Doctor Skill

Note: All

~/.codex/...

paths in this guide respect

CODEX_HOME

when that environment variable is set.

Canonical skill root

OMX installs skills to

${CODEX_HOME:-~/.codex}/skills/

— this is the path current Codex CLI natively loads as its skill root.

~/.agents/skills/

is a historical legacy path from an older Codex CLI release, before Codex settled on

~/.codex

as its home directory. Current Codex CLI and OMX no longer write there.

In a mixed OMX + plain Codex environment:

• Use:

  ${CODEX_HOME:-~/.codex}/skills/

  (user scope) or

  .codex/skills/

  (project scope)
• Clean up if present:

  ~/.agents/skills/

  — if this still exists alongside the canonical root, Codex's Enable/Disable Skills UI will show duplicate entries for any skill present in both trees
• Interop rule: OMX writes only to the canonical path; archive or remove

  ~/.agents/skills/

  once you have confirmed

  ${CODEX_HOME:-~/.codex}/skills/

  is your active root

Task: Run Installation Diagnostics

You are the OMX Doctor - diagnose and fix installation issues.

Step 1: Check Plugin Version

# Get installed version
INSTALLED=$(ls ~/.codex/plugins/cache/omc/oh-my-codex/ 2>/dev/null | sort -V | tail -1)
echo "Installed: $INSTALLED"

# Get latest from npm
LATEST=$(npm view oh-my-codex version 2>/dev/null)
echo "Latest: $LATEST"

Diagnosis:

• If no version installed: CRITICAL - plugin not installed
• If INSTALLED != LATEST: WARN - outdated plugin
• If multiple versions exist: WARN - stale cache

Step 2: Check Hook Configuration (config.toml + legacy settings.json)

Check

~/.codex/config.toml

first (current Codex config), then check legacy

~/.codex/settings.json

only if it exists.

Look for hook entries pointing to removed scripts like:

• bash $HOME/.codex/hooks/keyword-detector.sh

• bash $HOME/.codex/hooks/persistent-mode.sh

• bash $HOME/.codex/hooks/session-start.sh

Diagnosis:

• If found: CRITICAL - legacy hooks causing duplicates

Step 3: Check for Legacy Bash Hook Scripts

ls -la ~/.codex/hooks/*.sh 2>/dev/null

Diagnosis:

• If

  keyword-detector.sh

  ,

  persistent-mode.sh

  ,

  session-start.sh

  , or

  stop-continuation.sh

  exist: WARN - legacy scripts (can cause confusion)

Step 4: Check AGENTS.md

# Check if AGENTS.md exists
ls -la ~/.codex/AGENTS.md 2>/dev/null

# Check for OMX marker
grep -q "oh-my-codex Multi-Agent System" ~/.codex/AGENTS.md 2>/dev/null && echo "Has OMX config" || echo "Missing OMX config"

Diagnosis:

• If missing: CRITICAL - AGENTS.md not configured
• If missing OMX marker: WARN - outdated AGENTS.md

Step 5: Check for Stale Plugin Cache

# Count versions in cache
ls ~/.codex/plugins/cache/omc/oh-my-codex/ 2>/dev/null | wc -l

Diagnosis:

• If > 1 version: WARN - multiple cached versions (cleanup recommended)

Step 6: Check for Legacy Curl-Installed Content

Check for legacy agents, commands, and historical legacy skill roots from older installs/migrations:

# Check for legacy agents directory
ls -la ~/.codex/agents/ 2>/dev/null

# Check for legacy commands directory
ls -la ~/.codex/commands/ 2>/dev/null

# Check canonical current skills directory
ls -la ${CODEX_HOME:-~/.codex}/skills/ 2>/dev/null

# Check historical legacy skill directory
ls -la ~/.agents/skills/ 2>/dev/null

Diagnosis:

• If

  ~/.codex/agents/

  exists with oh-my-codex-related files: WARN - legacy agents (now provided by plugin)
• If

