Software-reliant systems permeate all aspects of modern society. The resulting interconnectedness and associated complexity has resulted in a proliferation of diverse stakeholders with conflicting goals. Thus, contemporary software engineering is plagued by incentive conflicts, in settling on design features, allocating resources during the development of products, and allocating computational resources at runtime. In this position paper, we describe some of these problems and outline a research agenda in bridging to the economic theory of mechanism design, which seeks to align incentives in multi-agent systems with private information and conflicting goals. The ultimate goal is to advance a principled methodology for the design of incentive-compatible approaches to manage the dynamic processes of software engineering.