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.