I'm working on a project where we prototype signal-processing algorithms with MATLAB, and then implement them on an embedded controller in C.
We're still in the early stages of the project, and we're still exploring alternative algorithms. We're also getting feedback from the controller tests that inform the further development of our MATLAB prototypes.
In this related question, the question was how to structure the SVN repository to support the parallel development of prototypes and the real implementation. However, the answers that were given did not address the issue of the development workflow.
For example, in our current project we have decided that only prototype code can be committed on trunk, whereas any implementation code must be committed on a dedicated branch.
I'd like to hear your experience in managing the workflow of a parallel development of prototype code and its implementation.