fix(codex): persist desktop settings in atom state

[shunkakinoki]

Summary

• store managed Codex Desktop preferences in electron-persisted-atom-state, which version 26.721.41059 actually reads
• remove ignored top-level duplicates while preserving unrelated global and atom state
• add regression coverage for app-owned nesting, stale top-level cleanup, rewrite recovery, and idempotency

Verification

• shellspec spec/activate_config_spec.sh — 55 examples, 0 failures (3 failures before the fix)
• full ShellSpec phase — 1,720 examples, 0 failures
• make nix-format-check — 533 files, 0 changed
• bash -n and ShellCheck on the synchronizer
• make build — successful Galactica Darwin generation
• live Home Manager activation — nested keep count 300, top-level copy absent, LaunchAgent last exit 0

Note

• the Fish sub-suite did not start because its nix develop environment evaluation stalled and was interrupted; no Fish assertion failed
• unrelated worktrunk/yek macOS Cargo activation failures remain tracked in shunkakinokisoftware-uvkd

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Summary by cubic

Persist Codex Desktop managed settings in electron-persisted-atom-state and remove stale top‑level copies. Matches current Desktop behavior, preserves unrelated state, and avoids unnecessary rewrites.

• Bug Fixes
  • Store managed keys under electron-persisted-atom-state (UI ignores top-level keys).
  • Merge managed keys into atom state and keep unrelated keys; strip stale top-level duplicates.
  • Skip writes when values already match to prevent launchd churn; add regression tests for merge, rewrite recovery, and idempotency.

^{Written for commit 1ad11da. Summary will update on new commits.}

[gemini-code-assist]

Caution

The consumer version of Gemini Code Assist on GitHub has been sunset. All code review activity has officially ceased.

[indent-zero]

PR Summary

Corrects where the Codex Desktop settings synchronizer persists managed values so that the app-controlled UI actually reads them. Previously the managed keys were written at the top level of ~/.codex/.codex-global-state.json and the nested electron-persisted-atom-state copies were being stripped as "legacy" — Codex Desktop actually reads from the atom-state object, so the UI was ignoring managed values and effectively reverting them. This PR inverts the write target, treats top-level copies as stale, and updates the ShellSpec suite accordingly.

• Rewrites sync-desktop-settings.sh to merge managed keys into electron-persisted-atom-state (via $atoms + $managed) and strip managed keys from the top level.
• Inverts the idempotency guard to require managed values in atom-state AND their absence at the top level, keeping the launchd watch loop stable.
• Changes the initial-file branch to write {"electron-persisted-atom-state": $settings[0]} when no state file exists.
• Updates the default.nix activation comment to describe atom-state persistence.
• Updates four ShellSpec cases (merge, restore-after-app-rewrite, remove-stale-top-level, idempotency) with new fixtures and has(...) assertions confirming top-level cleanup.

Issues

No issues found.

CI Checks

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[coderabbitai]

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Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 62c2ac88-e617-4c22-8a4d-c65524f4cffd

📥 Commits

Reviewing files that changed from the base of the PR and between 6221a9d and 1ad11da.

📒 Files selected for processing (3)

• config/codex/default.nix
• config/codex/sync-desktop-settings.sh
• spec/activate_config_spec.sh

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📝 Walkthrough

Summary by CodeRabbit

• Bug Fixes
  • Improved synchronization of Codex Desktop preferences by storing managed settings in the app’s persisted state.
  • Preserved unrelated application state during preference updates.
  • Prevented unnecessary rewrites when preferences are already synchronized.
  • Removed outdated top-level preference entries after migration to the persisted state structure.

Walkthrough

Codex Desktop preference synchronization now stores managed values in persisted electron-persisted-atom-state, removes conflicting top-level copies, preserves unrelated atom state, and updates activation tests for nested persistence and no-op behavior.

Changes

Codex Desktop state synchronization

Layer / File(s)	Summary
Persist managed preferences in atom state config/codex/sync-desktop-settings.sh, config/codex/default.nix	Synchronization reads and writes managed preferences under electron-persisted-atom-state, removes overlapping top-level keys, preserves unrelated state, and documents the updated behavior.
Validate activation and no-op behavior spec/activate_config_spec.sh	Activation tests verify nested merging, restoration, stale top-level key removal, and avoidance of rewrites when persisted values already match.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Possibly related PRs

• shunkakinoki/dotfiles#2085: Updates related Codex Desktop persistence and activation expectations.
• shunkakinoki/dotfiles#2165: Modifies the same synchronization script and activation specifications for persisted global state.

Poem

A bunny tucked the settings deep,
Where atom-state can safely sleep.
Old top-level copies hopped away,
While matching values skip the write today.
Merge the state, preserve the rest—
Codex preferences pass the test!

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/fix-codex-desktop-atom-state

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