audit-discovery-symlinks

Use When

• After add new skills/agents/teams → almanac
• After repo rename/move → abs symlinks may break
• Slash cmds/agents not found in Claude Code
• Periodic health check → drift registries vs discovery
• Onboard new project → should discover shared almanac

Do NOT use → creating initial symlink hub from scratch. See symlink-architecture guide for first-time setup.

In

Do

Step 1: Identify Almanac Path

Locate agent-almanac root dir.

# Auto-detect from current project's .claude/agents symlink
ALMANAC_PATH=$(readlink -f .claude/agents 2>/dev/null | sed 's|/agents$||')

# Fallback: check if cwd is the almanac
if [ -z "$ALMANAC_PATH" ] || [ ! -f "$ALMANAC_PATH/skills/_registry.yml" ]; then
  if [ -f "skills/_registry.yml" ]; then
    ALMANAC_PATH=$(pwd)
  fi
fi

# Fallback: check global agents symlink
if [ -z "$ALMANAC_PATH" ] || [ ! -f "$ALMANAC_PATH/skills/_registry.yml" ]; then
  ALMANAC_PATH=$(readlink -f ~/.claude/agents 2>/dev/null | sed 's|/agents$||')
fi

echo "Almanac path: $ALMANAC_PATH"

→ ALMANAC_PATH points to dir w/ skills/_registry.yml, agents/_registry.yml, teams/_registry.yml.

If err: Auto-detect fails → ask user for almanac_path. Root = dir w/ skills/, agents/, teams/ + registries.

Step 2: Inventory Registries

Extract canonical lists from registries.

# Count registered skills (entries with "- id:" under domain sections)
REGISTERED_SKILLS=$(grep '^ \{6\}- id:' "$ALMANAC_PATH/skills/_registry.yml" | awk '{print $3}' | sort)
REGISTERED_SKILL_COUNT=$(echo "$REGISTERED_SKILLS" | wc -l)

# Count registered agents
REGISTERED_AGENTS=$(grep '^ \{2\}- id:' "$ALMANAC_PATH/agents/_registry.yml" | awk '{print $3}' | sort)
REGISTERED_AGENT_COUNT=$(echo "$REGISTERED_AGENTS" | wc -l)

# Count registered teams
REGISTERED_TEAMS=$(grep '^ \{2\}- id:' "$ALMANAC_PATH/teams/_registry.yml" | awk '{print $3}' | sort)
REGISTERED_TEAM_COUNT=$(echo "$REGISTERED_TEAMS" | wc -l)

echo "Registered: $REGISTERED_SKILL_COUNT skills, $REGISTERED_AGENT_COUNT agents, $REGISTERED_TEAM_COUNT teams"

→ Counts match total_skills, total_agents, total_teams in registry headers.

If err: Counts diverge → registry out of sync. Note discrepancy → continue using actual - id: entries as source of truth.

Step 3: Audit Project-Level Symlinks

Check .claude/skills/*, .claude/agents, .claude/teams in cwd.

PROJECT_CLAUDE=".claude"

# --- Skills ---
# Items on disk (excluding _template)
PROJECT_SKILLS=$(ls "$PROJECT_CLAUDE/skills/" 2>/dev/null | grep -v '^_template$' | sort)
PROJECT_SKILL_COUNT=$(echo "$PROJECT_SKILLS" | grep -c .)

# Missing: in registry but not in project .claude/skills/
MISSING_PROJECT_SKILLS=$(comm -23 <(echo "$REGISTERED_SKILLS") <(echo "$PROJECT_SKILLS"))

# Broken: symlink exists but target doesn't resolve
BROKEN_PROJECT_SKILLS=$(find "$PROJECT_CLAUDE/skills/" -maxdepth 1 -type l ! -exec test -e {} \; -printf '%f\n' 2>/dev/null | sort)

# Extraneous: in project but not in registry (and not external)
EXTRA_PROJECT_SKILLS=$(comm -13 <(echo "$REGISTERED_SKILLS") <(echo "$PROJECT_SKILLS"))

# --- Agents ---
if [ -L "$PROJECT_CLAUDE/agents" ] || [ -d "$PROJECT_CLAUDE/agents" ]; then
  PROJECT_AGENT_STATUS="OK"
  test -d "$PROJECT_CLAUDE/agents" || PROJECT_AGENT_STATUS="BROKEN"
  PROJECT_AGENT_COUNT=$(ls "$PROJECT_CLAUDE/agents/"*.md 2>/dev/null | wc -l)
else
  PROJECT_AGENT_STATUS="MISSING"
  PROJECT_AGENT_COUNT=0
fi

# --- Teams ---
# Teams are NOT symlinked. TeamCreate uses ~/.claude/teams/ for runtime state.
# A .claude/teams symlink is a misconfiguration — warn if found.
if [ -L "$PROJECT_CLAUDE/teams" ]; then
  PROJECT_TEAM_STATUS="MISCONFIGURED"
  PROJECT_TEAM_COUNT=0
  # Stale symlink — should be removed to avoid collision with TeamCreate
else
  PROJECT_TEAM_STATUS="OK"
  PROJECT_TEAM_COUNT=0
fi

→ Zero missing, zero broken. Extraneous classified + explained.

