~/.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

Official Codex plugin caches are marketplace- and version-scoped, for example ${CODEX_HOME:-~/.codex}/plugins/cache/$MARKETPLACE_NAME/oh-my-codex/$VERSION/. Local installs may use local as the version identifier.

# Get installed plugin cache versions across marketplaces.
# Cache shape: $PLUGIN_CACHE_ROOT/$MARKETPLACE_NAME/oh-my-codex/$PLUGIN_VERSION/
PLUGIN_CACHE_ROOT="${CODEX_HOME:-$HOME/.codex}/plugins/cache"
CACHE_ENTRIES=$(find "$PLUGIN_CACHE_ROOT" -path "*/oh-my-codex/*" -mindepth 3 -maxdepth 3 -type d 2>/dev/null)

if [[ -z "$CACHE_ENTRIES" ]]; then
  echo "Installed plugin cache: none"
else
  while IFS= read -r VERSION_DIR; do
    MARKETPLACE_NAME=$(basename "$(dirname "$(dirname "$VERSION_DIR")")")
    PLUGIN_VERSION=$(basename "$VERSION_DIR")
    printf 'Installed plugin cache: marketplace=%s version=%s path=%s\n' "$MARKETPLACE_NAME" "$PLUGIN_VERSION" "$VERSION_DIR"
  done <<< "$CACHE_ENTRIES"
fi

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

Diagnosis:

If no cache entry exists: INFO - plugin marketplace artifact not cached; this may be normal when OMX was installed only through npm/setup
Compare each printed PLUGIN_VERSION with LATEST; if it differs and is not local: WARN - outdated plugin cache
If one marketplace has multiple version directories: WARN - stale cache for that marketplace/plugin pair
Remember: plugin install/discovery is not a replacement for npm install -g oh-my-codex plus omx setup; the packaged plugin carries plugin-scoped companion metadata for optional MCP compatibility servers and apps, with first-party MCP disabled by default, while native/runtime hooks and the rest of OMX runtime wiring stay setup-owned

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

# List marketplace/version cache entries for this plugin
PLUGIN_CACHE_ROOT="${CODEX_HOME:-$HOME/.codex}/plugins/cache"
find "$PLUGIN_CACHE_ROOT" -path "*/oh-my-codex/*" -mindepth 3 -maxdepth 3 -type d 2>/dev/null \
  | while IFS= read -r VERSION_DIR; do
      MARKETPLACE_NAME=$(basename "$(dirname "$(dirname "$VERSION_DIR")")")
      PLUGIN_VERSION=$(basename "$VERSION_DIR")
      printf '%s\t%s\n' "$MARKETPLACE_NAME" "$PLUGIN_VERSION"
    done

Diagnosis:

If a single marketplace lists multiple versions: WARN - multiple cached versions for that marketplace/plugin pair (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 generated agents or hand-installed role files. The Codex plugin can package reusable workflows plus plugin-scoped companion metadata for optional MCP/apps; legacy setup installs native agents, while plugin setup archives stale legacy native-agent files and keeps config/hooks current.
If ~/.codex/commands/ exists with oh-my-codex-related files: WARN - legacy command files from older installs. Current OMX uses skills/workflows plus setup-managed native surfaces.
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

# Global cache reset across all marketplaces for this plugin.
# If you only want one marketplace, set MARKETPLACE_NAME and remove just that subtree instead.
PLUGIN_CACHE_ROOT="${CODEX_HOME:-$HOME/.codex}/plugins/cache"
find "$PLUGIN_CACHE_ROOT" -path "*/oh-my-codex" -type d -prune -exec rm -rf {} +
echo "Plugin cache cleared across all marketplaces. Restart Codex CLI to fetch the latest marketplace entry."

Fix: Stale Cache (multiple versions)

# Keep only the newest version inside the selected marketplace/plugin cache.
# Set MARKETPLACE_NAME to the exact marketplace printed in Step 1.
PLUGIN_CACHE_ROOT="${CODEX_HOME:-$HOME/.codex}/plugins/cache"
PLUGIN_CACHE_DIR="$PLUGIN_CACHE_ROOT/$MARKETPLACE_NAME/oh-my-codex"
KEEP_VERSION=$(for dir in "$PLUGIN_CACHE_DIR"/*; do [[ -d "$dir" ]] && basename "$dir"; done | sort -V | tail -1)
if [[ -n "$KEEP_VERSION" ]]; then
  find "$PLUGIN_CACHE_DIR" -mindepth 1 -maxdepth 1 -type d ! -name "$KEEP_VERSION" -exec rm -rf {} +
fi

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.