Use a separate config overlay for the desktop app

What variant of Codex are you using?

Codex App (desktop)

What feature would you like to see?

Please give the desktop app its own app-managed config overlay, for example $CODEX_HOME/config-desktop.toml (defaulting to ~/.codex/config-desktop.toml), instead of writing desktop state into the user-managed $CODEX_HOME/config.toml.

For desktop sessions, configuration should be loaded in this order:

1. $CODEX_HOME/config.toml as the user defaults.
2. $CODEX_HOME/config-desktop.toml as desktop-specific overrides.

When the same key exists in both files, the desktop overlay should win for the desktop app only. Desktop-originated writes—including feature availability, Computer Use hooks, migrations, and settings changed through the app—should target the overlay. The CLI should continue to use the user config without inheriting desktop-only state.

This preserves shared defaults across Codex surfaces while establishing a clear ownership boundary: users and their tooling own config.toml; the desktop app owns its overlay.

Additional information

The current shared-file behavior makes simply opening the app mutate global configuration and can change CLI behavior or create persistent config churn. Related reports demonstrate several variants of the same ownership problem:

• https://github.com/openai/codex/issues/28404
• https://github.com/openai/codex/issues/28184
• https://github.com/openai/codex/issues/24387
• https://github.com/openai/codex/issues/33635

The exact filename is not important; the important properties are separate storage, $CODEX_HOME awareness, deterministic merge precedence, and no desktop writes to the user-owned defaults file.

Start by tracing how desktop sessions load configuration and how desktop-originated writes handle feature availability, Computer Use hooks, migrations, and app settings; compare those paths with the CLI's use of config.toml. Confirm how $CODEX_HOME is resolved and how configuration keys are merged. Done means desktop uses a separate overlay with deterministic precedence and desktop writes no longer modify the user-owned defaults file.