I've been using a project called SX https://github.com/sleuth-io/sx to manage them. It has its quirks, but overall I find it to be very useful.

One thing I've had to write as a layer on top of it is a way to assemble agent-specific CLAUDE.md / AGENTS.md from fragments.

For example, I have a little fragment that has all agents respond to me in ordered list format. (Since they often ask a bunch of question all jumbled throughout a response, the ordered list format allows me to respond to those specific questions.) And I also have a growing anti-Claudeism fragment as well.

Then I combine this with project-specific fragments and have it assembled into into a single CLAUDE.md / AGENTS.md. The layer also does a little reporting on the length of the resulting files and notifies me if it ever grows beyond a certain size.