I wonder if instead of checking the prompts into the repo as files, a better idea would be to store them inside the commit messages.
If prompts are specifications for a change of the system's behavior, then it seems natural to manage them as changes and not as resources.
This would also keep them in the right "historical context" of the repo and avoid the "prompt rot" you were talking about.
Git history is a bit annoying to navigate, but that may just be a tooling issue. I've long been bothered by the loss of the review history when merging a PR. Would actually be pretty cool to click on a row of code and see the commit messages that formed that row of code in a little sidebar, and the technical discussions that were behind it.
Functional safety development processes often demand code-review, technical design decisions, changes of plans, or intentional compromises; to be linked together with reference IDs in the code they effect. But the workflow for this is usually extremely manual and absolute misery. But a codebase made like this is like magic to read later.