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>2.3.2</version> <configuration> <useDefaultManifestFile>true</useDefaultManifestFile> </configuration> ... </plugin> </plugins> </build> ... </project>