Cyber-Physical Systems are embedded computers that control complex physical processes and components while cooperating as agents in distributed networks. Due to the scale and complexity of the interactions that occur within cyber-physical systems, requirements traceability strategies that are accurate and easy to manage are hard to implement and maintain. However, the information traces provide is crucial in managing the development and completeness of an application. Existing requirements management systems do not scale well and traceability is difficult in such highly heterogeneous environments. We present TORUS (Traceability Of Requirements Using Splices), a novel traceability framework that operates outside of yet connects to diverse requirements and development environments. Our approach introduces splices, autonomous traceability data structures that persist trace information through the inevitable changes that occur during system design and development. We demonstrate how this framework can be applied to cyber-physical systems that employ the IEC 61499 Function Blocks architecture. Example requirements are expressed as CESAR boilerplates for a workpiece color sorter system. Formal mathematical models of requirements, splices and function blocks are presented to show how trace information can be mined, delivering important project algorithms and metrics to stakeholders. By capturing not only the current state of the system but also historical information, TORUS allows project teams to see a much richer view of their system's artifacts. Preliminary results indicate that the TORUS framework scales well and that the splices generate metrics that will allow us to perform code-level validation and completeness checking in the future.