In case when user runs "mvn clover2:setup install", JARs containing instrumented code will be installed into ~/.m2 local cache. It may cause NoClassDefFoundError in case when such JAR is picked in another build in which Clover is not enabled.
Similarly, when user runs "mvn clover2:setup deploy", instrumented JARs will be deployed to a repository.
Clover should allow to protect users from polluting their repositories.
This repository pollution protection feature will be enabled by default for builds where automatic Clover integration is used. In case of manual Clover integration, user can enable this protection by the -Dmaven.clover.repositoryPollutionProtection=true flag.