My answer is 10 years later but in case like that, you need to use a more precise model for the maven shade plugin. Use this form of this plugin:

<build>
  <plugins>
    <plugin>
      <!-- Create a FAT JAR -->
      <groupId>org.apache.maven.plugins</groupId>
      <artifactId>maven-shade-plugin</artifactId>
      <version>3.6.0</version>
      <executions>
        <execution>
          <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <transformers>
                  <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                    <mainClass>flag.yourCompany.yourMainClass</mainClass>
              </transformer>
            </transformers>
            <shadedArtifactAttached>true</shadedArtifactAttached>
            <shadedClassifierName />
          </configuration>
        </execution>
      </executions>
    </plugin>
  </plugins>
</build>

Now, If you have an IDE like JetBrains IntelliJ IDEA, put this command on it for the maven configuration:

clean compile verify

If you want to perform a command in the folder of your project that contains pom.xml, you can just do it:

mvn verify

Now to check if your jar has a manifest, copy-paste the shaded version Name-1.0-SNAPSHOT-shaded.jar in a file named Name.zip (note that you must change the extension) and go to META-INF folder. You can finally see a MANIFEST.MF file in the list of files. Extract it and see the content, it must be like that:

Manifest-Version: 1.0
Created-By: Maven JAR Plugin 3.4.1
Build-Jdk-Spec: 24
Main-Class: flag.yourCompany.yourMainClass

The command (replace with your yourMainClass-yourVersion-shaded.jar):

java -jar Name-1.0-SNAPSHOT-shaded.jar

now works in the terminal if you have correctly configurated your JAVA_HOME environment variable! (but I don't know if it is executable directly by Windows cause I have differents versions of Java in my PATH)