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Several Eclipse projects, such as GMF Tooling, use custom scripts at build time in order to have a documentation plugin which is made of the javadocs from several other bundles. See http://dev.eclipse.org/viewcvs/viewvc.cgi/org.eclipse.gmp/org.eclipse.gmf.tooling/doc/org.eclipse.gmf.doc/buildDoc.xml?view=markup&root=Modeling_Project It would be nice to provide a Tycho plugin for this use case. Using maven-antrun-plugin won't work since path to other bundles are resolved using the old PDE Build convention, which is not working with Maven.
Did you try the standard maven javadoc plugin? http://maven.apache.org/plugins/maven-javadoc-plugin/ Tycho should inject compile classpath and source folders correctly now so that this plugin can be used.
Honestly, I didn't try yet, but I'll do this ASAP!
Mickael: Please re-open if the maven-javadoc-plugin doesn't work for you. (And please share your results if it does :-)