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>

... and code within modules to be excluded by configuring the agent to be more selective ...

<plugin>
    <groupId>org.jacoco</groupId>
    <artifactId>jacoco-maven-plugin</artifactId>
    <version>${jacoco-plugin.version}</version>
    <executions>
        <execution>
            <goals>
                <goal>prepare-agent</goal>
            </goals>
            <configuration>
                <includes>
                    <include>com.foo.*</include>
                </includes>
            </configuration>
        </execution>
    </executions>
</plugin>
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