Using the XML file, you can include the files or directories you want to process, and exclude the ones you do not. PHPUnit Manual Entry
<filter>
<whitelist processUncoveredFilesFromWhitelist="true">
<file>BankAccount.php</file>
<directory suffix=".class">.</directory>
<directory suffix=".fn">.</directory>
<directory suffix=".php">.</directory>
<exclude>
<directory>ExternalLibraries</directory>
</exclude>
</whitelist>
</filter>