Merging Integration and Unit test reports with JaCoCo

I recently implemented this: after some headaches and a lot of testing, I have a configuration that works beautifully.

<plugin>
    <groupId>org.jacoco</groupId>
    <artifactId>jacoco-maven-plugin</artifactId>
    <version>${jacoco.version}</version>
    <executions>
        <execution>
            <id>pre-unit-test</id>
            <goals>
                <goal>prepare-agent</goal>
            </goals>
            <configuration>
                <destFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</destFile>
                <propertyName>surefireArgLine</propertyName>
            </configuration>
        </execution>
        <execution>
            <id>pre-integration-test</id>
            <goals>
                <goal>prepare-agent-integration</goal>
            </goals>
            <configuration>
                <destFile>${project.build.directory}/coverage-reports/jacoco-it.exec</destFile>
                <propertyName>testArgLine</propertyName>
            </configuration>
        </execution>
        <execution>
            <id>post-integration-test</id>
            <phase>post-integration-test</phase>
            <goals>
                <goal>report</goal>
            </goals>
            <configuration>
                <dataFile>${project.build.directory}/coverage-reports/jacoco-it.exec</dataFile>
                <outputDirectory>${project.reporting.outputDirectory}/jacoco-it</outputDirectory>
            </configuration>
        </execution>
        <execution>
            <id>post-unit-test</id>
            <phase>prepare-package</phase>
            <goals>
                <goal>report</goal>
            </goals>
            <configuration>
                <dataFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</dataFile>
                <outputDirectory>${project.reporting.outputDirectory}/jacoco-ut</outputDirectory>
            </configuration>
        </execution>
        <execution>
            <id>merge-results</id>
            <phase>verify</phase>
            <goals>
                <goal>merge</goal>
            </goals>
            <configuration>
                <fileSets>
                    <fileSet>
                        <directory>${project.build.directory}/coverage-reports</directory>
                        <includes>
                            <include>*.exec</include>
                        </includes>
                    </fileSet>
                </fileSets>
                <destFile>${project.build.directory}/coverage-reports/aggregate.exec</destFile>
            </configuration>
        </execution>
        <execution>
            <id>post-merge-report</id>
            <phase>verify</phase>
            <goals>
                <goal>report</goal>
            </goals>
            <configuration>
                <dataFile>${project.build.directory}/coverage-reports/aggregate.exec</dataFile>
                <outputDirectory>${project.reporting.outputDirectory}/jacoco-aggregate</outputDirectory>
            </configuration>
        </execution>
    </executions>
</plugin>
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-surefire-plugin</artifactId>
    <version>2.18.1</version>
    <configuration>
        <argLine>${surefireArgLine}</argLine>
        <skipTests>${skip.unit.tests}</skipTests>
        <includes>
            <include>**/*UT.java</include>
            <include>**/*MT.java</include>
            <include>**/*Test.java</include>
        </includes>
        <skipTests>${skipUTMTs}</skipTests>
    </configuration>
</plugin>
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-failsafe-plugin</artifactId>
    <version>2.12.4</version>
    <configuration>
        <skipTests>${skipTests}</skipTests>
        <skipITs>${skipITs}</skipITs>
        <argLine>${testArgLine}</argLine>
        <excludes>
            <exclude>**/*UT*.java</exclude>
        </excludes>
    </configuration>
    <executions>
        <execution>
            <goals>
                <goal>integration-test</goal>
                <goal>verify</goal>
            </goals>
        </execution>
    </executions>
</plugin>

As you can see, there are 6 distinct Jacoco executions to run the tests, merge the files and create an aggregate report. On top of the Jacoco config, you also need to configure Surefire and Failsafe to take an argument from Jacoco (Surefire runs the unit tests and Failsafe runs the integration tests).

All of the configuration that I used should be there, what you do with it is your design architecture to make it fit within your desired requirements. Personally, I recommend a look into what I exclude and include within surefire and failsafe if you are having issues with files not being read.