Cleaning Up Research Sessions

Cleaning Up Research Sessions

Overview

Remove intermediate files created during research workflow while preserving all important data.

Core principle: Conservative cleanup with user confirmation. Never delete anything important.

When to Use

Use this skill when:

• Research session is complete and consolidated
• Preparing to archive or share research session folder
• Research folder has accumulated temporary/intermediate files
• User explicitly asks to clean up

When NOT to use:

• Research is still in progress
• User hasn't reviewed final outputs yet
• Unsure what files are safe to delete

Files That Are ALWAYS KEPT

NEVER delete these (protected list):

Core outputs:

• SUMMARY.md - Enhanced findings with methodology
• relevant-papers.json - Filtered relevant papers
• papers-reviewed.json - Complete screening history
• papers/ directory - All PDFs and supplementary files
• citations/citation-graph.json - Citation relationships

Methodology documentation:

• screening-criteria.json - Rubric definition (if exists)
• test-set.json - Rubric validation papers (if exists)
• abstracts-cache.json - Cached abstracts for re-screening (if exists)
• rubric-changelog.md - Rubric version history (if exists)

Auxiliary documentation (if exists):

• README.md - Project overview
• TOP_PRIORITY_PAPERS.md - Curated priority list
• evaluated-papers.json - Rich structured data

Project configuration:

• .claude/ directory - Permissions and settings
• *.py helper scripts that were created - Keep for reproducibility

Files That May Be Cleaned Up

Candidates for removal (with confirmation):

Intermediate search results:

• initial-search-results.json - Raw PubMed results before screening
  • Safe to delete: Data is in papers-reviewed.json
  • Reason to keep: Shows raw search results for reproducibility

Temporary files:

• *.tmp files
• *.swp files (vim swap files)
• .DS_Store (macOS)
• __pycache__/ (Python cache)
• *.pyc (Python compiled)