Linux Desktop loses saved local projects and task-to-project associations while config.toml remains intact #46428

mise ~/.config/mise/config.toml tools: gh@2.100.0

Environment

• Codex Desktop package: 26.901.20858-1
• Bundled Codex CLI: 0.153.0-alpha.5
• Platform: Arch Linux x86_64, Wayland
• Codex mode in the ChatGPT desktop app

Summary

The Codex Desktop project list disappeared even though the local project folders, Codex sessions, and project trust entries in ~/.codex/config.toml remain intact.

Re-adding a local folder recreates the visible project, but existing Codex tasks are not automatically grouped under it. Their working directories match the project paths, but their project association is missing.

Observed behavior

1. Before recovery, the Desktop project registry reported an empty project list.
2. Existing Codex tasks and their local working directories were still present.
3. ~/.codex/config.toml parses successfully and contains approximately 126 [projects."<path>"] entries, including trusted entries for the affected repositories.
4. After manually re-adding one project, the project became visible again.
5. Existing tasks still had no project association (projectId: null) even when their cwd matched the re-added project path.
6. The local folders and task/session data were not deleted.

Expected behavior

• Desktop should preserve or recover its saved local-project registry after an update/restart.
• Existing tasks should retain their project associations.
• If project metadata is rebuilt from local state, tasks whose working directory matches a project should either be re-associated or offered a recovery/migration path.
• Re-adding a project should not require manually rebuilding all historical task associations.

Reproduction / evidence

1. Use Codex Desktop on Linux with multiple local projects and existing tasks.
2. Keep the corresponding trusted project entries in ~/.codex/config.toml.
3. Restart or update the Desktop app.
4. Observe that the Projects area is empty or missing previously saved projects.
5. Confirm that the local folders and task history still exist.
6. Re-add one affected folder through the UI.
7. Observe that the project appears, but historical tasks remain ungrouped because their project association is null.

This is not the ChatGPT-vs-Codex mode mix-up described in some recent reports; the behavior was observed inside Codex mode, and the project registry itself was empty before manual re-addition.

Related reports:

• Desktop app sidebar hides existing local Codex sessions after restart/update #36504 — Desktop app sidebar hides existing local Codex sessions after restart/update
• ChatGPT Desktop Codex: existing chats missing from sidebar after migration #37853 — ChatGPT Desktop Codex: existing chats missing from sidebar after migration
• Config architecture: separate user-owned settings from generated runtime/plugin/project state #45627 — Config architecture: separate user-owned settings from generated runtime/plugin/project state

Please advise whether there is an official project/session index rebuild or migration-repair procedure. I have not deleted, reset, or manually modified Codex state databases.