How to exclude and include properly classes, packages and jar classes, lib from the jacoco report (Instrumentation offline)

Try includes instead of excludes. Notice that you need .class at the end. try something like that:

<configuration>
    <includes>
        <include>com/company/package/**/*.class</include>
    </includes>
</configuration>

Base on your example:

           <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>${jacoco.version}</version>
                <executions>
                    <execution>
                    <goals>
                        <goal>instrument</goal>
                        <goal>restore-instrumented-classes</goal>
                        <goal>report</goal>
                    </goals>
                    <configuration>
                        <!-- this configuration affects all goals -->
                        <includes>
                            <include>com/company/packageToInclude/**/*.class</include>                                               
                        </includes>
                    </configuration>
                    </execution>
                </executions>
            </plugin>

I don't know how you generate lib directory, because you don't provide complete example.

However in case of the following example

src/main/java/Example.java

class Example {
}

src/test/java/ExampleTest.java

public class ExampleTest {
    @org.junit.Test
    public void test() {
        new Example();
    }
}

and pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
  <modelVersion>4.0.0</modelVersion>

  <groupId>org.example</groupId>
  <artifactId>example</artifactId>
  <version>0.1-SNAPSHOT</version>

  <properties>
    <jacoco.version>0.8.4</jacoco.version>
  </properties>

  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.12</version>
    </dependency>
    <dependency>
      <groupId>org.jacoco</groupId>
      <artifactId>org.jacoco.agent</artifactId>
      <classifier>runtime</classifier>
      <version>${jacoco.version}</version>
      <scope>test</scope>
    </dependency>
  </dependencies>

  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-dependency-plugin</artifactId>
        <executions>
          <execution>
            <phase>test-compile</phase>
            <goals>
              <goal>copy-dependencies</goal>
            </goals>
            <configuration>
              <includeArtifactIds>junit</includeArtifactIds>
              <outputDirectory>${project.build.directory}/classes/lib</outputDirectory>
            </configuration>
          </execution>
        </executions>
      </plugin>

      <plugin>
        <groupId>org.jacoco</groupId>
        <artifactId>jacoco-maven-plugin</artifactId>
        <version>${jacoco.version}</version>
        <executions>
          <execution>
            <goals>
              <goal>instrument</goal>
              <goal>restore-instrumented-classes</goal>
              <goal>report</goal>
            </goals>
          </execution>
        </executions>
      </plugin>

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <configuration>
          <systemPropertyVariables>
            <jacoco-agent.destfile>target/jacoco.exec</jacoco-agent.destfile>
          </systemPropertyVariables>
        </configuration>
      </plugin>
    </plugins>
  </build>

</project>

execution of mvn clean verify produces

$ ls -R target/classes
target/classes:
Example.class  lib

target/classes/lib:
junit-4.12.jar

and following report

And after addition of following <configuration>

      <plugin>
        <groupId>org.jacoco</groupId>
        <artifactId>jacoco-maven-plugin</artifactId>
        <version>${jacoco.version}</version>
        <executions>
          <execution>
            <goals>
              <goal>instrument</goal>
              <goal>restore-instrumented-classes</goal>
              <goal>report</goal>
            </goals>
            <configuration>
              <excludes>
                <exclude>lib/**</exclude>
              </excludes>
            </configuration>
          </execution>
        </executions>
      </plugin>

execution of the same command mvn clean verify produces following report

If the above doesn't help, then please provide absolutely complete example allowing everybody else to reproduce exactly the same what you do.