UseCase:
Create aggregated javadocs for both source code in the default location and 
source code in an additional location.  I include the "additional source code directory"
using the "build-helper-maven-plugin" which is included in the parent pom: 
JavaDocTestCase/pom.xml.

Problem:
When I run the command:
mvn javadoc:javadoc -Daggregate=true
using javadoc version 2.4, the classes in the "additional" source code directory
is not included in the aggregated javadocs.  
*******Using javadoc version 2.3, works correctly.

Assumption:
The java files are already compiled using the command: "mvn install".

To use one version of javadoc vs the other, edit the "JavaDocTestCase/pom.xml" file to 
change the version of the javadoc to use in the plugin "version" element for the 
maven-javadoc-plugin.

        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>2.3</version>
          <executions>
            <execution>
              <id>buildJavadoc</id>
              <phase>package</phase>
              <goals>
                <goal>jar</goal>
              </goals>
              <configuration>
                <additionalJOption>-J-Xmx512m</additionalJOption>
                <quiet>true</quiet>
                <aggregate>true</aggregate>
                <links>
                  <link>http://java.sun.com/j2se/1.5.0/docs/api</link>
                </links>
              </configuration>
            </execution>
          </executions>
        </plugin>

The javadoc 2.4 incorrectly does not include the "GeneratedTest1" and "GeneatedTest2" class
API in the apidocs at:
JavaDocTestCase/target/site/apidocs/index.html

The javadoc 2.3 correctly includes the "GeneratedTest1" and "GeneatedTest2" class
API in the apidocs at:
JavaDocTestCase/target/site/apidocs/index.html

I ran two tests.  One test ran the command "mvn javadoc:javadoc -Daggregate=true"
using the version 2.3 of javadoc and one test using the version 2.4 of javadoc.
The output for the two runs I made are in JavaDocTestCase/javadoc2.3out.txt and 
JavaDocTestCase/javadoc2.4out.txt.

Notice that the output when using javadoc 2.3 runs the "build-helper:add-source"
before the javadoc is executed.  I believe that is why the javadocs correctly include 
the additional source files in the javadoc.

***************************JavaDoc 2.3***************************************
. . . . . . . . . 
[INFO] Preparing javadoc:javadoc
[INFO] ------------------------------------------------------------------------
[INFO] Building Javadoc Test Project
[INFO] ------------------------------------------------------------------------
[INFO] [build-helper:add-source {execution: add-source}]
[INFO] Source directory: D:\JavaDocTestCase\generated-src\main\java added.
[INFO] ------------------------------------------------------------------------
[INFO] Building Module 1 of the JavaDoc Test Project
[INFO] ------------------------------------------------------------------------
[INFO] [build-helper:add-source {execution: add-source}]
[INFO] Source directory: D:\JavaDocTestCase\module1\generated-src\main\java added.
[INFO] ------------------------------------------------------------------------
[INFO] Building Module 2 of the JavaDoc Test Project
[INFO] ------------------------------------------------------------------------
[INFO] [build-helper:add-source {execution: add-source}]
[INFO] Source directory: D:\JavaDocTestCase\module2\generated-src\main\java added.
. . . . . . . . . 
[INFO] [javadoc:javadoc]
Loading source files for package test...
Constructing Javadoc information...
Standard Doclet version 1.5.0_12
Building tree for all the packages and classes...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\GeneratedTest1.html...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\GeneratedTest2.html...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\Test1.html...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\Test2.html...
. . . . . . . . . 
*****************************************************************************

Notice that the output when using the javadoc 2.4 runs the javadoc first and then
will run thru the modules and does not even call the "build-helper:add-source"
plugin.

**************************JavaDoc 2.4******************************************
. . . . . . . . . 
[INFO] [javadoc:javadoc]
[WARNING] -top option is not supported on Java version < 1.6. Ignore this option.
Loading source files for package test...
Constructing Javadoc information...
Standard Doclet version 1.5.0_12
Building tree for all the packages and classes...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\Test1.html...
Generating D:/JavaDocTestCase/target/site/apidocs\test/\Test2.html...
. . . . . . . . . 
[INFO] ------------------------------------------------------------------------
[INFO] Building Module 1 of the JavaDoc Test Project
[INFO]    task-segment: [javadoc:javadoc]
[INFO] ------------------------------------------------------------------------
[INFO] [javadoc:javadoc]
[INFO] ------------------------------------------------------------------------
[INFO] Building Module 2 of the JavaDoc Test Project
[INFO]    task-segment: [javadoc:javadoc]
[INFO] ------------------------------------------------------------------------
[INFO] [javadoc:javadoc]
. . . . . . . . . 
*****************************************************************************