For those using pom-scijava 1.126 or 1.127: there is a problem with the javadoc configuration. Specifically, this problematic commit:
The change doesn't work the way I had hoped, and the maven-javadoc-plugin configuration does not get picked up in all cases. E.g., the "use=false" hack can be off, resulting in an NPE when building javadoc for code in the default package using "mvn site".
I recommend using pom-scijava 1.125 until we can release 1.128 to resolve the issue.