Duo integrates with Shibboleth to add two-factor authentication for Shibboleth identity providers, complete with inline self-service enrollment and Duo Prompt. The code is open-source and available on GitHub.
Yes, Reference Shibboleth's Guide for implementing Duo Security for use upon request.
Yes, The Multi-Context Broker (MCB) is an extension to the Shibboleth IdP that improves Shibboleth's handling of multiple authentication methods, including multi-factor authentication, as well as multiple authentication contexts and assurance profiles. InCommon Assurance Multi-Context Broker