Use maven-shade-plugin rather than maven-assembly-plugin in order to package the artifact in an uber-jar
Now you have to give the target filtered file path.

For instance java -jar dojo69-1.0.0-SNAPHOT.jar f test-classes/config-filtered.properties test-classes/filter1.properties test-classes/filter2.properties
ignore generated dependency-reduced-pom.xml file by maven-shade-plugin
Improve REAMDE