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Codex skill toggle not working: still loads legacy directory ~/.agents/skills

Quick fix

Remove leftover copies in ~/.agents/skills or disable them in config; CC-Switch cannot manage that shared directory.

Symptom

Section titled “Symptom”
Error output
[Bug] Codex 技能开关不生效：codex 仍会加载遗留目录 ~/.agents/skills 中的技能副本
English translation

[Bug] Codex skill toggle not working: codex still loads skill copies from the legacy directory ~/.agents/skills

Cause

Section titled “Cause”

Codex CLI natively loads skills from two directories: the current canonical directory ${CODEX_HOME:-~/.codex}/skills and the legacy directory ~/.agents/skills (the user-level directory for the Agent Skills open standard). cc-switch manages only the former via symlinks. Turning a skill off in cc-switch removes only the link under ~/.codex/skills and does not touch the real copies in ~/.agents/skills. As a result, Codex still loads those skills from ~/.agents/skills even when the toggle is off, making the toggle appear ineffective.

If the user changes the storage location in cc-switch settings to ~/.agents/skills, that directory becomes the single source of truth (SSOT). cc-switch then creates a symlink in ~/.codex/skills pointing to it. Turning the toggle off removes only the symlink in ~/.codex/skills, while the files remain in ~/.agents/skills and Codex can still read them. Codex does not deduplicate skills with the same name, so the same skill present in both directories can also cause duplicate entries in the skill list.

Fix

Section titled “Fix”

  1. Identify which skill copies in ~/.agents/skills/ are marked off in cc-switch but are still loaded.

  2. Manually delete the corresponding skill folders under ~/.agents/skills/ to remove all copies accessible to Codex.

    # 路径: ~/.agents/skills/<skill-name>/

  3. Alternatively, edit the Codex config file config.toml to explicitly disable specific skills.

    路径: ~/.codex/config.toml
    [[skills.config]]
    path = "/Users/user-name/.agents/skills/<skill-name>/SKILL.md"
    enabled = false

Affected Versions

Section titled “Affected Versions”
ToolCodex
Version0.147.0
PlatformsmacOS

Source Issues

Section titled “Source Issues”

This page is distilled from 1 real issues

FAQ

Section titled “FAQ”
Why can't cc-switch automatically clean up ~/.agents/skills?
~/.agents/skills is the user-level directory for the Agent Skills open standard, and other tools (such as Claude Code and Copilot CLI) may also write skills there. cc-switch respects this shared standard and does not modify or delete content in that directory, to avoid breaking other tools' configurations.
How do I avoid duplicate skill entries?
Ensure skills exist in only one directory. Either set the cc-switch storage location to the default ~/.cc-switch/skills and clean up copies in ~/.agents/skills, or set the storage location to ~/.agents/skills and ensure there are no extra symlinks in ~/.codex/skills pointing to the same skills.
Section titled “Related problems”
Atomic replace failed os error 50Change the Claude Code configuration directory from a WSL path back to a Windows local path, or roll back to v3.19.0.1 issues mergedsettings.json overwritten by proxy takeover causing plugin config loss - Claude CodePlace custom fields such as hooks and statusLine into the "General Configuration" panel, or upgrade to v3.12.2+ to fix the legacy backup restore logic.15 issues merged[mcp_servers.node_repl] written back automatically by CC SwitchTurn off or delete node_repl in MCP management at the top right of CC Switch to stop it being written back into the Codex config file.2 issues merged

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