ghost-directory-detection-pattern

name	ghost-directory-detection-pattern
description	Methodology for detecting and resolving 'ghost directories' in ai_collection skill synchronization where skill directories exist but SKILL.md files are missing. This pattern addresses a chronic sync failure mode observed in automated research cron jobs.
license	Complete terms in LICENSE.txt

Ghost Directory Detection Pattern

Problem Description

A subtler sync failure occurs when the skill DIRECTORY exists in the ai_collection repo (collection/skills/{name}/ with subdirs like assets/, references/, scripts/) but the SKILL.md file itself is MISSING — creating a "ghost" directory that passes ls -d but fails ls SKILL.md.

This happens when:

1. init_skill.py creates the directory structure with nested subdirectories
2. The SKILL.md write was interrupted or failed
3. The copy operation missed the top-level SKILL.md file
4. Only the inner directory structure was copied

Detection Pattern

# Bulk ghost detection
for d in ~/ai_github/ai_collection/collection/skills/*/; do
  name=$(basename "$d")
  if [ -d "$d" ] && [ ! -f "$d/SKILL.md" ]; then
    echo "GHOST DIR: $name"
    # Fix by copying from local skills
    cp ~/.hermes/skills/ai_collection/$name/SKILL.md $d/SKILL.md
  fi
done

Real-World Examples

This pattern found 5 ghost dirs in a single sweep on 2026-07-03:

• membrane-potential-alignment
• rats-register-attention
• brainworld-4d-fmri
• boosting-brain-to-image-tribe-v2
• braindyn-sheaf-neural-ode

Integration with Domain Saturation Workflow

When domain saturation is detected (all papers have local skills), run ghost directory detection as part of the validation workflow:

1. Check for missing skill files: [ -f ~/ai_github/ai_collection/collection/skills/$name/SKILL.md ]
2. Check for ghost directories: [ -d ~/ai_github/ai_collection/collection/skills/$name/ ] && [ ! -f ~/ai_github/ai_collection/collection/skills/$name/SKILL.md ]
3. Fix both cases by copying from local skills
4. Verify INDEX.md entries exist for all skills
5. Commit fixes with message: "fix: resolve ghost directories and sync gaps"

Prevention

After any init_skill.py run, verify the SKILL.md was actually written before proceeding to sync:

if [ ! -f ~/.hermes/skills/ai_collection/$name/SKILL.md ]; then
  echo "ERROR: SKILL.md not created - aborting sync"
  exit 1
fi

This prevents ghost directories from being created in the first place.

When to Use This Skill

Use this methodology when:

• Running automated research cron jobs that create and sync skills
• Validating ai_collection repository integrity
• Debugging missing skill content despite directory existence
• Performing bulk sync gap detection and resolution

Related Skills

• domain-saturation-workflow - Overall validation workflow for saturated domains
• automated-research-workflow - Complete cron job automation patterns
• git-cleanup-patterns - Git workflow patterns for skill synchronization