A shaded jar will have multiple version.properties, e.g.
file:/mnt/var/lib/hadoop/tmp/hadoop-unjar7817209360894770970/cascading/version.properties
jar:file:/mnt/single-load/./load-hadoop2-tez-20150729.jar!/cascading/version.properties
only warn if there are duplicates within a protocol, not across since we should only be seeing file: and jar: