If you use the following configuration, the file found in ${project.build.outputDirectory}/META-INF/MANIFEST.MF will be used as the manifest file in the jar.
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<useDefaultManifestFile>true</useDefaultManifestFile>
</configuration>
...
</plugin>
</plugins>
</build>
...
</project>