Earlier quoted context omitted.
You can put them in subdirectories like CODEOWNERS files. https://ampcode.com/AGENT.md#multiple-agent-files
>When multiple files exist, tools SHOULD merge the configurations with more specific files taking precedence over general ones. How is the tool supposed to merge multiple md files?
However, if you look through the source code or network requests, you’ll see that merging just means naive “concatenation”.