Comma separated exception list for PHP Mess Detector for short variable names like $id or other valid shortnames. I include this using Sublime PHPcs settings.

phpcs.sublime-settings

{
    // other settings
    // Execute phpmd
    "phpmd_run": true,

    // Execute the phpmd on file save
    "phpmd_command_on_save": true,

    // It seems python/sublime cannot always find the phpmd application
    // If empty, then use PATH version of phpmd, else use the set value
    "phpmd_executable_path": "c:\\wamp\\bin\\php\\php5.4.12\\pear\\phpmd.bat",

    // Additional arguments you can specify into the application
    //
    // Example:
    // {
    //     "codesize,unusedcode"
    // }
    "phpmd_additional_args": {
        "codesize,unusedcode,naming,~/.phpmd/rules.xml": "" // add path to custom ruleset file here
    }
}

rules.xml

 <?xml version="1.0"?>
 <rule ref="rulesets/naming.xml/ShortVariable" >
    <properties>
        <property name="exceptions" value="id,em" />
    </properties>
</rule>

for anyone that finds this when searching for a solution.... I only had luck when omitting naming from phpmd_additional_args