Is it possible to create an “uber” jar containing the project classes and the project dependencies as jars with a custom manifest file?

Actually, I didn’t check what the maven-shade-plugin is doing exactly (or any other plugin) as maven 2 has everything built-in to create a megajar or uberjar. You just have to use the maven-assembly-plugin with the predefined jar-with-dependencies descriptor.

Just add this snippet to your pom.xml to customize the manifest:

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-assembly-plugin</artifactId>
  <configuration>
    <archive>
      <manifest>
        <mainClass>my.package.to.my.MainClass</mainClass>
      </manifest>
    </archive>
  </configuration>
</plugin>

And the following command will generate your uberjar:

mvn assembly:assembly -DdescriptorId=jar-with-dependencies

But, again, the default behavior of this descriptor is to unpack dependencies (like the maven-shade-plugin). To be honest, I don’t get why this is a problem but, if this is really not what you want, you can use your own custom assembly descriptor.

To do so, first, create your assembly descriptor, let’s say src/assembly/uberjar.xml, with the following content:

<assembly>
  <id>uberjar</id>
  <formats>
    <format>jar</format>
  </formats>
  <includeBaseDirectory>false</includeBaseDirectory>
  <dependencySets>
    <dependencySet>
      <unpack>false</unpack>
      <scope>runtime</scope>
      <useProjectArtifact>false</useProjectArtifact>
    </dependencySet>
  </dependencySets>
  <fileSets>
    <fileSet>
      <directory>${project.build.outputDirectory}</directory>
      <outputDirectory>/</outputDirectory>
    </fileSet>
  </fileSets>
</assembly>

Then, configure the maven-assembly-plugin to use this descriptor and to add the dependencies to the Class-Path entry of the manifest:

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-assembly-plugin</artifactId>
  <configuration>
    <descriptors> 
      <descriptor>src/assembly/uberjar.xml</descriptor>
    </descriptors>
    <archive>
      <manifest>
        <mainClass>my.package.to.my.MainClass</mainClass>
        <addClasspath>true</addClasspath>
      </manifest>
    </archive>
  </configuration>
  <!--
  <executions>
    <execution>
      <phase>package</phase>
      <goals>
        <goal>single</goal>
      </goals>
    </execution>
  </executions>
  -->
</plugin>

Finally run mvn assembly:assembly to produce your uberjar.

Optionally, uncomment the executions element to bind the assembly plugin on the package phase (and have the assembly produced as part of the normal build).