Cross Agent Skill Audit

Cross-Agent Skill Audit

When to Use

• User reports a skill isn't visible to one or more agents
• After migrating skills between locations (~/.hermes/ vs .claude/)
• When adding a new repo to the workspace
• After hermes update or harness-update to verify nothing broke

Architecture Overview

All 4 agents access skills through different mechanisms:

Hermes:         external_dirs in ~/.hermes/config.yaml (reads 6 repos' .claude/skills/)
Claude Code:    .claude/skills/ (native, on-demand via slash commands)
Codex CLI:      .codex/skills/ → symlink → ../.claude/skills/
Gemini CLI:     .gemini/skills/ → symlink → ../.claude/skills/

Per-repo: each repo that has agents must have .codex/skills and .gemini/skills symlinks pointing to ../../.claude/skills.

Audit Procedure

Step 1: Count skills per agent

WS=/mnt/local-analysis/workspace-hub

# Claude Code (native .claude/skills/)
echo "CC: $(find -L $WS/.claude/skills -name 'SKILL.md' -not -path '*/_archive/*' | wc -l)"

# Codex (symlink → .claude/)
echo "Codex: $(find -L $WS/.codex/skills -name 'SKILL.md' -not -path '*/_archive/*' | wc -l)"

# Gemini (symlink → .claude/)
echo "Gemini: $(find -L $WS/.gemini/skills -name 'SKILL.md' -not -path '*/_archive/*' | wc -l)"

# Hermes (external_dirs)
grep -A7 'external_dirs' ~/.hermes/config.yaml | grep '.claude/skills' | wc -l
echo "(count of external_dirs paths)"

Expected: All three symlink agents should show the same count. A mismatch means broken symlink or real directory takeover.

Step 2: Verify symlink integrity

# Check if .codex/skills is a symlink (NOT a real directory)
test -L $WS/.codex/skills && echo "OK: symlink" || echo "BROKEN: real dir or missing"
test -L $WS/.gemini/skills && echo "OK: symlink" || echo "BROKEN: real dir or missing"

# Check per-repo symlinks
for repo in CAD-DEVELOPMENTS digitalmodel worldenergydata achantas-data assetutilities; do
  if [ -d "$WS/$repo/.codex" ]; then
    target=$(readlink "$WS/$repo/.codex/skills" 2>/dev/null || echo "MISSING")
    echo "  $repo/.codex/skills → $target"
  fi
done

Step 3: Check external_dirs coverage

for d in $(grep 'external_dirs' ~/.hermes/config.yaml -A10 | grep '.claude/skills' | sed 's/.*- //'); do
  count=$(find -L "$d" -name 'SKILL.md' -not -path '*/_archive/*' | wc -l 2>/dev/null)
  label=$(basename $(dirname $(dirname "$d")))
  echo "  $label: $count skills"
done

Step 4: Check for local-only skills

# Any skills left in ~/.hermes/skills/ not covered by external_dirs?
find ~/.hermes/skills -name 'SKILL.md' 2>/dev/null | while read f; do
  echo "  LOCAL ONLY: $f"
done

Expected: 0 results. Any local skills should be migrated to repo .claude/skills/.

Common Fixes

Fix 1: .codex/skills is a real directory instead of symlink

cd $WS
# Verify all 57 GSD skills exist in .claude/skills/ first
mv .codex/skills .codex/skills.bak
ln -s ../.claude/skills .codex/skills
rm -rf .codex/skills.bak  # after verification
git add .codex/skills
git commit -m "fix(codex): replace .codex/skills real dir with symlink"

Fix 2: Missing per-repo symlinks

cd $WS/GEMINI-REPO
rm -rf .codex/skills 2>/dev/null
rm -rf .gemini/skills 2>/dev/null
ln -s ../../.claude/skills .codex/skills
ln -s ../../.claude/skills .gemini/skills
git add .codex/skills .gemini/skills
git commit -m "feat(harness): add .codex/.gemini symlinks for GEMINI-REPO"

Fix 3: Hermes external_dirs missing a repo

Edit ~/.hermes/config.yaml:

skills:
  external_dirs:
    - /path/to/repo/.claude/skills  # ADD missing repo here

Then run: scripts/_core/sync-agent-configs.sh

Fix 4: Skills in ~/.hermes/skills/ not migrated to repo

# Use the backfill script
bash scripts/hermes/backfill-skills-to-repo.sh --commit
# Manually: copy skill to repo .claude/skills/ then delete local copy

Pitfalls

1. find without -L doesn't follow symlinks: Always use find -L when counting skills through .codex/skills or .gemini/skills. Plain find returns 0 for symlinked directories.

2. Codex symlink takeover: A common bug where .codex/skills somehow becomes a real directory (e.g., from a git checkout that dereferences symlinks). Always check with test -L.

3. Per-repo vs workspace-hub access: When Codex/Gemini work inside a sub-repo (e.g., CAD-DEVELOPMENTS/), their symlinks point to ../../.claude/skills which is the sub-repo's local skills only. They do NOT automatically see workspace-hub canonical skills. This is by design to limit context budget.

4. external_dirs path changes: If workspace-hub moves to a different path, update __WS_HUB_PATH__ in config/agents/hermes/config.yaml.template and re-run sync-agent-configs.sh.

5. _archive directory: The 2166 archived skills in workspace-hub .claude/skills/ should NOT be counted. Always exclude with -not -path '*/_archive/*'.

6. Empty category dirs in ~/.hermes/skills/: After migration, empty dirs remain. Clean with: find ~/.hermes/skills -mindepth 1 -maxdepth 1 -type d -empty -delete

Validation Checklist

After any change to the skill ecosystem:

• CC count = Codex count = Gemini count (workspace-hub baseline)
• .codex/skills is a symlink (test -L)
• .gemini/skills is a symlink (test -L)
• 0 skills in ~/.hermes/skills/ (find returns nothing)
• All 6 external_dirs paths exist in config.yaml
• hermes skills_list shows expected count
• skill_view works for both Hermes and CC
• git status clean (no unstaged symlink changes)