setup-brain

A setup helper for a Zettelkasten-style Brain vault, a linked knowledge system made from organized notes. It creates folders for captures, source material, permanent notes, indexes, articles, projects, templates, and other records.

In plain words
What is it for?
Use it to initialize a vault for general knowledge, coding notes, research, learning, or mixed topics.
Why use it?
It gives a new knowledge base a consistent structure before you start storing information.

Skill for Claude CodeCodex

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 skills/abilityai/abilities/setup-brain
Any agent
npx skills add Abilityai/abilities --skill setup-brain
Clone the repo
git clone --depth 1 https://github.com/Abilityai/abilities

Made for: Claude Code, Codex.

Per session 16 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 726 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 $0.00016 $0.00726
Opus 5 $0.00008 $0.00363
Sonnet 5 $0.00003 $0.00145
Haiku 4.5 $0.00002 $0.00073

Measured yesterday against content hash 5c4d69640ac0, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

setup-brain 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.

plugins/agent-dev/memory-templates/brain/setup-brain/SKILL.md · 122 lines

How it starts

The opening of the file, as written. The whole thing — 122 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Setup Brain Vault

Initialize a Zettelkasten-style knowledge management system.

Step 1: Ask Configuration

Use AskUserQuestion:

Question 1: "Where should the Brain vault be created?"

  • Options:
    • "Brain/ folder (Recommended)" - Standard location
    • "Custom location" - Specify a different path

Question 2: "What type of knowledge will you primarily store?"

  • Options:
    • "General knowledge & insights" - Broad topics
    • "Technical/coding notes" - Development focused
    • "Research & learning" - Academic style
    • "Mixed/All types"

Step 2: Create Directory Structure

Create the Brain vault structure:

mkdir -p Brain/00-Inbox/Quick\ Captures
mkdir -p Brain/00-Inbox/Raw\ Materials
mkdir -p Brain/01-Sources/Books
mkdir -p Brain/02-Permanent
mkdir -p Brain/03-MOCs
mkdir -p Brain/04-Output/Articles
mkdir -p Brain/04-Output/Draft\ Posts
mkdir -p Brain/04-Output/Projects
mkdir -p Brain/05-Meta/Changelogs
mkdir -p Brain/05-Meta/Templates
mkdir -p Brain/Document\ Insights

Step 3: Create Essential Files

Brain/CHANGELOG.md:

# Brain Changelog

## [Session Date]
- Brain vault initialized
- Structure created with standard directories

Brain/04-Output/Articles/ARTICLE-INDEX.md:

# Article Index

Central registry of all articles in the vault.

| Title | Created | Status | Topics |
|-------|---------|--------|--------|
| (none yet) | - | - | - |

Brain/05-Meta/Templates/permanent-note.md:

---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: [agent-name]
updated_by: [agent-name]
tags: []
---

# Note Title

[Content goes here]

## Connections

- [[Related Note 1]]
- [[Related Note 2]]

Step 4: Update CLAUDE.md

Add brain configuration to CLAUDE.md:

## Brain Vault

Knowledge management using Zettelkasten method.

### Structure
- `Brain/00-Inbox/` - New captures, raw ideas
- `Brain/02-Permanent/` - Atomic, interconnected notes
- `Brain/03-MOCs/` - Maps of Content (indexes)
- `Brain/04-Output/` - Generated content
- `Brain/05-Meta/` - Changelogs and templates

### Note Format
All notes MUST have YAML frontmatter:
- created, updated (dates)
- created_by, updated_by (agent attribution)
- tags (array)

### Commands
- `/create-note` - Create a new permanent note
- `/search-brain` - Search the vault
- `/find-connections` - Discover note relationships

Read the full file on GitHub · 122 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 · 122 lines · 16 tokens per session scan A 5c4d69640ac0

Subscribe to this mod's changes

setup-brain is a skill published in the GitHub repository Abilityai/abilities (11 stars, last pushed 14d ago), licensed MIT. It adds 16 tokens to every session and 726 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.

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