If err: No .claude/ → no discovery setup. Note → skip to global audit.

Step 4: Audit Global Symlinks

Check ~/.claude/skills/* + ~/.claude/agents. Verify ~/.claude/teams is NOT a symlink (absent or real dir for TeamCreate runtime).

GLOBAL_CLAUDE="$HOME/.claude"

# --- Skills ---
GLOBAL_SKILLS_ALL=$(ls "$GLOBAL_CLAUDE/skills/" 2>/dev/null | sort)

# Classify each entry: almanac vs external
ALMANAC_GLOBAL_SKILLS=""
EXTERNAL_GLOBAL_SKILLS=""
for item in $GLOBAL_SKILLS_ALL; do
  target=$(readlink -f "$GLOBAL_CLAUDE/skills/$item" 2>/dev/null)
  if [ -z "$target" ]; then
    # Real directory (not a symlink) — external
    EXTERNAL_GLOBAL_SKILLS="$EXTERNAL_GLOBAL_SKILLS $item"
  elif echo "$target" | grep -q "^$ALMANAC_PATH"; then
    ALMANAC_GLOBAL_SKILLS="$ALMANAC_GLOBAL_SKILLS $item"
  else
    EXTERNAL_GLOBAL_SKILLS="$EXTERNAL_GLOBAL_SKILLS $item"
  fi
done

# Filter: _template is always extraneous for almanac content
ALMANAC_GLOBAL_SKILLS=$(echo "$ALMANAC_GLOBAL_SKILLS" | tr ' ' '\n' | grep -v '^_template$' | grep -v '^$' | sort)

# Missing: in registry but not in global almanac skills
MISSING_GLOBAL_SKILLS=$(comm -23 <(echo "$REGISTERED_SKILLS") <(echo "$ALMANAC_GLOBAL_SKILLS"))

# Broken: symlink exists but target doesn't resolve
BROKEN_GLOBAL_SKILLS=$(find "$GLOBAL_CLAUDE/skills/" -maxdepth 1 -type l ! -exec test -e {} \; -printf '%f\n' 2>/dev/null | sort)

# Stale almanac entries: in global almanac set but not in registry
STALE_GLOBAL_SKILLS=$(comm -13 <(echo "$REGISTERED_SKILLS") <(echo "$ALMANAC_GLOBAL_SKILLS"))

# --- Agents ---
if [ -L "$GLOBAL_CLAUDE/agents" ] || [ -d "$GLOBAL_CLAUDE/agents" ]; then
  GLOBAL_AGENT_STATUS="OK"
  test -d "$GLOBAL_CLAUDE/agents" || GLOBAL_AGENT_STATUS="BROKEN"
  GLOBAL_AGENT_COUNT=$(ls "$GLOBAL_CLAUDE/agents/"*.md 2>/dev/null | wc -l)
else
  GLOBAL_AGENT_STATUS="MISSING"
  GLOBAL_AGENT_COUNT=0
fi

# --- Teams ---
# Teams are NOT symlinked. TeamCreate uses ~/.claude/teams/ for runtime state.
# A ~/.claude/teams symlink is a misconfiguration — warn if found.
if [ -L "$GLOBAL_CLAUDE/teams" ]; then
  GLOBAL_TEAM_STATUS="MISCONFIGURED"
  GLOBAL_TEAM_COUNT=0
  # Stale symlink — should be removed to avoid collision with TeamCreate
else
  GLOBAL_TEAM_STATUS="OK"
  GLOBAL_TEAM_COUNT=0
fi

→ Zero missing almanac skills, zero broken. External listed, not flagged err.

If err: No ~/.claude/ → global hub not set up. See symlink-architecture guide for initial setup.

Step 5: Generate Audit Report

Summary table both layers.

# Discovery Symlink Audit Report

**Date**: YYYY-MM-DD
**Almanac**: <almanac_path>
**Scope**: both | project | global

## Summary

| Content | Registered | Project | Global (almanac) | Global (external) |
|---------|------------|---------|-------------------|-------------------|
| Skills  | N          | N       | N                 | N                 |
| Agents  | N          | STATUS  | STATUS            | —                 |
| Teams   | N          | STATUS  | STATUS            | —                 |

## Issues

### Missing (registered but no symlink)
- Project skills: [list or "none"]
- Global skills: [list or "none"]

### Broken (symlink exists, target gone)
- Project: [list or "none"]
- Global: [list or "none"]

### Extraneous
- Stale almanac (in discovery but not registry): [list or "none"]
- _template in discovery path: [yes/no]
- External content (non-almanac): [list — informational only]

→ Clear actionable report. Zero issues = clean.

If err: Report gen fails → raw counts + lists to console as fallback.

Step 6: Repair (Optional)

If fix_mode = auto/interactive → fix found issues.

