The course is scaffolded to help you progress through key cognitive stages of understanding, analysis, application and reflection.
The meaning of "scaffolded" seems to be clear from the context. I think I can paraphrase like this: The course is designed... . Is my understanding correct?
I haven't found "scaffold" as a verb on https://www.merriam-webster.com/dictionary/scaffold and the Collins dictionary says that "to scaffold" means to provide with a scaffold or to support by means of a scaffold, which is related to building.