The easy answer is the maven-helper-plugin: 
http://mojo.codehaus.org/build-helper-maven-plugin/add-source-mojo.html.

src/main/java-gen probably means that your sources are generated by 
someone. If this someone is a Maven plugin, then it probably does the job 
of adding the source directory to your POM (which may not be what you 
want, but that is not point now). If you generate the sources using the 
AntRun plugin, you can add *one* extra source directory.

And if you care (this is a convention): generated sources are placed under 
target/generated-sources, and never under src.


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