6a. Create missing project symlinks:

for skill in $MISSING_PROJECT_SKILLS; do
  ln -s "../../skills/$skill" "$PROJECT_CLAUDE/skills/$skill"
done

6b. Create missing global symlinks:

for skill in $MISSING_GLOBAL_SKILLS; do
  ln -s "$ALMANAC_PATH/skills/$skill" "$GLOBAL_CLAUDE/skills/$skill"
done

6c. Remove broken symlinks:

# Project
for broken in $BROKEN_PROJECT_SKILLS; do
  rm "$PROJECT_CLAUDE/skills/$broken"
done

# Global
for broken in $BROKEN_GLOBAL_SKILLS; do
  rm "$GLOBAL_CLAUDE/skills/$broken"
done

6d. Remove stale almanac entries:

# Only remove items that target the almanac path but aren't in the registry
for stale in $STALE_GLOBAL_SKILLS; do
  rm "$GLOBAL_CLAUDE/skills/$stale"
done

# Remove _template if present
rm -f "$GLOBAL_CLAUDE/skills/_template"
rm -f "$PROJECT_CLAUDE/skills/_template"

6e. Fix missing directory symlinks (agents/teams):

# Project agents
if [ "$PROJECT_AGENT_STATUS" = "MISSING" ]; then
  ln -s ../agents "$PROJECT_CLAUDE/agents"
fi

# Project teams
if [ "$PROJECT_TEAM_STATUS" = "MISSING" ]; then
  ln -s ../teams "$PROJECT_CLAUDE/teams"
fi

# Global agents
if [ "$GLOBAL_AGENT_STATUS" = "MISSING" ]; then
  ln -s "$ALMANAC_PATH/agents" "$GLOBAL_CLAUDE/agents"
fi

# Global teams
if [ "$GLOBAL_TEAM_STATUS" = "MISSING" ]; then
  ln -sf "$ALMANAC_PATH/teams" "$GLOBAL_CLAUDE/teams"
fi

Important: Never remove items classified as external. Belong to other projects (peon-ping) → preserve.

→ All missing created, broken removed, stale cleaned. External untouched.

If err: ln -s fails due to existing file/dir at target (empty dir instead of symlink) → remove blocker first w/ rmdir (empty) or flag for manual review (non-empty).

Step 7: Verify

Re-run Steps 3-4 checks → confirm repairs.

echo "=== Post-repair verification ==="
echo "Project skills: $(ls "$PROJECT_CLAUDE/skills/" 2>/dev/null | grep -v '^_template$' | wc -l)"
echo "Global skills (almanac): $(echo "$ALMANAC_GLOBAL_SKILLS" | wc -w)"
echo "Broken project: $(find "$PROJECT_CLAUDE/skills/" -maxdepth 1 -type l ! -exec test -e {} \; -print 2>/dev/null | wc -l)"
echo "Broken global:  $(find "$GLOBAL_CLAUDE/skills/" -maxdepth 1 -type l ! -exec test -e {} \; -print 2>/dev/null | wc -l)"
echo "Project agents: $PROJECT_AGENT_STATUS ($PROJECT_AGENT_COUNT .md files)"
echo "Global agents:  $GLOBAL_AGENT_STATUS ($GLOBAL_AGENT_COUNT .md files)"
echo "Project teams:  $PROJECT_TEAM_STATUS ($PROJECT_TEAM_COUNT .md files)"
echo "Global teams:   $GLOBAL_TEAM_STATUS ($GLOBAL_TEAM_COUNT .md files)"

→ Zero missing, zero broken. Counts match registered totals (almanac). External listed separately.

If err: Issues remain post-repair → report specific failures. Common: perms on ~/.claude/, NTFS path length on /mnt/, non-empty dir blocking symlink.

Check

• Almanac path identified + contains all 3 registries
• Registry counts match total_* headers (or discrepancy noted)
• Project-level skills/agents/teams audited
• Global-level skills/agents/teams audited
• External content identified + excluded from issue counts
• _template entries flagged extraneous
• Audit report generated w/ counts + lists
• fix_mode=auto → safe repairs applied, external untouched
• Post-repair verification → zero missing, zero broken

Traps

1. External vs missing almanac: ~/.claude/skills/ may contain skills from other projects (peon-ping). Check symlink target is under almanac path before classifying stale/extraneous.

2. Remove external: Never delete items not targeting almanac. Belong to other projects, intentional.

3. Symlink _template dirs: Scaffolding, not consumable. Should never appear in .claude/skills/ or .claude/agents/. Bulk sync scripts must skip.

4. Stale .claude/teams symlink: Symlink pointing to team defs = misconfig. TeamCreate uses ~/.claude/teams/ for runtime (config.json, inboxes). If this path symlinks almanac teams/ → runtime artifacts written to git-tracked repo. Remove any .claude/teams symlink found.

5. Relative vs absolute paths: Project-level skill symlinks = relative (../../skills/<name>). Global = absolute (/path/to/almanac/skills/<name>). Mixing → breakage on moves.

6. Registry header vs actual count: total_skills in header may be stale if entries added w/o count update. Trust actual - id: entries, not header.

→

• repair-broken-references — general broken link/ref repair
• tidy-project-structure — project dir org
• create-skill — inc. symlink creation for new skills (Step 13)
• create-agent — inc. discovery verification (Step 10)
• create-team — team creation w/ registry integration