Everyone should be running with safe_mode on in /etc/php.ini (on Centos) as it makes exploiting your system more difficult is PHP can't execute anything on the system if a script is exploited.

For example with Safe_Mode on the only executable files on the system are ones in the safe_mode_exec_dir = /safephp

This is crucial, if you must execute anything from PHP then you have to copy the binary and assign to the user that Apache runs your site under.  This makes things much more secure.

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