audit-discovery-symlinks

When Use

• After adding new skills, agents, teams to almanac
• After repository rename or move — may break absolute symlinks
• Slash commands or agents not found in Claude Code
• Periodic health check — catch drift between registries and discovery paths
• Onboarding new project — should discover shared almanac content

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

Inputs

Parameter	Type	Required	Description
almanac_path	string	No	Absolute path to agent-almanac root. Auto-detected from .claude/ symlink targets or cwd if omitted
scope	enum	No	project, global, or both (default: both)
fix_mode	enum	No	report (default: audit only), auto (fix all safe issues), interactive (prompt before each fix)

Steps

Step 1: Identify Almanac Path

Locate agent-almanac root directory.

# 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"

Got: ALMANAC_PATH points to directory containing skills/_registry.yml, agents/_registry.yml, teams/_registry.yml.

If fail: Auto-detection fails? Ask user for almanac_path input. Almanac root = directory with skills/, agents/, teams/, registries.

Step 2: Inventory Registries

Extract canonical lists of skills, agents, teams 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"

Got: Counts match total_skills, total_agents, total_teams values in each registry header.

If fail: Counts diverge from header totals? Registry out of sync. Note discrepancy in report, continue with actual - id: entries as source of truth.

Step 3: Audit Project-Level Symlinks

Check .claude/skills/*, .claude/agents, .claude/teams in current project directory.

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

Got: Zero missing, zero broken. Extraneous items classified and explained.

If fail: .claude/ doesn't exist? Project has no discovery setup. Note and skip to global audit.

Step 4: Audit Global Symlinks

Check ~/.claude/skills/* and ~/.claude/agents. Also check ~/.claude/teams NOT a symlink (should be absent or directory for TeamCreate runtime state).

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

Got: Zero missing almanac skills, zero broken. External content (peon-ping, etc.) listed but not flagged as errors.

If fail: ~/.claude/ doesn't exist? Global hub not set up. See symlink-architecture guide for initial setup.

Step 5: Generate Audit Report

Produce summary table covering 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]

Got: Clear, actionable report. Zero issues = clean bill of health.

If fail: Report generation itself fails? Output raw counts and lists to console as fallback.

Step 6: Repair (Optional)

If fix_mode is auto or interactive, fix issues found.

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.

Got: All missing symlinks created, broken removed, stale almanac entries cleaned. External content untouched.

If fail: ln -s fails due to existing file/directory at target (e.g., empty directory instead of symlink)? Remove blocker first with rmdir (empty dirs) or flag for manual review (non-empty dirs).

Step 7: Verify

Re-run audit checks from Steps 3-4 to 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)"

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

If fail: Issues remain after repair? Report specific failures. Common causes: permission errors on ~/.claude/, NTFS path length limits on /mnt/ paths, non-empty directory blocking symlink creation.

Checks

• Almanac path correctly identified, contains all three registries
• Registry counts match total_* header values (or discrepancy noted)
• Project-level skills, agents, teams audited
• Global-level skills, agents, teams audited
• External content (non-almanac) identified and excluded from issue counts
• _template entries flagged as extraneous (never belongs in discovery paths)
• Audit report generated with clear counts and actionable lists
• If fix_mode is auto: all safe repairs applied, external content untouched
• Post-repair verification confirms zero missing, zero broken

Pitfalls

1. Confusing external content with missing almanac content: ~/.claude/skills/ may hold skills from other projects (peon-ping). Always check if symlink target under almanac path before classifying stale/extraneous.

2. Removing external content: Never delete items not targeting almanac. Belong to other projects. Intentional.

3. Symlinking _template directories: Templates are scaffolding, not consumable content. _template should never appear in .claude/skills/ or .claude/agents/. Bulk sync scripts must skip it.

4. Stale .claude/teams symlink: .claude/teams symlink pointing to team definitions = misconfiguration. Claude Code's TeamCreate uses ~/.claude/teams/ for runtime state (config.json, inboxes). Symlink to almanac's teams/ = runtime artifacts written into git-tracked repo. Remove any .claude/teams symlink at project or global level.

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

6. Registry header vs actual count: total_skills field in registry header may be stale if someone added entries without updating count. Trust actual - id: entries, not header.

See Also

• repair-broken-references -- general broken link and reference repair
• tidy-project-structure -- project directory organization
• create-skill -- includes symlink creation for new skills (Step 13)
• create-agent -- includes discovery verification (Step 10)
• create-team -- team creation with registry integration