Adding custom source paths to javadoc

I ran into the same problem. To fix it, you'll need to insert javadoc plugin into the build lifecycle at such point where any additional compile source roots have already been added to the project.

E.g.:

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<phase>process-sources</phase>
<goals>
<goal>javadoc</goal>
</goals>
</execution>
</executions>
</plugin>

<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<executions>
<execution>
<phase>generate-sources</phase>
<configuration>
<sourceRoot>$

/generated/java</sourceRoot>
<tasks>
... some ant tasks
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>

Here javadoc plugin is invoked after antrun plugin and therefore given sourceRoot is added to projects compile source roots. This may not be the right way to do it but that's how I got it working. Also notice that your code generator must be run from a plugin that adds the compile source root into the project like antrun does. Hope this is of any help.

personally I would prefer to see a solution where it is possible to have additional source directories while having configured the plugin only in the 'reporting' section

Used executedProject.getCompileSourceRoots() instead of project.getCompileSourceRoots() to return the source paths.
NB: if your code generator is a maven plugin, it should handle the compileSourceRoots ie:
project.addCompileSourceRoot( outputDirectory );

I have a similar issue with source generated with antrun plugin.

I have a multimodule project, and when I run mvn package -DperformRelease=true, the Javadoc of my generated source is generated and packaged, but when I run mvn site, I don't have the Javadoc of my generated class. Perhaps there is a problem with aggregate=true ?