The way I've been storing prompts is a directory in the project called 'prompts' and an .md file for each topic/feature. Since I usually iterate a lot on the same prompt (to minimise context rot), I store many versions of the same prompt ordered chronologically (newest at top).

That way if I need to find a prompt from some feature from the past, I just find the relevant .md file and it's right at the top.

Interestingly, my projects are way better documented (via prompts) than they ever were in the pre-agentic era.