iOS App Signer
This is an app for OS X that can (re)sign apps and bundle them into ipa files that are ready to be installed on an iOS device.
Supported input types are: ipa, deb, app, xcarchive
This app requires Xcode to be installed, it has only been successfully tested on OS X 10.11 at this time.
You need a provisioning profile and signing certificate, you can get these from Xcode by creating a new project.
You can then open up iOS App Signer and select your input file, signing certificate, provisioning file, and optionally specify a new application ID and/or application display name.
maciekish / iReSign: The basic process was gleaned from the source code of this project.