Cupcake (Apollic Software) has been the company behind Flynn (and Tent) since day 0 (we tend to downplay the branding because we think both projects can stand on their own).

Most of the development on Flynn (nearly all of the 2014 work) was done by Jonathan Rudenberg (@titanous), one of the founders of Cupcake. We brought in Jeff as a contractor and paid him out of the crowdfunding campaign. He contributed to the initial architecture and prototypes but stepped back in December.

I don't want to speak for Jeff (@progrium) but my understanding is that he'll keep evangelizing the project at conferences and may be working on a proprietary version/components at Digital Ocean.

The Cupcake team (especially Jonathan) will keep developing Flynn (of course with open source contributions) full time in the future.