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I have the same problem. The includes/excludes appear to be evaluated relative to the class directory. It is onerous and brittle to add specific exclusions on a package by package basis.
IMHO, rather than an option to exclude specific maven modules, the plugin should ignore un-instrumented class files.
This would address the problem without being maven specific. In the maven configuration, modules could then be excluded by configuring them to skip jacoco instrumentation...
<plugin> <groupId>org.jacoco</groupId> <artifactId>jacoco-maven-plugin</artifactId> <configuration> <skip>true</skip> </configuration> </plugin>