The clover2:setup goal has proven more reliable and also easier for users to understand than the clover2:instrument goal.
We should update the documentation so that the clover2:setup goal is used by default and
the clover2:instrument goal is only used when users absolutely must - for keeping instrumented source/artifacts separate.
Maven has issues when a plugin forks the lifecycle (clover2:instrument) and it has been recommended by the maven team to not rely on this.
see also suggestions here: http://forums.atlassian.com/thread.jspa?messageID=257315111