How can I specify a Class-Path: entry in the manifest of an EJB JAR?

You just have to configure it:

<project>
  ...
  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-ejb-plugin</artifactId>
        <version>2.5</version>
        ...
        <configuration>
          <archive>
            <manifest>
              <addClasspath>true</addClasspath>
            </manifest>
          </archive>
        </configuration>
        ...
      </plugin>
    </plugins>
  </build>
  ...
</project>
         
Please see the Maven Archiver Reference for more information about controlling the exact format of the generated class path entries.

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How does the classifier affect artifacts in my EJB project?

When used, the copy of the artifact in your project will have the classifier appended to its filename. This can be used to differentiate multiple artifacts.

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