We present a process for the development of safety and security critical components in transportation systems targeting a high-level certification (CENELEC 50126/50128, DO 178, CC ISO/IEC 15408). The process adheres to the objectives of an "agile development" in terms of evolutionary flexibility and continuous improvement. Yet, it enforces the overall coherence of the development artifacts (ranging from proofs over tests to code) by a particular environment (CVCE). In particular, the validation process is built around a formal development based on the interactive theorem proving system Isabelle/HOL, by linking the business logic of the application to the operating system model, down to code and concrete hardware models thanks to a series of refinement proofs. We apply both the process and its support in CVCE to a case-study that comprises a model of an odometric service in a railway-system with its corresponding implementation integrated in seL4 (a secure kernel for which a comprehensive Isabelle development exists). Novel techniques implemented in Isabelle enforce the coherence of semi-formal and formal definitions within specific certification processes in order to improve their cost-effectiveness . This paper has been published at ERTS2018.