Organize Files

Process

1. Audit

Get the current state:

bash .coral/public/skills/organize-files/scripts/audit.sh

Or manually: ls -R {shared_dir}/notes/ and count files per directory.

Also check for content-level issues:

• Contradictions — do any notes claim opposite things? Update or flag them in _open-questions.md.
• Stale info — research notes that experiments have disproven. Update with actual results.
• Orphan pages — notes not listed in index.md. Add them.
• Missing cross-references — related notes that don't link to each other.
• Gaps — techniques mentioned but never researched, or researched but never tried.

2. Plan

Write out your target structure before moving anything. Organize within research/ and experiments/ — add subdirectories by topic when a dir has 5+ files:

research/
├── algorithms/       (3+ notes)
├── optimization/     (3+ notes)
└── ...

experiments/
├── optimization/     (3+ notes)
├── debugging/        (3+ notes)
└── ...

Rules:

• Minimum 3 files per subdirectory — don't create a dir for 1-2 files
• Max 2 levels deep — experiments/optimization/learning-rate.md is the limit
• Name by topic — algorithms/ not agent1-work/
• Don't touch raw/ — immutable source material
• Don't touch _synthesis/, _connections.md, _open-questions.md — owned by consolidate

3. Deduplicate

Find near-duplicates:

python .coral/public/skills/organize-files/scripts/find_duplicates.py .coral/public/notes --threshold 0.5

Merge confirmed duplicates. Move originals to _archive/. Don't merge notes that contradict each other — flag those in _open-questions.md.

4. Move and Rename

Use the move script for safe moves with frontmatter tracking:

python .coral/public/skills/organize-files/scripts/move_note.py SOURCE DEST

Naming: kebab-case-like-this.md, topic first, no agent IDs, no bare dates, under 60 chars.

5. Update Index

Regenerate index.md:

python .coral/public/skills/organize-files/scripts/generate_index.py .coral/public/notes

The index should only list research/ and experiments/ entries — not raw/.

6. Log

Append a summary to _organization-log.md: what you moved, merged, or renamed, and why.