Create a profile for the fat jar and configure the maven assembly plugin to create the fat jar in this profile.
For example use this profile:
<profiles>
<profile>
<id>fatjar</id>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
Then you can build it by activating the profile
mvn -P fatjar clean install
where fatjar
is the profile id.
Multiple profiles can also be activated
mvn -P fatjar,release install