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I tried the first answer by using maven-resource-plugin to copy the org.ops4j.pax.logging.cfg file with custom log settings into target folder after a build. I copied the following into my karaf pom file. It does copy the file but I guess the original org.ops4j.pax.logging.cfg file is produced after this plugin is executed. So the base log file without custom log settings overrides our log setting file. But it does work when I copy the plugin into my parent pom, so not the exact solution but hits nearby for now.

        <plugin>
            <artifactId>maven-resources-plugin</artifactId>
            <version>3.0.1</version>
            <executions>
              <execution>
                <id>copy-resources</id>
                <phase>validate</phase>
                <goals>
                  <goal>copy-resources</goal>
                </goals>
                <configuration>
                  <outputDirectory>${basedir}/target/assembly/etc</outputDirectory>
                  <overwrite>true</overwrite>         
                  <resources> 
                    <resource>
                      <directory>res</directory>
                      <filtering>true</filtering>
                    </resource>
                  </resources>              
                </configuration>            
              </execution>
            </executions>
          </plugin>