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For Atlan, brain, the open-source Agent Registry CLI, with the Atlan adapter replaces the deprecated atlanai CLI. atlanai published skills, read registry objects, and captured traces through hooks in Claude Code and Codex. If you used registry, the earlier package manager that brain grew out of, Atlan Desktop moves that setup for you too. How you move depends on whether you use Atlan Desktop.

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If you use Atlan Desktop

Atlan Desktop does the move when it starts. You don’t run anything. From registry (macOS and Linux). The app stops the old CLI’s background service and moves your setup to brain: your settings, the registries you declared, what you installed for your user, what you installed in each project the old CLI’s jobs kept in sync, your adapters, and your jobs. It then removes the old CLI’s files from ~/.registry, keeping a backup under ~/.brain/handoff-backup/. If the move fails, the app tries again later, and doesn’t start the brain background service until the move is done. From atlanai. After you sign in, and once brain is signed in to all your organizations, the app turns off atlanai in your coding agents:
  • It stops the atlanai background service, and removes its macOS login item if an older version added one.
  • It uninstalls the Atlan plugins that atlanai added to Claude Code, and removes the Atlan plugin marketplaces they came from.
  • It removes atlanai hooks from ~/.claude/settings.json, and saves the previous file as settings.json.pre-registry.
  • In Codex, it removes the Atlan plugin marketplaces, any Atlan plugins left behind, and atlanai hooks in ~/.codex/hooks.json. It saves the previous hooks file as hooks.json.pre-registry.
It leaves the ~/.atlanai folder in place, including ~/.atlanai/auth.json, which Atlan Desktop uses for your sign-in. It doesn’t move skills you installed with atlanai skill install or atlanai skill pull. Atlan Desktop installs your organization’s skills for your user on its own; to install one into a project, use brain add.

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If you use the command line only: from registry

Moving a registry setup to brain is covered by the open-source project. Tokens stored in your OS keychain don’t carry over, so sign in to Atlan again as shown in Use brain with Atlan.

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If you use the command line only: from atlanai

Nothing moves you off atlanai automatically. Until you do these steps, atlanai keeps capturing sessions through its hooks and keeps updating itself.
1

Set up brain

Install brain and the Atlan adapter and sign in, as described in Use brain with Atlan. Do this before you remove atlanai: while you’re still signed in to atlanai, you can pass its token to brain:
That token lasts only as long as the atlanai session’s current token, and brain cannot refresh it. brain has no browser sign-in yet.
2

Install your skills again

brain doesn’t read .atlan/package.json or the folders atlanai skill pull wrote. In each project, install the skills you need:
3

Capture traces with brain

If you used atlanai to capture sessions, add a brain traces job:
See Capture traces.
4

Remove the atlanai hooks

This removes the hooks atlanai wrote to ~/.claude/settings.json and ~/.codex/hooks.json. It asks the atlanai background service to do it. If it says no daemon is running, run atlanai daemon start and try again.
5

Remove the Atlan plugins from Claude Code

List your plugins:
Uninstall atlanai@atlanai, atlan-claude-plugin@atlan, and any plugin from an Atlan marketplace, then remove that marketplace. An Atlan marketplace is one whose source in ~/.claude/plugins/known_marketplaces.json is https://api.atlan.com/marketplace.git or another Atlan address.
Remove a marketplace only after every plugin from it is gone.
6

Remove the Atlan marketplaces from Codex

For each Atlan marketplace in ~/.codex/config.toml:
Codex keeps a removed marketplace’s plugins. Remove any that are left:
7

Stop the atlanai background service

Stop it last: until the plugins and hooks are gone, a coding-agent session can start it again. On macOS, if ~/Library/LaunchAgents/Atlan.plist exists and runs atlanai, an older version added it as a login item. Unload and delete it:
If you added the pre-push publishing hook with atlanai skill hooks install, run atlanai skill hooks uninstall in each of those repositories. Atlan Desktop leaves ~/.atlanai in place, and you can too. Nothing runs from it after these steps.

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Command map: atlanai

“Not in brain yet” means neither brain nor the Atlan adapter has the feature today. Where the API has it, the last column links to the SDK. The Atlan SkillSync GitHub Action publishes skills with atlanai. Replace it with the brain workflow in Sync skills from GitHub.