Updated the systemCommand() static function to handle both an array and string value for arguments, this resolves issues on Windows Servers where Apache fails to reload. As the systemCommand() function now uses core PHP function calls instead of other static functions inside the class, I've now depreciated the now redundent files to enable existing third-party modules to keep working whilst making it clear we will be removing these methods/functions in future.

Closes several bugs #647, #646 and #632