Clover works on a source code instrumentation level, which means it needs access to source code in order to generate code coverage data.
It works well in multi-module Maven projects, however if you depend on any (external or local) Maven repository to fetch the dependencies (they are not part of multi module project) then you have to manage this by your own. Either by tracking coverage in every module separately (recommended) or by sharing instrumented JAR files (I would rather not recommend it because instrumented JARs can end up in a production system which is rather a bad thing)
Cheers,
Grzegorz Lewandowski
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