The problem occurs with dependencies like commons-logging, which have runtime dependencies to other logging engines. As workaround one can use
<assembly>
<inclusions>
<inclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</inclusion>
...
</assembly>
but all these dependencies are already listed as optional / provided in the dependency tree. Thus they should be added as "-libraryjars" to avoid warnings.
List of warnings:
[proguard] Warning: org.apache.commons.logging.impl.AvalonLogger: can't find referenced class org.apache.avalon.framework.logger.Logger
[proguard] Warning: org.apache.commons.logging.impl.Log4JLogger: can't find referenced class org.apache.log4j.Category
[proguard] Warning: org.apache.commons.logging.impl.Log4JLogger: can't find referenced class org.apache.log4j.Priority
[proguard] Warning: org.apache.commons.logging.impl.Log4JLogger: can't find referenced class org.apache.log4j.Logger
[proguard] Warning: org.apache.commons.logging.impl.LogKitLogger: can't find referenced class org.apache.log.Hierarchy
[proguard] Warning: org.apache.commons.logging.impl.LogKitLogger: can't find referenced class org.apache.log.Logger
[proguard] Warning: org.apache.commons.logging.impl.ServletContextCleaner: can't find referenced class javax.servlet.ServletContextListener
[proguard] Warning: org.apache.commons.logging.impl.ServletContextCleaner: can't find referenced class javax.servlet.ServletContextEvent