You need to go via the pom configuration like this:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9</version>
<configuration>
<!-- Default configuration for all reports -->
...
</configuration>
<executions>
<execution>
<id>aggregate</id>
<goals>
<goal>aggregate</goal>
</goals>
<phase>site</phase>
<configuration>
<!-- Specific configuration for the aggregate report -->
...
</configuration>
</execution>
...
</executions>
</plugin>
...
</plugins>
</build>
...
</project>
and than you need to call mvn site ...