The files pdfunit.config and the license key file can be placed outside of the classpath. But then their location has to be declared by Java system properties. The keys of the properties are:

Dependent on your test system (Eclipse, ANT or Maven) these parameters can be set in many ways. Use the common information to see, how Java system properties are set in your specific environment. A less known option is the operating system environment variable _JAVA_OPTIONS which works for all test systems:

set _JAVA_OPTIONS=-Dpdfunit.configfile=..\myfolder\pdfunit.config

If you have questions about this topic, write a mail to info[at]pdfunit.com.