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Jacoco Code coverage report generated after on Jenkins build does not respect the jacoco configurations mentioned in pom.xml

I am trying to get Jenkins to respect the jacoco code coverage configurations from the pom.xml instead of the configurations excplicitly set on the Jenkins code coverage plugin UI.
If I mention exclusions explicitly on the jacoco code coverage plugin UI, it is respected.
But this does not seem to be feasible for more number of different projects which may have different configurations(exclusions, inclusions, coverage criteria).
The below jacoco snippet in pom.xml is respected when I run this locally using mvn clean install. The code coverage report generated excludes the exclusions.
Any suggestions on how to make the coverage report generated on jenkins respect the exclusions from my pom.xml ?
Jacoco configurations respected from Jenkins code coverage UI
The goal mentioned in the jenkins configuration page is clean -U source:jar install -Pbundle.
I tried removing the jacoco code coverage report from Jenkins configuration post-build actions thinking that it may respect the configurations in pom.xml but that ended up not generating the coverage report itself.
Snippet of jacoco from pom.xml
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.17</version>
<configuration>
<!-- Sets the VM argument line used when unit tests are run. -->
<argLine>${surefireArgLine}</argLine>
<systemPropertyVariables>
<jacoco-agent.destfile>${project.basedir}/target/jacoco.exec</jacoco-agent.destfile>
</systemPropertyVariables>
</configuration>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.6</version>
<configuration>
<excludes>
<exclude>com/package/subpackage1/subpackage2/server/config/*.class</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>jacoco-initialize</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<!-- Sets the name of the property containing the settings for JaCoCo
runtime agent. -->
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<execution>
<id>jacoco-site</id>
<phase>test</phase>
<goals>
<goal>report</goal>
<goal>check</goal>
</goals>
<configuration>
<rules>
<rule>
<element>PACKAGE</element>
<limits>
<limit>
<counter>CLASS</counter>
<value>COVEREDRATIO</value>
<minimum>50%</minimum>
</limit>
</limits>
</rule>
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

Exclude test directories in multi-module maven projecty from JaCoCo when using Azure build pipeline

This feels like it should be easy, so please help point me in the correct direction.
I am successfully using maven to build my java project using a Azure Pipeline. I am also successfully getting JaCoCo coverage reports.
I have a maven project with multiple modules. Below is a sample project structure. I want to exclude everything in all the sub src/test/java directories/packages.
myproject
mod1
src/main/java/...
src/test/java/...
pom.xml
mod2
src/main/java/...
src/test/java/...
pom.xml
pom.xml
I would have expected something like setting codeCoverageClassFilter to -:*.src.test.java*.*, but none of my variations have worked. What is the correct statement to exclude all these test directories?

For excluded test add next configuration in pom parent
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.6</version>
<configuration>
<excludes>
<exclude>com/acme/test/*</exclude>
</excludes>
</configuration>
<executions>
<!-- prepare agent for measuring integration tests -->
<execution>
<id>jacoco-initialize</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>jacoco-site</id>
<phase>package</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>

Not able to generate coverage report using jacoco plugin for test cases written using jmockit library

I have unit test cases written using jmockit(version:1.44) library in my application. I am able to run the test cases using maven surefire plugin and generate coverage reports using below dependency-
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>
-javaagent:${project.basedir}/repo/org/jmockit/1.44/jmockit-1.44.jar
</argLine>
<forkMode>once</forkMode>
</configuration>
</plugin>
However, I want to integrate coverage report with sonar qube and started using jacoco plugin instead of surefire.
But I am getting the exception -
[ERROR] PwdResetControllerTest.setUp:76 NoClassDefFound mockit.MockUp
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.2</version>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<!-- attached to Maven test phase -->
<execution>
<id>report</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
Please help.

Code coverage of client/server web application

I am writing a multi-module application. Some of the modules are just basic Java libraries which are then included in the WAR of a webapp.
I would like to run code coverage in the following scenario:
I am running the webapp through an embedded Jetty that is started via Maven.
I have tests which are executing HTTP requests against the webapp.
I would like to get code covered in the webapp and also by the tests.
Is this possible and how can it be achieved with Cobertura, JaCoCo or Emma? From what I understand, the code coverage will only cover the client-side code in this scenario. Am I correct?

