yg init installs one universal set of agent-rules files — the same files, the same content, regardless of which agent you use. There is no platform question to answer.

By default it writes all three:

• A short summary block inside marker comments in AGENTS.md.
• A one-line @AGENTS.md import added to CLAUDE.md, because Claude Code does not read AGENTS.md on its own.
• A copy of the same summary at .clinerules/yggdrasil.md, because Cline looks there instead of AGENTS.md.

Each one can be switched off independently with yg init --no-agents-md, --no-claude-md or --no-clinerules. The choice is recorded durably under rules_artifacts in .yggdrasil/yg-config.yaml, so it holds on every later run and reaches the team through the repository rather than through everyone's command line — see the CLI reference and Configuration. A disabled artifact is never written, never created, and never touched.

That summary tells the agent to run yg prime before making any change. yg prime prints the complete, current operating manual straight from your installed Yggdrasil CLI — so an agent's instructions are always up to date and are never cut short by a small instruction budget.

yg check also watches whichever of these files this project has enabled under rules_artifacts, and warns if one of those goes missing, gets hand-edited, falls behind after you upgrade the CLI, or ends up duplicated — always pointing you at yg init --upgrade to fix it. An artifact switched off is never mentioned.

Upgrading a project that requires its whole tree

The files above (and the .gitattributes entry yg init maintains) are new in your repository, so a project that requires every tracked file to belong to a component will report them as unmapped errors on the next check. That is any project whose yg-config.yaml has no coverage: block at all, or whose coverage.required covers the repository root. They're repository plumbing, not project source — exclude them. A project carrying all three artifacts excludes all four paths:

coverage:
  excluded:
    - AGENTS.md
    - CLAUDE.md
    - .clinerules/
    - .gitattributes

A project that has switched an artifact off under rules_artifacts never gets that file written, so its stanza is shorter by that line. yg init --upgrade tells you when this applies to your project and prints the stanza for the artifacts your project actually has; it never edits the file for you. Mapping them to a component instead works just as well if you'd rather keep them under enforcement. A freshly initialized project requires nothing and is unaffected.

How each agent picks up the rules

Agent	How it gets the rules
Claude Code	The @AGENTS.md import line in CLAUDE.md
Cline	.clinerules/yggdrasil.md
GitHub Copilot, Cursor, Codex, OpenCode, Amp, Zed, and any other agent confirmed to read a repository's AGENTS.md	AGENTS.md directly

No agent gets a bespoke file of its own anymore — every agent reads one of these three universal artifacts. If your agent reads none of them natively, point it at AGENTS.md by hand, or have it run yg prime directly.

Agents that need a one-time manual setup

These are left off the table above because we can't confirm they read AGENTS.md on their own — not because they're unsupported. Each takes one small step, once:

• Windsurf — folded into another product; last we checked, its current status and whether that product reads AGENTS.md natively were both in flux. yg init deletes the rules file the retired installer wrote at .windsurf/rules/yggdrasil.md.
• Aider — needs an explicit read: entry in .aider.conf.yml pointing at AGENTS.md. yg init no longer writes one; add the entry yourself if you use Aider. It also removes the entry an earlier version wrote, which pointed at a file that no longer exists. If you wrote that entry by hand rather than letting yg init add it, it is left alone on purpose — check .aider.conf.yml for a read: line still pointing at .yggdrasil/agent-rules.md and repoint it at AGENTS.md.
• CodeBuddy — reads its own CODEBUDDY.md, not AGENTS.md; we have no confirmation of native AGENTS.md support. yg init deletes the rules file the retired installer wrote at .codebuddy/rules/yggdrasil/RULE.mdc.
• Roo Code — reported to have shut down, so this is here for anyone still running an older install. yg init deletes the rules file the retired installer wrote at .roo/rules/yggdrasil.md.
• Gemini CLI — retired as a standalone tool as far as we can tell, so this is likewise here for anyone still running it. yg init removes the import line the retired installer added to GEMINI.md (and the file itself, if that line was all it held).

For any of these, point the agent at AGENTS.md by hand — for the last two, in whichever file that agent reads — or have it run yg prime directly. Both give it the same rules every other agent gets.

The same sweep covers every other file the retired per-platform installers used to write, whether or not the agent appears above: .cursor/rules/yggdrasil.mdc, the old single rules file at .yggdrasil/agent-rules.md, and the yggdrasil marker block inside .github/copilot-instructions.md — only our own block is cut out, the rest of the file stays byte-exact, and the file itself is deleted only when nothing but that block remained. Whatever it removes is listed in the yg init --upgrade output as cleaned-up legacy artifacts, so nothing disappears silently.