codemap agents init copies these files into <your-project>/.agents/. Use codemap agents init --mcp (or the interactive prompt) to write IDE MCP config — see agents.md § MCP wiring. Since v1, both rules/codemap.md and skills/codemap/SKILL.md are thin pointers. The full content is served live by codemap rule / codemap skill (CLI), codemap://rule / codemap://skill (MCP), and GET /resources/{encoded-uri} against codemap serve (HTTP) — all three resolve to the same source under templates/agent-content/.
Package upgrades carry today's content automatically; you don't normally edit the pointer files. To add your own project-specific rules / skills, drop sibling files (e.g. .agents/rules/my-team-conventions.md, .agents/skills/my-domain/SKILL.md) — the codemap pointers stay package-managed.
Full docs: docs/agents.md on GitHub — pointer protocol, section assembler, IDE wiring (Cursor, Copilot, …), staleness detection.