second-brain-mapping

second-brain-mapping is a skill for Claude Code from mycelium-hq/ai-brain-starter. It costs 116 tokens per session (4,501 once invoked), scanned A, original, MIT.

A process that turns an Obsidian vault—a folder of linked notes—into a searchable, structured knowledge base. It extracts metadata, adds links between related notes, and can find connections across note types.

In plain words
What is it for?
Use it to refresh metadata, process typed notes such as meetings or journals, identify missing links, sanitize graph reports, and surface patterns across the vault.
Why use it?
Important relationships are hard to see when information is spread across many separate files. Mapping makes the vault easier to query and can reveal cross-topic insights.

Skill for Claude Code

Written for Claude Code: argument-hint in frontmatter. Also seen: mentions subagents; positional $N argument.

Part of the ai-brain-starter plugin — 38 skills, 17 commands, 3 agents, 1 hook shipped together

Good fit Use it to refresh metadata, process typed notes such as meetings or journals, identify missing links, sanitize graph reports, and surface patterns across the vault.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/mycelium-hq/ai-brain-starter/second-brain-mapping
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 mycelium-hq/ai-brain-starter --skill second-brain-mapping
Clone the repo
git clone --depth 1 https://github.com/mycelium-hq/ai-brain-starter

Made for: Claude Code.

Or install ai-brain-starter, the plugin that ships this one along with the rest of its 38 skills, 17 commands, 3 agents, 1 hook.

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 second-brain-mapping

README.md
[![agentmods](https://agentmods.dev/badge/skills/mycelium-hq/ai-brain-starter/second-brain-mapping/github.svg)](https://agentmods.dev/skills/mycelium-hq/ai-brain-starter/second-brain-mapping)
Your own site
<a href="https://agentmods.dev/skills/mycelium-hq/ai-brain-starter/second-brain-mapping"><img src="https://agentmods.dev/badge/skills/mycelium-hq/ai-brain-starter/second-brain-mapping/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 second-brain-mapping

Your own site · 80×15
<a href="https://agentmods.dev/skills/mycelium-hq/ai-brain-starter/second-brain-mapping"><img src="https://agentmods.dev/badge/skills/mycelium-hq/ai-brain-starter/second-brain-mapping.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 116 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,501 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. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
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 $0.00116 $0.04501
Opus 5 $0.00058 $0.02250
Sonnet 5 $0.00023 $0.00900
Haiku 4.5 $0.00012 $0.00450

Measured 10d ago against content hash ff119a46ead1, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

second-brain-mapping 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 10d 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.

skills/second-brain-mapping/SKILL.md · 350 lines

How it starts

The opening of the file, as written. The whole thing — 350 lines — stays where its author put it; the contents beside it link to each section on GitHub.

/second-brain-mapping

{SKILL_DIR} = this skill's own folder (locally: the directory this SKILL.md lives in; a served brain substitutes the real absolute path before you read this). Shared starter files live at the repo root two levels up: {SKILL_DIR}/../... If a path does not resolve, name the missing file and stop — never guess another location.

Your vault is a database. This skill makes it queryable.

What it does

Phase Tool LLM cost Always runs?
1 vault-metadata-extract.py (dispatcher → type-specific extractors) 0 tokens Yes
2 /graphify (optional) ~100k–1M tokens No — asks first
2b graphify_report_sanitize.py --check — keeps the graph report from flooding the vault's graph view 0 tokens Yes, whenever a report exists
3 Wikilink gaps + interactive apply ~5k tokens If graph exists
4 vault-insight-engine.py — cross-type surprise finder 0 tokens Yes

Phases 1, 2b and 4 are free. Phase 2 is expensive and opt-in. Phase 3 needs interactive approval so it skips gracefully in non-TTY contexts. 2b runs even when 2 is skipped — a report left by an earlier run is the thing it protects against.

Setup

Run once after cloning ai-brain-starter:

/setup-vault-types

Interactive wizard asks which doc types you have (journal, book, article, meeting, person, project, podcast, client, etc.) and installs the matching extractors. You can add custom types later by editing scripts/extractors/schemas.yaml or running /setup-vault-types --add <name>.

Usage

/second-brain-mapping                 # full pipeline
/second-brain-mapping --metadata-only # skip graphify + wikilinks, keep insights
/second-brain-mapping --insights-only # only run Phase 4 on existing metadata
/second-brain-mapping --type book     # only process files with `type: book`
/second-brain-mapping --dry-run       # preview without writes
/second-brain-mapping --sample        # preview 1 file per configured type (cold-start safe)
/second-brain-mapping --sample 3      # preview 3 files per configured type

Read the full file on GitHub · 350 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. 10d ago First seen · 350 lines · 116 tokens per session scan A ff119a46ead1

Subscribe to this mod's changes

second-brain-mapping is a skill published in the GitHub repository mycelium-hq/ai-brain-starter (36 stars, last pushed today), licensed MIT. It adds 116 tokens to every session and 4,501 once invoked, about $0.0006 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.

Related

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