Alex Taylor , what you've described, regarding the exclude block in the maven plugin not taking affect in Jenkins, is the issue I've seen and am interested in a fix for, and seems to align with the initial description (which is specific to maven based projects).

Thanks for the update Gabriel Stanek just wanted make sure I was understanding everyone's issue and how best I can fix it

I am still seeing this as an open issue. Even I exclude the package from the pom.xml as well as from the Jenkins "exclusions" fields, those packages are still being included in the JaCoCo report.

my workaround: in the pom.xml I save all patterns  as properties:

<coverage-exclusion-01>*/com/company/product//config//.</coverage-exclusion-01><coverage-exclusion-02>/com/company/cfa//CallDTO.</coverage-exclusion-02><coverage-exclusion-03>*/com/company/cfa/*/DAO.</coverage-exclusion-03>

And I use them to configure the maven jacoco plugin

<configuration> <excludes> <exclude>${coverage-exclusion-01}</exclude> <exclude>${coverage-exclusion-02}</exclude>

etc...

And then, in the pipeline file y read again the properties

script{      props = readMavenPom().getProperties()     exclusionPattern = props.entrySet().findAll\{entry -> entry.key.startsWith('coverage-exclusion-')}.collect{it.value}.join(',')
    echo "exclusionPattern = ${exclusionPattern}"
}
jacoco( execPattern: '**/target/jacoco.exec', exclusionPattern: exclusionPattern)

It works, but is ugly