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The configuration specified in the parent pom does not seem to be used in the subprojects, although inherited is set to true and excludeSubProjects to false.
Besides that, RAT only checks for headers and is able to fix/put them if necessary. This is a rather simply check/fix which can also be done by checkstyle and the ClassHeadersMojo. I will implement this in checkstyle so that the headers are checked, instead of being ignored.