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I have had this same issue. I find that the versions of Jenkins can cause this. For example, getting the version of Jenkins from the Synaptic Package Manager installs one version than the one online or even from the Ubuntu software store. Debian vs tomcat, etc. I had downloaded the .war version, but it did no good, stating that there is already file of that type in Jenkins-commons, as well as in var/usr/share file. And it was conflicting. But, I still got that message even after I deleted that extra .war file. I did a delete of the Jenkins Jenkins commons, yet still got errors. I will try figuring this out and then report back what I figure out.