How can I tell jaxb / Maven to generate multiple schema packages?

I had to specify different generateDirectory (without this, the plugin was considering that files were up to date and wasn’t generating anything during the second execution). And I recommend to follow the target/generated-sources/<tool> convention for generated sources so that they will be imported in your favorite IDE automatically. I also recommend to declare several execution instead of declaring the plugin twice (and to move the configuration inside each execution element):

<plugin>
  <groupId>org.jvnet.jaxb2.maven2</groupId>
  <artifactId>maven-jaxb2-plugin</artifactId>
  <version>0.7.1</version>
  <executions>
    <execution>
      <id>schema1-generate</id>
      <goals>
        <goal>generate</goal>
      </goals>
      <configuration>
        <schemaDirectory>src/main/resources/dir1</schemaDirectory>
        <schemaIncludes>
          <include>shiporder.xsd</include>
        </schemaIncludes>
        <generatePackage>com.stackoverflow.package1</generatePackage>
        <generateDirectory>${project.build.directory}/generated-sources/xjc1</generateDirectory>
      </configuration>
    </execution>
    <execution>
      <id>schema2-generate</id>
      <goals>
        <goal>generate</goal>
      </goals>
      <configuration>
        <schemaDirectory>src/main/resources/dir2</schemaDirectory>
        <schemaIncludes>
          <include>books.xsd</include>
        </schemaIncludes>
        <generatePackage>com.stackoverflow.package2</generatePackage>
        <generateDirectory>${project.build.directory}/generated-sources/xjc2</generateDirectory>
      </configuration>
    </execution>
  </executions>
</plugin>

With this setup, I get the following result after a mvn clean compile

$ tree target/
target/
├── classes
│   ├── com
│   │   └── stackoverflow
│   │       ├── App.class
│   │       ├── package1
│   │       │   ├── ObjectFactory.class
│   │       │   ├── Shiporder.class
│   │       │   ├── Shiporder$Item.class
│   │       │   └── Shiporder$Shipto.class
│   │       └── package2
│   │           ├── BookForm.class
│   │           ├── BooksForm.class
│   │           ├── ObjectFactory.class
│   │           └── package-info.class
│   ├── dir1
│   │   └── shiporder.xsd
│   └── dir2
│       └── books.xsd
└── generated-sources
    ├── xjc
    │   └── META-INF
    │       └── sun-jaxb.episode
    ├── xjc1
    │   └── com
    │       └── stackoverflow
    │           └── package1
    │               ├── ObjectFactory.java
    │               └── Shiporder.java
    └── xjc2
        └── com
            └── stackoverflow
                └── package2
                    ├── BookForm.java
                    ├── BooksForm.java
                    ├── ObjectFactory.java
                    └── package-info.java

Which seems to be the expected result.