A tool for examining the link structure of a note vault, meaning a collection of connected notes. It finds isolated notes, missing connections, important concepts, and concepts that connect different parts of the vault.

Use it to map a vault, find orphan notes, discover links to add, identify bridge concepts, or check structural vault health.

It helps reveal where notes are disconnected or where useful relationships have not been recorded. Its graph analysis runs across the full vault rather than a small sample.

vault-graph — Skill for Claude Code by tuan3w

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.

Any agent

npx skills add tuan3w/obsidian-vault-agent --skill vault-graph

Clone the repo

git clone --depth 1 https://github.com/tuan3w/obsidian-vault-agent

Made for: Claude Code.

Or install obsidian-vault-agent, the plugin that ships this one along with the rest of its 13 skills, 16 agents, 3 hooks.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/tuan3w/obsidian-vault-agent/vault-graph/github.svg)](https://agentmods.dev/skills/tuan3w/obsidian-vault-agent/vault-graph)

Your own site

<a href="https://agentmods.dev/skills/tuan3w/obsidian-vault-agent/vault-graph"><img src="https://agentmods.dev/badge/skills/tuan3w/obsidian-vault-agent/vault-graph/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/tuan3w/obsidian-vault-agent/vault-graph"><img src="https://agentmods.dev/badge/skills/tuan3w/obsidian-vault-agent/vault-graph.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 59 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,304 The whole file, excluding the scripts and references it only reads on demand.

Security scan C 2 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.

Model	Per session	Once invoked
Fable 5.1	$0.00059	$0.01304
Opus 5	$0.00030	$0.00652
Sonnet 5	$0.00012	$0.00261
Haiku 4.5	$0.00006	$0.00130

Measured 10d ago against content hash 2c6c0d03c373, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade C, and why

vault-graph scanned grade C with 2 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 10d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/analyze_vault_graph.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Downloads and executes remote codehighSupply chain

curl | sh runs whatever the server returns today, which is not necessarily what it returned when this was reviewed.

Requires `uv` installed (`brew install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`). Dependencies auto-install on first run.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

Requires `uv` installed (`brew install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`). Dependencies auto-install on first run.

skills/vault-graph/SKILL.md · 152 lines

How it starts

The opening of the file, as written. The whole thing — 152 lines — stays where its author put it; the contents beside it link to each section on GitHub.

<Use_When>

User asks about vault structure, connections, or health
User wants to find orphan notes (unlinked, isolated)
User wants to discover missing connections between notes
User wants to identify the most important concepts in the vault
User asks "what should I link?" or "what's disconnected?"
As part of /health workflow for structural metrics
User says "map", "graph", "network", "connections", "orphans", "bridges" </Use_When>

<Do_Not_Use_When>

User wants to search note CONTENT (use Grep/search_notes instead)
User wants to process a single note (use /process)
User wants tag analysis without graph structure (use /health) </Do_Not_Use_When>

<Execution_Policy>

Run the Python script first — it handles all graph math deterministically
Pipe script output to the graph-analyst agent for interpretation
Report progress via TodoWrite
If uv is not installed, provide install command and stop
Script runs on the full vault — no sampling needed (handles 5000+ notes) </Execution_Policy>

Stage 1: RUN GRAPH ANALYSIS

Run the analysis script from the skill directory:

SKILL_DIR="${CLAUDE_SKILL_DIR}"
uv run "$SKILL_DIR/scripts/analyze_vault_graph.py" "." --top 20

The script outputs JSON to stdout with:

summary: total notes, edges, orphans, density, clustering coefficient
top_pagerank: most influential notes
top_betweenness: bridge concepts connecting clusters
top_in_degree: most referenced notes
top_out_degree: most connecting notes
orphans: notes with zero links in/out
dead_ends: notes referenced but linking nowhere
clusters: connected components with dominant types
missing_links: wikilinks pointing to non-existent notes
type_distribution: counts by note type
status_distribution: counts by processing status

Requires uv installed (brew install uv or curl -LsSf https://astral.sh/uv/install.sh | sh). Dependencies auto-install on first run.

Read the full file on GitHub · 152 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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.

10d ago First seen · 152 lines · 59 tokens per session scan C 2c6c0d03c373

Subscribe to this mod's changes

vault-graph is a skill published in the GitHub repository tuan3w/obsidian-vault-agent (39 stars, last pushed 5mo ago), licensed MIT. It adds 59 tokens to every session and 1,304 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it C with 2 findings (downloads and executes remote code, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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