I was having trouble deploying the EJB in chapter 6 because the pom puts a Main-Class declaration in the Manifest. This causes glassfish to reject the jar, but no mention of this is made in the book, that I found.

The workaround is stated in this comment embedded in the Chapter 6 pom.xml:

To avoid multiple modules with Maven, here is what you need to manually do (it's not nice, but it works)

1. Comment the following section (maven-jar-plugin), package the jar, and deploy to GlassFish
2. Uncomment the following section, package the jar and run the Main class with app client

There is a simpler way to do this without resorting to commenting/uncommenting. Wrap the maven jar plugin with the main class declaration in a profile. The profile is inactive by default and activated with -Pclient added to the command line.

<profiles>
    <profile>
        <id>client</id>
        <activation>
            <activeByDefault>false</activeByDefault>
        </activation>
        <build>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <version>${plugin-jar-version}</version>
                    <configuration>
                        <archive>
                            <manifest>
                                <mainClass>org.beginningee6.book.chapter06.Main</mainClass>
                            </manifest>
                        </archive>
                    </configuration>
                </plugin>
            </plugins>
        </build>
    </profile>
</profiles>