By default, The RAR plugin retrieves the manifest file to use in this location $basedir/src/main/rar/META-INF/MANIFEST.MF. To be able to change the location, configure the manifestFile property and set the value to the new location.
<project> [...] <build> <plugins> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-rar-plugin</artifactId> <version>2.4</version> <configuration> <manifestFile>src/resources/META-INF/MANIFEST.MF</manifestFile> </configuration> </plugin> </plugins> </build> [...] </project>