I think you can try using the builder-helper-maven plugin, currently the latest version is 1.5. as described by http://docs.codehaus.org/display/SONAR/Analyzing+Java+Projects . However, just change the plugin version to 1.5 and use mvn sonar3: sonar. Most importantly, do not forget to <sonar.phase> generate sources </sonar.phase>, without this it does not work.
as for the output directory, if you use eclipse, you can specify the output directory for each module and point them to the same folder. Use this folder as the output directory for pom.xml. do not forget to disable the scrub if using eclipse.
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