In which case you'd have 1 markdown file and at least for the ones that are invoked via the CLI, just set up a Makefile entry point that leads them to the correct location.
Saw a repo recently with probably 80% of those
> This node.js CLI tool processes CLAUDE.md files with hierarchical collection and recursive @-import resolution. Walks directory tree from current to ~/.claude/, collecting all CLAUDE.md files and processing them with file import resolution. Saves processed context files with resolved imports next to the original CLAUDE.md files or in a specific location (configurable).
I mostly use Claude Code, but every now and then go with Gemini, and having to maintain two sets of (hierarchical) instructions was annoying. And then opencode showed up, which meant yet another tool I wanted to try out and …well.
Now I have a git repo I add as a submodule and tell each tool to read through and create their own WHATEVER.md
Library to help with this. Not great that a library is necessary, but useful until this converges to a standard (if it ever does).