I was used to sign my app with the following command
codesign --resource-rules=ResourceRules.plist -f -s \"SIGNER_NAME\" MYAPP.app
After install
Can you use iReSign? https://github.com/maciekish/iReSign
It's a GUI that allows to sign (or resign) ipa files with mobileProvision certificate.
I tried it with Yosemite and works like a charm.
Over on this post They answer your question. That post is more targeted towards using a build server (Jenkins CLI) but the answer is the same for you (and the author of the answer points out that it is NOT unique to Jenkins).
For the purpose of answering the question on this page, here is their answer:
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
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.