I have updated to OS X Yosemite and also Xcode 6.1 (downloaded from the developer site), from this time I have had the problem with the building as in the log file I see the
Everything is ok with Jenkins plugin. Just product settings is incorrect.
Open the "Build Settings" tab of your project. Searched "Code Signing Resource Rules Path", it was empty for me. Change to: $(SDKROOT)/ResourceRules.plist
credits goes to Adams Blair who described this problem with SDK2.2
https://stackoverflow.com/a/7919137/2124345
Update
This solution doesn't remove the warning itself. But i'm pretty sure that warning isn't a problem. The problem is that without this setting ResourceRules.plist files isn't generated in Payload folder, and build process stops because file is missing.
And again, it's not related with jenkins plugin at all. Same error happens with xcrun -sdk iphoneos PackageApplication. Jenkins just calling this command line as a build step.