[ChatGPT Chronicle] System Skill Creator is deleted from shared system Skills

Summary

A ChatGPT Chronicle/background run deletes the canonical system Skill Creator from the shared Codex system-Skills installation.

The Chronicle worker starts the bundled Codex runtime with skills.bundled.enabled=false. The resulting cleanup appears to remove the shared $CODEX_HOME/skills/.system directory instead of merely disabling bundled Skills for that worker. The system Skill Creator then becomes unavailable to unrelated, ordinary Codex tasks.

This report concerns the canonical OpenAI-provided system Skill Creator—not a personal or copied substitute.

This have been like that since codex app released months ago, this is unacceptable.

Affected environment

• ChatGPT Desktop: 26.803.41515 (build 6321)
• Bundled Codex CLI: 0.147.0-alpha.6.5
• macOS: 26.6.1, Apple silicon

Reproduction

1. Start ChatGPT Desktop and confirm the canonical system Skill Creator is present under $CODEX_HOME/skills/.system/skill-creator.
2. Enable Chronicle and allow a Chronicle background task to start.
3. Observe that the Chronicle worker invokes the bundled Codex runtime with skills.bundled.enabled=false.
4. Inspect the shared system-Skills installation after the worker starts.
5. Start an unrelated Codex task and attempt to use the system Skill Creator.

Actual result

• $CODEX_HOME/skills/.system is removed.
• The canonical system Skill Creator disappears and cannot be discovered by later ordinary tasks.
• The system OpenAI Docs Skill disappears in the same event, confirming that this is a shared system-directory mutation rather than a failure isolated to one Skill.
• A fresh normal Codex startup can restore the bundled system Skills, but a later Chronicle run removes them again.
• Turning Chronicle off prevents recurrence only after any already-running Chronicle worker exits.

The deletion is also reproducible with a disposable CODEX_HOME, without user cleanup scripts or scheduled automations.

Expected result

skills.bundled.enabled=false should control availability only for that worker. It must not delete, overwrite, or mutate the shared canonical system-Skills installation.

In particular, a Chronicle task must never uninstall the system Skill Creator used by other tasks.

Related upstream work

This may share the cleanup defect reported in #19265 and addressed by #36989, but the currently distributed ChatGPT Desktop build above still reproduces the Chronicle-specific Skill Creator failure.

Please confirm:

1. which released ChatGPT Desktop/Codex build first contains the fix;
2. whether Chronicle workers are covered by that fix; and
3. whether a guard will prevent background tasks configured with bundled Skills disabled from mutating $CODEX_HOME/skills/.system.

Start by tracing handling of skills.bundled.enabled=false and the cleanup that affects $CODEX_HOME/skills/.system. Reproduce with a disposable CODEX_HOME, then verify that a Chronicle worker leaves the shared system-Skills installation unchanged while still disabling bundled Skills for that worker.