In the past it was the recommended way to run goal sonar:sonar
alone. This is no more the case since SonarQube Scanner for Maven stopped trying to run unit tests + collect coverage for you by forking a new Maven lifecycle.
General advice is now to run goals in a single command. For example mvn clean package sonar:sonar
In the case of Clover the clover:setup
goal will alter the Maven Model to make all other plugins (like surefire) use instrumented classes instead of original source code. This is indeed a problem because it will prevent SonarQube to match class files. So in your case you should either stick with two separate goals, or manually configure sonar.sources
to refer to original source code.