shade-jar utility is means for changing JAR file namespaces. Basically it replaces all occurences of given pattern with a given replacement. The replacament is performed on class file names and inside the class files themselves. This is commonly known as shading.
shade-jar org.apache.log4j com.example.shaded.log4j /usr/share/java/log4j.jar lib/shaded-log4j.jar will replace all occurences of org.apache.log4j in JAR file /usr/share/java/log4j.jar with com.example.shaded.log4j and store the resulting JAR in lib/shaded-log4j.jar.
Bugs should be reported through Java Packages Tools issue tracker at Github: m[blue]https://github.com/fedora-java/javapackages/issuesm.