Solution:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-ear-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
<jboss>
<version>4</version>
</jboss>
<bundleFileName>
binbase-quality-control.ear
</bundleFileName>
<modules>
<webModule>
<groupId>edu.ucdavis.genomics.metabolomics.binbase.quality
</groupId>
<artifactId>quality-war</artifactId>
<contextRoot>/quality-war</contextRoot>
</webModule>
</modules>
</configuration>
</plugin>