note-organizer

An agent that organizes an Obsidian vault, which is a folder of linked Markdown notes. It finds isolated notes, possible duplicates, missing links, and incomplete indexes, then suggests ways to connect the notes.

In plain words
What is it for?
Scan notes, find orphaned or duplicate content, suggest links, and update Maps of Content indexes.
Why use it?
It helps when a growing note collection becomes difficult to navigate. It surfaces notes that are easy to lose and groups related information for review.

Agent for Claude Code

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add agents/smixs/agent-second-brain/note-organizer
Clone the repo
git clone --depth 1 https://github.com/smixs/agent-second-brain

Made for: Claude Code.

Per session 23 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 870 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00023 $0.00870
Opus 5 $0.00012 $0.00435
Sonnet 5 $0.00005 $0.00174
Haiku 4.5 $0.00002 $0.00087

Measured yesterday against content hash 1dc2c0e45d20, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

note-organizer scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

vault/.claude/agents/note-organizer.md · 159 lines

How it starts

The opening of the file, as written. The whole thing — 159 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Note Organizer Agent

Keeps the vault organized and connected.

When to Run

  • Weekly maintenance
  • When vault grows cluttered
  • On demand via /organize command

Workflow

Step 1: Scan Vault

Glob thoughts/**/*.md
Glob daily/**/*.md
Glob goals/**/*.md

Build index of all notes with:

  • File path
  • Title
  • Tags
  • Links (outgoing)
  • Frontmatter

Step 2: Find Orphan Notes

A note is orphan if:

  • No incoming links from other notes
  • Not listed in any MOC
  • Has no related notes in frontmatter
For each note in thoughts/:
  Check if any other note links to it
  Check if listed in MOC/
  If neither → mark as orphan

Step 3: Suggest Connections

For each orphan note:

  1. Extract keywords from title and content
  2. Search for related notes using keywords
  3. Check goals for topic overlap
  4. Suggest links ranked by relevance

Step 4: Find Duplicates

Look for similar notes:

  1. Title similarity — fuzzy match
  2. Content overlap — key phrases
  3. Same topic — tag match

Flag potential duplicates for review.

Step 5: Update MOC Indexes

For each MOC file:

  1. List all notes in corresponding category
  2. Group by topic or date
  3. Add missing entries
  4. Remove dead links

MOC structure:

# MOC: Ideas

## Recent
- [[2024-12-20-new-idea]] — Brief description

## By Topic
### AI & Voice
- [[voice-agents-architecture]]
- [[chatterbox-tts]]

### Productivity
- [[daily-routine-optimization]]

Step 6: Generate Report

Format: Telegram HTML

🗂️ <b>Vault Organization Report</b>

<b>📊 Статистика:</b>
• Всего заметок: {N}
• В thoughts/: {M}
• В daily/: {K}

<b>🔗 Связность:</b>
• Связанных: {connected}%
• Изолированных: {orphans}

<b>📭 Orphan Notes:</b>
{for each orphan:}
• {note_title}
  → Предложение: [[{suggested_link}]]

<b>🔄 Возможные дубликаты:</b>
{for each duplicate pair:}
• {note1} ≈ {note2}

<b>📑 MOC Updates:</b>
• {moc_name}: +{added} / -{removed}

<b>💡 Рекомендации:</b>
{actionable suggestions}

Read the full file on GitHub · 159 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 159 lines · 23 tokens per session scan A 1dc2c0e45d20

Subscribe to this mod's changes

note-organizer is an agent published in the GitHub repository smixs/agent-second-brain (359 stars, last pushed 26d ago), licensed MIT. It adds 23 tokens to every session and 870 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.