Hi Andras Bokor, hadoop-build-tools/src/main/resources/checkstyle/checkstyle.xml is correct. IIUC checkstyle only flags new issues introduced by your patch.
The RunJar's package directory has package.html. You see a warning in your run because checkstyle.xml is not configured to allow it. See http://checkstyle.sourceforge.net/config_javadoc.html#JavadocPackage.
I think you can just ignore this error, we use package.html all over the place.