bash

manu@Samweis PHP_PMD-git $ src/bin/phpmd --version
PHPMD 2.2.0
manu@Samweis PHP_PMD-git $ src/bin/phpmd /tmp/short.php text /tmp/naming.xml 

manu@Samweis PHP_PMD-git $ 

ruleset.xml

<?xml version="1.0" encoding="UTF-8"?>
<ruleset name="Naming Rules"
         xmlns="http://pmd.sf.net/ruleset/1.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://pmd.sf.net/ruleset/1.0.0 http://pmd.sf.net/ruleset_xml_schema.xsd"
         xsi:noNamespaceSchemaLocation="http://pmd.sf.net/ruleset_xml_schema.xsd">
    <description>
The Naming Ruleset contains a collection of rules about names - too long, too short, and so forth.
    </description>

    <rule ref="rulesets/naming.xml/ShortVariable">
        <properties>
            <property name="exceptions" value="id,q,i,j,v,e,f,fp" />
        </properties>
    </rule>

</ruleset>

short.php

<?php
class Foo
{
    public function foo($id) {
        return $id * $id;
    }
}