cd research-sessions/YYYY-MM-DD-description/
 
# List all files with sizes
find . -type f -exec ls -lh {} \; | awk '{print $5, $9}' | sort -rh

🧹 Cleanup Analysis for: research-sessions/2025-10-11-btk-selectivity/
 
Files to KEEP (protected):
  ✅ SUMMARY.md (45 KB)
  ✅ relevant-papers.json (12 KB)
  ✅ papers-reviewed.json (28 KB)
  ✅ papers/ (14 PDFs, 32 MB)
  ✅ citations/citation-graph.json (5 KB)
  ✅ screening-criteria.json (2 KB)
  ✅ abstracts-cache.json (156 KB)
 
Files that CAN be removed (intermediate):
  🗑️  initial-search-results.json (8 KB) - Raw PubMed results
  🗑️  .DS_Store (6 KB) - macOS metadata
 
Total space to recover: 14 KB
 
Proceed with cleanup? (y/n/review)

About to delete:
- initial-search-results.json (8 KB)
 
This file contains raw PubMed search results. The data is preserved in
papers-reviewed.json, so this is safe to delete.
 
Confirm deletion? (y/n)

# Move to trash instead of rm (safer)
# On macOS:
mv initial-search-results.json ~/.Trash/
 
# On Linux:
mv initial-search-results.json ~/.local/share/Trash/files/
 
# Or use rm if user confirms
rm initial-search-results.json

✅ Cleanup complete!
 
Removed:
- initial-search-results.json (8 KB)
- .DS_Store (6 KB)
 
Space recovered: 14 KB
 
Protected files preserved:
- All 8 core files kept
- All 14 PDFs kept
- All methodology documentation kept

# Check core files exist
test -f SUMMARY.md && echo "✓ SUMMARY.md"
test -f relevant-papers.json && echo "✓ relevant-papers.json"
test -f papers-reviewed.json && echo "✓ papers-reviewed.json"
test -d papers && echo "✓ papers/ directory"
 
# Verify JSON files are valid
jq empty relevant-papers.json && echo "✓ relevant-papers.json valid JSON"
jq empty papers-reviewed.json && echo "✓ papers-reviewed.json valid JSON"

✅ Integrity check passed
   - All core files present
   - All JSON files valid
   - All PDFs intact

⚠️  abstracts-cache.json is 256 MB
 
This file enables re-screening if you update the rubric. Options:
1. Keep (recommended if you might refine rubric)
2. Compress (gzip to ~50 MB, can decompress later)
3. Delete (only if research is final and won't be updated)
 
Choice? (1/2/3)

gzip abstracts-cache.json
# Creates abstracts-cache.json.gz
 
echo "Compressed abstracts-cache.json to $(du -h abstracts-cache.json.gz | cut -f1)"

📝 Found helper scripts:
   - screen_papers.py (created for batch screening)
   - deep_dive_papers.py (created for data extraction)
 
These scripts document your methodology. Recommendations:
- Keep for reproducibility
- Add comments if not already documented
- Reference in SUMMARY.md under "Reproducibility" section
 
Keep scripts? (y/n)

# Find all research sessions
find research-sessions/ -maxdepth 1 -type d
 
# For each session:
for session in research-sessions/*/; do
    echo "Analyzing: $session"
    # Run cleanup analysis
done

Found 5 completed research sessions.
 
Clean up all sessions? (y/n/select)
- y: Analyze and clean all sessions
- n: Cancel
- select: Choose which sessions to clean

PROTECTED_PATTERNS = [
    'SUMMARY.md',
    'relevant-papers.json',
    'papers-reviewed.json',
    'papers/*.pdf',
    'papers/*.zip',
    'citations/citation-graph.json',
    'screening-criteria.json',
    'test-set.json',
    'abstracts-cache.json',
    'rubric-changelog.md',
    'README.md',
    'TOP_PRIORITY_PAPERS.md',
    'evaluated-papers.json',
    '*.py',  # Helper scripts
    '.claude/*',  # Project settings
]

def is_protected(filepath):
    """Check if file matches any protected pattern"""
    for pattern in PROTECTED_PATTERNS:
        if fnmatch(filepath, pattern):
            return True
    return False
# Never delete protected files
if is_protected(file_to_delete):
    print(f"⚠️  ERROR: {file_to_delete} is protected and cannot be deleted")
    return

# Dry run (show only, don't delete)
echo "DRY RUN - No files will be deleted"
 
for file in $candidate_files; do
    if is_safe_to_delete "$file"; then
        echo "Would delete: $file ($(du -h $file | cut -f1))"
    fi
done
 
echo ""
echo "Proceed with actual deletion? (y/n)"

### Optional: Cleanup
 
After reviewing outputs, optionally clean up intermediate files:
 
"Research session is complete. Would you like me to clean up intermediate files?
I'll show you what will be deleted before removing anything."
 
If yes: Use `cleaning-up-research-sessions` skill

User: "Can you clean up the research session folder?"
 
Agent: "I'll analyze the research session and show you what can be safely cleaned up."
 
[Analyzes folder]
 
Agent: "🧹 Cleanup Analysis for: research-sessions/2025-10-11-btk-selectivity/
 
Files to KEEP (protected):
  ✅ SUMMARY.md (45 KB) - Final findings
  ✅ relevant-papers.json (12 KB) - Filtered results
  ✅ papers-reviewed.json (28 KB) - Complete history
  ✅ papers/ (14 PDFs, 32 MB) - Downloaded papers
  ✅ citations/citation-graph.json (5 KB) - Citation network
  ✅ screening-criteria.json (2 KB) - Rubric definition
  ✅ abstracts-cache.json (156 KB) - Cached abstracts
 
Files that CAN be removed:
  🗑️  initial-search-results.json (8 KB) - Raw PubMed results
     → Data is preserved in papers-reviewed.json
  🗑️  .DS_Store (6 KB) - macOS metadata
     → Not needed
 
Total space to recover: 14 KB
 
Proceed with cleanup? (y/n/review)"
 
User: "y"
 
Agent: "Final confirmation - About to delete:
- initial-search-results.json (8 KB)
- .DS_Store (6 KB)
 
All protected files will be preserved. Confirm? (y/n)"
 
User: "y"
 
Agent: [Deletes files]
 
"✅ Cleanup complete!
 
Removed:
- initial-search-results.json (8 KB)
- .DS_Store (6 KB)
 
Space recovered: 14 KB
 
Running integrity check...
✅ All core files intact
✅ All JSON files valid
✅ All 14 PDFs present
 
Research session is ready for archiving or sharing."