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As documented, most Maven plugins are not supported by the `init` from existing Maven project. It just covers some basic standard things and all special things need to be translated manually.

To generate source code properly,
• define a task that generates those files
• make sure its inputs and outputs are configured properly
• do not generate into some existing source folder or similar, but into a dedicated directory like `layout.buildDirectory.dir("generated/whatever")
• wire that task as producing sources like `sourceSets { main { java.srcDir(theTaskThatGeneratesSources) } }`, then all source needing tasks automatically see those sources and also automatically have the necessary task dependencies

Thanks. I saw some discussion along these lines on Stack Overflow.