You can upload a jar with the java stack but you still need to specify the class and classpath (http://developer.cloudbees.com/bin/view/RUN/Java+Container). The java container does not currently use "java -jar"
Example:
bees app:deploy -t java -R java_version=1.7
-R class=org.springframework.boot.loader.JarLauncher app.jar
An example repo: