By name: organize-files description: "Organize the shared notes directory when it becomes hard to navigate. Restructure within research/ and experiments/, deduplicate, update index.md."
Organize Files
Restructure the shared notes directory so every agent can find what they need quickly.
For a complete before/after walkthrough on a realistic messy notes/ tree — including the dedup pass, naming fixes, subdirectory creation, link repair, and audit-log entry — see references/worked-example.md. Read it once before your first reorganization; it makes the abstract steps below concrete.
For recovery procedures and judgment calls (move script aborted partway, false-positive duplicates, files that look misplaced in _synthesis/, contradicting _open-questions.md, races between agents…), see references/edge-cases.md.
When to Use
- Too many flat files in
research/orexperiments/ - Duplicate or near-duplicate notes
- Inconsistent naming (spaces, uppercase, agent IDs in filenames)
- After a deep-research or consolidate phase that created many files
- You can't find a note you know exists
Notes Directory Structure
notes/
├── index.md ← table of contents (research + experiments only)
├── raw/ ← immutable sources (DON'T touch)
├── research/ ← deep-research findings (organize within)
│ ├── <topic>/ ← group by topic or theme
│ └── ...
├── experiments/ ← eval reflections and results (organize within)
│ ├── <approach>/ ← group by approach or technique
│ └── ...
├── _synthesis/ ← consolidate owns this (DON'T touch)
├── _connections.md ← consolidate owns this
├── _open-questions.md
└── _organization-log.md ← append-only log of what you changed
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.mdis the limit - Name by topic —
algorithms/notagent1-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
For pairs above the threshold where the verdict is not immediately obvious from a quick read — same topic vs. different angle vs. different topic with shared boilerplate vs. genuinely contradicting — spawn the Dedup Judge subagent. It reads both notes blinded (no author / timestamp / length metadata) and returns a structured verdict (same-topic-merge / different-angle-fold / contradicting-do-not-merge / keep-both-rename) with concrete merge or rename instructions. See agents/dedup-judge.md. Use it especially when:
- The two notes were written by different agents (recency / author bias is highest).
- One note is much longer than the other (length bias makes the long one feel authoritative).
- The notes appear to disagree but you can't tell if it's a real conflict or a scope difference.
For obvious cases — verbatim duplicates, or clearly different topics that shared a paragraph — just decide directly.
When merging confirmed duplicates, preserve provenance from both notes — never just pick one and discard:
- Union the
## Referenceslists (de-duplicated by URL orraw/filename). Losing a citation loses an audit trail that an agent may need months later. - Keep the more specific claims from each note, not just whichever was longer. A short note with concrete numbers usually has higher information density than a long one with vague prose.
- Combine
tagsandaliasesrather than picking one set. Both were correct in their original context.
Move originals to _archive/ so the merge is reversible.
When two notes contradict each other, don't merge:
- Flag the conflict in
_open-questions.md(existing rule). - Also stamp
contradictedBy: [other-note-slug]into each note's frontmatter so future readers see the conflict at the note level —_open-questions.mdcollects them, but agents reading the note directly should see the warning without a separate lookup.
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/.
Then resolve cross-links — moves and renames break any [[old-slug]] references in note bodies:
python .coral/public/skills/organize-files/scripts/resolve_links.py .coral/public/notes --dry-run
# review the diff, then:
python .coral/public/skills/organize-files/scripts/resolve_links.py .coral/public/notes
The resolver walks every note, scans the body for plain-text mentions of every other note's title, and wraps them as [[slug|Title]]. It skips text already inside wikilinks, citation markers, code blocks, and inline code. Run this after moves and renames, not before — the resolver needs final paths.
6. Log
Append a summary to _organization-log.md: what you moved, merged, or renamed, and why.