I think if you would manage to attach the JaCoCo-agent to the jvm that runs the jetty, it should be able to measure which code has been called over the time you run the integration tests against your webapp. So you should get a statistic that shows you the code coverage.
There is a JaCoCo Maven Plugin - though I'm not sure if this will help with you scenario. Just used it during unit tests.
Edit: found a blog-post that seems to point in the right direction here
Measure Code Coverage by Integration Tests with Sonar

Here's how I achieved it
Assuming you already have a minimal pom.xml config:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</
<version>0.7.4.201502262128</vers
</plugin>
Download JaCoCo's agent and copy jacocoagent.jar to a suitable location (e.g. $HOME/tools/jacocoagent0.7.4.jar)
Attach JaCoCo's agent to Maven's JVM via:
export MAVEN_OPTS="$MAVEN_OPTS \
-javaagent:$HOME/tools/jacocoagent0.7.4.jar=output=tcpserver,port=6300"
Run your application with embedded jetty server e.g. mvn jetty:run
Run your integration tests
In another shell, dump and report via mvn jacoco:dump jacoco:report
Open your report on ./target/site/index.html (by default)

You can use Jacoco plugin to generate code coverage Here is the plugin configuration I used for junit test code coverage.
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.5.10.201208310627</version>
<configuration>
<skip>${maven.test.skip}</skip>
<output>file</output>
<append>true</append>
</configuration>
<executions>
<execution>
<id>jacoco-initialize</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>jacoco-site</id>
<phase>verify</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
Note: you may get life cycle not covered error in maven while using eclipse, one way is you explicitly mention the life cycle using plugin management. I installed the jacoco plugin from the market place which resolved my problem

We had a similar scenario where integration test were run on a jetty server. Also we needed a combined report for all the tests unit and integration. The solution we implemented was to run-forked jetty and pass the jvmargs with the jacoco javaagent details. Our code coverage reports covered all the rest api's and the service layer java code.
The pom config for jacoco
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<configuration>
<append>true</append>
</configuration>
<executions>
<execution>
<id>prepare-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<destFile>${project.build.directory}/jacoco.exec</destFile>
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<execution>
<id>prepare-integration</id>
<goals>
<goal>prepare-agent-integration</goal>
</goals>
<configuration>
<destFile>${project.build.directory}/jacoco.exec</destFile>
<propertyName>failsafeArgLine</propertyName>
</configuration>
</execution>
</executions>
</plugin>
With the above config we generated a common exec file for both unit and integration test. Next we configured jetty to run-forked
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>${jetty-maven-plugin.version}</version>
<configuration>
<stopKey>foo</stopKey>
<stopPort>9999</stopPort>
<webApp>
<contextPath>/myway</contextPath>
<descriptor>src/main/webapp/WEB-INF/web.xml</descriptor>
</webApp>
<!-- passing the jacoco plugin as a jvmarg -->
<jvmArgs>${failsafeArgLine}</jvmArgs>
</configuration>
<executions>
<execution>
<id>start-jetty</id>
<phase>pre-integration-test</phase>
<configuration>
<daemon>true</daemon>
<waitForChild>false</waitForChild>
</configuration>
<goals>
<goal>run-forked</goal>
</goals>
</execution>
<execution>
<id>stop-jetty</id>
<phase>post-integration-test</phase>
<goals>
<goal>stop</goal>
</goals>
</execution>
</executions>
</plugin>
This would launch jetty in a separate jvm with the jvmargs. Finally we generated the report in the reporting tag of the pom. We noticed that adding the report to the build plugins did not capture the integration tests run by the jetty.
<reporting>
</plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<reportSets>
<reportSet>
<id>jacoco-report</id>
<reports>
<report>report</report>
</reports>
</reportSet>
</reportSets>
</plugin>
</plugins>
</reporting>
The reports can be accessed at target/site/jacoco/index.html, alternately you can run it from the command line.
mvn jacoco:report
Hope it helps.

Emma does not display uncovered packages in the report

I am using maven with emma to generate coverage report on linux red hat. After I run command mvn emma:emma, packages which are not covered by JUnit tests are not displayed in the report.
I am using following configuration:
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>emma-maven-plugin</artifactId>
<version>1.0-alpha-3</version>
</plugin>
Any idea what is going on?
Or any way to make sure all packages including uncovered are part of report?

note this was supposed to be a comment, and It doesn't answer not answer the question directly. It questions the usefulness of the question.
Quit using emma and start using jacoco. AFAIK, emma has been dormant since around 2007. The latest version of the emma plugin on maven central is from 2010.
As of today (fist quarter 2013). There is a version on maven central from feb-2013.
<dependency>
<groupId>org.jacoco</groupId>
<artifactId>jacoco</artifactId>
<version>0.6.2.201302030002</version>
</dependency>
And it is synchronized with the maven plugin. Here is an example of a configuration of mine
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<excludes>
<exclude>**/entities/*</exclude>
</excludes>
</configuration>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>prepare-package</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
The reports from jacoco also look nicer than the ones in emma.
Compare:
with