  ~/.codex/commands/

  exists with oh-my-codex-related files: WARN - legacy commands (now provided by plugin)
• If

  ${CODEX_HOME:-~/.codex}/skills/

  exists with OMX skills: OK - canonical current user skill root
• If

  ~/.agents/skills/

  exists: WARN - historical legacy skill root that can overlap with

  ${CODEX_HOME:-~/.codex}/skills/

  and cause duplicate Enable/Disable Skills entries

Look for files like:

• architect.md

  ,

  researcher.md

  ,

  explore.md

  ,

  executor.md

  , etc. in agents/

• ultrawork.md

  ,

  deepsearch.md

  , etc. in commands/
• Any oh-my-codex-related

  .md

  files in skills/

---

Report Format

After running all checks, output a report:

## OMX Doctor Report

### Summary
[HEALTHY / ISSUES FOUND]

### Checks

| Check | Status | Details |
|-------|--------|---------|
| Plugin Version | OK/WARN/CRITICAL | ... |
| Hook Config (config.toml / legacy settings.json) | OK/CRITICAL | ... |
| Legacy Scripts (~/.codex/hooks/) | OK/WARN | ... |
| AGENTS.md | OK/WARN/CRITICAL | ... |
| Plugin Cache | OK/WARN | ... |
| Legacy Agents (~/.codex/agents/) | OK/WARN | ... |
| Legacy Commands (~/.codex/commands/) | OK/WARN | ... |
| Skills (${CODEX_HOME:-~/.codex}/skills) | OK/WARN | ... |
| Legacy Skill Root (~/.agents/skills) | OK/WARN | ... |

### Issues Found
1. [Issue description]
2. [Issue description]

### Recommended Fixes
[List fixes based on issues]

---

Auto-Fix (if user confirms)

If issues found, ask user: "Would you like me to fix these issues automatically?"

If yes, apply fixes:

Fix: Legacy Hooks in legacy settings.json

If

~/.codex/settings.json

exists, remove the legacy

"hooks"

section (keep other settings intact).

Fix: Legacy Bash Scripts

rm -f ~/.codex/hooks/keyword-detector.sh
rm -f ~/.codex/hooks/persistent-mode.sh
rm -f ~/.codex/hooks/session-start.sh
rm -f ~/.codex/hooks/stop-continuation.sh

Fix: Outdated Plugin

rm -rf ~/.codex/plugins/cache/omc/oh-my-codex
echo "Plugin cache cleared. Restart Codex CLI to fetch latest version."

Fix: Stale Cache (multiple versions)

# Keep only latest version
cd ~/.codex/plugins/cache/omc/oh-my-codex/
ls | sort -V | head -n -1 | xargs rm -rf

Fix: Missing/Outdated AGENTS.md

Fetch latest from GitHub and write to

~/.codex/AGENTS.md

:

WebFetch(url: "https://raw.githubusercontent.com/Yeachan-Heo/oh-my-codex/main/docs/AGENTS.md", prompt: "Return the complete raw markdown content exactly as-is")

Fix: Legacy Curl-Installed Content

Remove legacy agents/commands plus the historical

~/.agents/skills

tree if it overlaps with the canonical

${CODEX_HOME:-~/.codex}/skills

install:

# Backup first (optional - ask user)
# mv ~/.codex/agents ~/.codex/agents.bak
# mv ~/.codex/commands ~/.codex/commands.bak
# mv ~/.agents/skills ~/.agents/skills.bak

# Or remove directly
rm -rf ~/.codex/agents
rm -rf ~/.codex/commands
rm -rf ~/.agents/skills

Note: Only remove if these contain oh-my-codex-related files. If user has custom agents/commands/skills, warn them and ask before removing.

---

Post-Fix

After applying fixes, inform user:

Fixes applied. Restart Codex CLI for changes to take effect.