Java – Maven generates duplicate pom.xml and pom.properties files in a jar

<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>

and you run it with

mvn clean compile assembly:single

Compile goal should be added before assembly:single or otherwise the code on your own project is not included.

See more details in comments.

Commonly this goal is tied to a build phase to execute automatically. This ensures the JAR is built when executing mvn install or performing a deployment/release.

<plugin>
  <artifactId>maven-assembly-plugin</artifactId>
  <configuration>
    <archive>
      <manifest>
        <mainClass>fully.qualified.MainClass</mainClass>
      </manifest>
    </archive>
    <descriptorRefs>
      <descriptorRef>jar-with-dependencies</descriptorRef>
    </descriptorRefs>
  </configuration>
  <executions>
    <execution>
      <id>make-assembly</id> <!-- this is used for inheritance merges -->
      <phase>package</phase> <!-- bind to the packaging phase -->
      <goals>
        <goal>single</goal>
      </goals>
    </execution>
  </executions>
</plugin>

You can add local dependencies directly (as mentioned in build maven project with propriatery libraries included) like this:

<dependency>
    <groupId>com.sample</groupId>
    <artifactId>sample</artifactId>
    <version>1.0</version>
    <scope>system</scope>
    <systemPath>${project.basedir}/src/main/resources/Name_Your_JAR.jar</systemPath>
</dependency>

Update

In new releases this feature is marked as deprecated but still working and not removed yet ( You just see warning in the log during maven start). An issue is raised at maven group about this https://issues.apache.org/jira/browse/MNG-6523 ( You can participate and describe why this feature is helpful in some cases). I hope this feature remains there!

If you are asking me, as long as the feature is not removed, I use this to make dependency to only one naughty jar file in my project which is not fit in repository. If this feature is removed, well, there are lots of good answers here which I can chose from later!