obsidian-llm-wiki: Command for Claude Code

.claude/commands/organize-vault.md

organize-vault is a command for Claude Code from mickeytony0215-png/obsidian-llm-wiki. It costs 14 tokens per session (430 once invoked), scanned A, original, MIT.

A command that scans an entire note vault, adds missing paper details, and creates two-way links between related notes. It marks links to notes that have not been reviewed or that are disputed.

In plain words
What is it for?
Use it to inventory paper notes, concept notes, seminar reports, and other notes; add YAML metadata to paper notes; and connect notes that share methods, problems, or sources.
Why use it?
It removes the need to find related notes and repair missing metadata by hand. Visible markers help you notice information that still needs checking.

Command for Claude Code

Written for Claude Code: installed under .claude/.

This is mickeytony0215-png/obsidian-llm-wiki's own configuration. It tells Claude Code how to work on obsidian-llm-wiki itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything obsidian-llm-wiki configures →

Reuse

Borrowing it

Nothing to install: this file belongs to mickeytony0215-png/obsidian-llm-wiki. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/mickeytony0215-png/obsidian-llm-wiki/main/.claude/commands/organize-vault.md
Clone the repo
git clone --depth 1 https://github.com/mickeytony0215-png/obsidian-llm-wiki

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for organize-vault

README.md
[![agentmods](https://agentmods.dev/badge/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault/github.svg)](https://agentmods.dev/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault)
Your own site
<a href="https://agentmods.dev/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault"><img src="https://agentmods.dev/badge/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for organize-vault

Your own site · 80×15
<a href="https://agentmods.dev/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault"><img src="https://agentmods.dev/badge/commands/mickeytony0215-png/obsidian-llm-wiki/organize-vault.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 14 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 430 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
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 5.1 $0.00014 $0.00430
Opus 5 $0.00007 $0.00215
Sonnet 5 $0.00003 $0.00086
Haiku 4.5 $0.00001 $0.00043

Measured 12d ago against content hash 27e2dd26792b, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

organize-vault 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 12d ago.

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.

.claude/commands/organize-vault.md · 54 lines

What it actually says

Review-gate check (soft)

When scanning and encountering a note with review_status: unreviewed:

  • In the final report, list these under a separate section: "Unreviewed notes (N)"
  • When adding a link pointing to an unreviewed note, append an [UNREVIEWED] marker to the link
  • For disputed notes, append a [DISPUTED] marker on links pointing to them
  • At the end of the report, remind the user: "Run /review-note on each of these N unreviewed notes. After review, the [UNREVIEWED] markers can be cleared by grep or by the next run of /organize-vault."

Do not skip unreviewed notes — build the links, but carry the visible marker.

Main flow

Scan every note in the vault and perform:

Step 1: Inventory

List all notes in the vault, grouped by: paper notes, concept notes, seminar reports, other.

Step 2: Backfill frontmatter

For every paper note missing YAML frontmatter, add title, authors, year, venue, tags, status.

Step 3: Build bidirectional links

Analyze the contents of all notes and find related pairs, then add [[links]] in both directions.

Relatedness criteria:

  • Same method or technique
  • Same problem
  • Same referenced literature
  • Same sub-field

Step 4: Create missing concept notes

Extract recurring core concepts from all paper notes. Create a concept note if one does not already exist.

Step 5: Produce the report

On completion, list:

  • Which notes were modified
  • Which concept notes were added
  • How many new links were created

Requirements

  • Use the output language specified in SKILL.md (keep technical terms in their original form).
  • Do not delete existing content — only add links and frontmatter.
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. 12d ago First seen · 54 lines · 14 tokens per session scan A 27e2dd26792b

Subscribe to this mod's changes

organize-vault is a command published in the GitHub repository mickeytony0215-png/obsidian-llm-wiki (2 stars, last pushed 2mo ago), licensed MIT. It adds 14 tokens to every session and 430 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 2026-08-31.