audit-discovery-symlinks

name	audit-discovery-symlinks
description	Audit and repair Claude Code discovery symlinks for skills, agents, and teams. Compares registries against .claude/ directories at project and global levels, detects missing, broken, and extraneous symlinks, distinguishes almanac content from external projects, and optionally repairs gaps. Use after adding new skills or agents, after a repository rename or move, when slash commands stop working, or as a periodic health check.
license	MIT
allowed-tools	Read Bash Grep Glob
metadata	{"author":"Philipp Thoss","version":"1.0","domain":"maintenance","complexity":"intermediate","language":"shell","tags":"maintenance, symlinks, discovery, claude-code, audit"}

audit-discovery-symlinks

When to Use

• After adding new skills, agents, or teams to the almanac
• After a repository rename or move that may have broken absolute symlinks
• When slash commands or agents are not found in Claude Code
• As a periodic health check to catch drift between registries and discovery paths
• When onboarding a new project that should discover shared almanac content

Do NOT use for creating the initial symlink hub from scratch. See the 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)

Procedure

Step 1: Identify Almanac Path

Locate the 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"

Expected: ALMANAC_PATH points to a directory containing skills/_registry.yml, agents/_registry.yml, and teams/_registry.yml.

On failure: If auto-detection fails, ask the user for the almanac_path input. The almanac root is the directory containing skills/, agents/, teams/, and their registries.

Step 2: Inventory Registries

Extract the canonical lists of skills, agents, and teams from their 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"

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

On failure: If counts diverge from the header totals, the registry itself is out of sync. Note the discrepancy in the report but continue with the actual - id: entries as the source of truth.

Step 3: Audit Project-Level Symlinks

Check .claude/skills/*, .claude/agents, .claude/teams in the 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 "$PROJECT_CLAUDE/agents" || PROJECT_AGENT_STATUS="BROKEN"
  PROJECT_AGENT_COUNT=$( *.md 2>/dev/null |  -l)

  PROJECT_AGENT_STATUS=
  PROJECT_AGENT_COUNT=0



 [ -L  ] || [ -d  ]; 
  PROJECT_TEAM_STATUS=
   -d  || PROJECT_TEAM_STATUS=
  PROJECT_TEAM_COUNT=$( *.md 2>/dev/null |  -l)

  PROJECT_TEAM_STATUS=
  PROJECT_TEAM_COUNT=0

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

On failure: If .claude/ does not exist at all, the project has no discovery setup. Note this and skip to global audit.

Step 4: Audit Global Symlinks

Check ~/.claude/skills/*, ~/.claude/agents, ~/.claude/teams.

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  | )


MISSING_GLOBAL_SKILLS=$( -23 <( ) <( ))


BROKEN_GLOBAL_SKILLS=$(find  -maxdepth 1 - l ! -  -e {} \; -  2>/dev/null | )


STALE_GLOBAL_SKILLS=$( -13 <( ) <( ))


 [ -L  ] || [ -d  ]; 
  GLOBAL_AGENT_STATUS=
   -d  || GLOBAL_AGENT_STATUS=
  GLOBAL_AGENT_COUNT=$( *.md 2>/dev/null |  -l)

  GLOBAL_AGENT_STATUS=
  GLOBAL_AGENT_COUNT=0



 [ -L  ] || [ -d  ]; 
  GLOBAL_TEAM_STATUS=
   -d  || GLOBAL_TEAM_STATUS=
  GLOBAL_TEAM_COUNT=$( *.md 2>/dev/null |  -l)

  GLOBAL_TEAM_STATUS=
  GLOBAL_TEAM_COUNT=0

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

On failure: If ~/.claude/ does not exist, the global hub is not set up. Refer to the symlink-architecture guide for initial setup.

Step 5: Generate Audit Report

Produce a 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]

Expected: A clear, actionable report. Zero issues means a clean bill of health.

On failure: If report generation itself fails, output raw counts and lists to the console as fallback.

Step 6: Repair (Optional)

If fix_mode is auto or interactive, fix the 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. These belong to other projects (e.g., peon-ping) and must be preserved.

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

On failure: If ln -s fails due to an existing file/directory at the target path (e.g., empty directory instead of symlink), remove the blocker first with rmdir (for empty dirs) or flag for manual review (for non-empty dirs).

Step 7: Verify

Re-run the 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)"

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

On failure: If issues remain after repair, report the specific failures. Common causes: permission errors on ~/.claude/, NTFS path length limits on /mnt/ paths, or a non-empty directory blocking symlink creation.

Validation

• Almanac path correctly identified and contains all three registries
• Registry counts match total_* header values (or discrepancy noted)
• Project-level skills, agents, and teams audited
• Global-level skills, agents, and 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

Common Pitfalls

1. Confusing external content with missing almanac content: ~/.claude/skills/ may contain skills from other projects (e.g., peon-ping). Always check whether a symlink target is under the almanac path before classifying it as stale or extraneous.

2. Removing external content: Never delete items that don't target the almanac. They belong to other projects and are intentional.

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

4. Empty directories blocking symlinks: ln -s fails if the target path is an existing directory. For teams, ~/.claude/teams/ may be an empty directory (from Claude Code runtime) that must be rmdir'd before creating a symlink.

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 these patterns causes breakage on moves.

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

Related Skills

• 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