Be sure that you use the full paths for each application in your application. According to APC documentation:
apc.stat integer
Use caution when changing this setting. This value is enabled by default, causing APC to stat (check) the script for each request to determine if it has changed. If it was changed, it will recompile and cache the new version. If this option is turned off, APC will not check, which usually means that to force the APC check, you need to restart the web server or clear the cache manually. Please note that FastCGI web server configurations may not clear the cache upon reboot. On a production server, where script files rarely change, significant performance gains can be achieved with disabled statistics.
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PHP , :
define('PATH_PROJECT', realpath(dirname(__FILE__)));
, :
include_once PATH_PROJECT . '/some/dir/file.php';
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