Systems-of-Systems (SoS) are complex infrastructures, which are characterized by a wide diversity of technologies and requirements imposed by the domain(s) they target. In this context, the software engineering community has been focusing on assisting the developers by providing them domain-specific languages, component-based software engineering frameworks and tools to leverage on the design and the development of such systems. However, the adoption of such approaches often prevents developers from combining several domains, which is a strong requirement in the context of SoS. Furthermore, only little attention has been paid to the definition of a modular toolset and an extensible runtime infrastructure for deploying and executing SoS. In this paper, we therefore propose a reference framework to leverage on the software engineering of SoS. Our reference framework has been validated on the development of two platforms, namely Hulotte and FraSCAti, to demonstrate that the resulting complexity is isolated in the core toolset, while the development of domain-specific extensions is leveraged and simplified by clearly identified abstractions.