Replying to myself:

It's a problem when NOT using the deprecated configuration (aggregate).
It already exists an issue [1] which I updated with some more info.

[1] http://jira.codehaus.org/browse/MJAVADOC-181

I think a crosspost on the dev list is not needed.

Felix Knecht schrieb:
> Hi all
> 
> In the new version of the javadoc plugin 2.5 <aggregate>true</..> is 
> deprecated. Using the new proposed configuration in
> the poms reporting section and running mvn site I don't get the javadoc 
> report anymore (wether in the generated site
> navigation nor as target/site/apidocs directory).
> What am I missing?
> 
> Deprectated, working reporting section:
> <plugin>
>   <groupId>org.apache.maven.plugins</groupId>
>   <artifactId>maven-javadoc-plugin</artifactId>
>   <version>2.5</version>
>   <configuration>
>     <aggregate>true</aggregate>
>   </configuration>
> </plugin>
> 
> Nonworking adapted section:
> <plugin>
>   <groupId>org.apache.maven.plugins</groupId>
>   <artifactId>maven-javadoc-plugin</artifactId>
>   <version>2.5</version>
>   <reportSets>
>     <reportSet>
>       <id>html</id>
>       <reports>
>         <report>aggregate</report>
>       </reports>
>     </reportSet>
>   </reportSets>
> </plugin>
> 
> Thanks and regards
> Felix
> 
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