Can you provide some more details, like a build log that shows what plugin is actually compiling the code or preferably a little example project to demonstrate the issue?

"mvn javadoc:javadoc" will return [INFO] ------------------------------------------------------------------------
[INFO] An error has occurred in JavaDocs report generation:Exit code: 1 - javadoc: error - Illegal package name: "example.doc-files"

Confirmed.

I guess we could add a filter for java files, but the doc for docfilessubdirs [1] doesnt speak about java files.
So we need to understand your use case to add java files in javadoc dir.
You could also provide a patch (always better).

[1] http://java.sun.com/j2se/1.4.2/docs/tooldocs/windows/javadoc.html#docfilessubdirs

fixed in r805778, snap deployed