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Question

I have a big maven project that uses the pmd plugin for code quality checks.

since I started using the pmd plugin i get the following warning message:

Answer 1

You should add the maven-jxr-plugin and run the jxr:jxr goal before the site lifecycle if the maven-jxr-plugin is added as a plugin like in your case:
clean jxr:jxr site

Otherwise you should add it as a report if you want it to work with mvn site. Take a look at the JXR Usage Documentation : JXR Usage