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Use the phpMD / PHP CodeSniffer Netbeans Plugin (see https://sourceforge.net/projects/phpmdnb/).
Use NetBeans plugin manager to install the plugin.
The "php cli file" should be already detected, if not set the path to your php installation file.
Set the "PHPCheckstyle run file" value to the "run.php" file in your PHPCheckstyle installation directory.
Set the "config" value to the name of the configuration file used.
You should them be able to use the "check style" contextual menu on any PHP file.