second-brain

---
name: second-brain
description: >
  Set up a new Obsidian knowledge base with the LLM Wiki pattern. Use when
  the user wants to create a second brain, initialize a vault, set up a
  personal knowledge base, or says "onboard". Guides through an interactive
  wizard to configure vault name, location, domain, agent support, and tooling.
allowed-tools: Bash Read Write Glob Grep
---

# Second Brain — Onboarding Wizard

Set up a new Obsidian knowledge base using the LLM Wiki pattern. The LLM acts as librarian — reading raw sources, compiling them into a structured interlinked wiki, and maintaining it over time.

## Wizard Flow

Guide the user through these 5 steps. Ask ONE question at a time. Each step has a sensible default — the user can accept it or provide their own value.

### Step 1: Vault Name

Ask:
> "What would you like to name your knowledge base? This will be the folder name."
> Default: `second-brain`

Accept any user-provided name. This becomes the folder name and the title in the agent config.

### Step 2: Vault Location

Ask:
> "Where should I create it? Give me a path, or I'll use the default."
> Default: `~/Documents/`

Accept any absolute or relative path. Resolve `~` to the user's home directory. The final vault path is `{location}/{vault-name}/`.

### Step 3: Domain / Topic

Ask:
> "What's this knowledge base about? This helps me set up relevant tags and describe the vault's purpose."
>
> Examples: "AI research", "competitive intelligence on fintech startups", "personal health and fitness"

Accept free text. Use this to:
- Write a one-line domain description for the agent config
- Generate 5-8 suggested domain-specific tags

### Step 4: Agent Config

Auto-detect which agent is running this skill. State it clearly:
> "I'm running in **[Agent Name]**, so I'll generate a **[config file]** for this vault."

Then ask:
> "Do you use any other AI agents you'd like config files for? Options: Claude Code, Codex, Cursor, Gemini CLI — or skip."

Skip the agent that was auto-detected. Generate configs for all selected agents.

**Agent detection logic:**
- If the `CLAUDE.md` convention is being used or the Skill tool is Claude Code's → Claude Code
- If the environment indicates Codex → Codex
- If `.cursor/` exists in the working directory → Cursor
- If `GEMINI.md` convention is being used → Gemini CLI
- If unsure, ask the user which agent they're using

### Step 5: Optional CLI Tools

Ask:
> "These tools extend what the LLM can do with your vault. All optional but recommended:"
>
> 1. **summarize** — summarize links, files, and media from the CLI
> 2. **qmd** — local search engine for your wiki (helpful as it grows)
> 3. **agent-browser** — browser automation for web research
>
> "Install all, pick specific ones (e.g. '1 and 3'), or skip?"

## Post-Wizard: Scaffold the Vault

After collecting all answers, execute these steps in order:

### 1. Create directory structure

Run the onboarding script, passing the full vault path:

```
bash <skill-directory>/scripts/onboarding.sh <vault-path>
```

This creates all directories and the initial `wiki/index.md` and `wiki/log.md` files.

### 2. Generate agent config file(s)

For each selected agent, read the corresponding template from `<skill-directory>/references/agent-configs/`:

| Agent | Template | Output File | Output Location |
|---|---|---|---|
| Claude Code | `claude-code.md` | `CLAUDE.md` | Vault root |
| Codex | `codex.md` | `AGENTS.md` | Vault root |
| Cursor | `cursor.md` | `second-brain.mdc` | `<vault>/.cursor/rules/` |
| Gemini CLI | `gemini.md` | `GEMINI.md` | Vault root |

For each template, replace the placeholders:

- `{{VAULT_NAME}}` → the vault name from Step 1
- `{{DOMAIN_DESCRIPTION}}` → a one-line description derived from Step 3
- `{{DOMAIN_TAGS}}` → generate 5-8 domain-relevant tags as a bullet list based on the domain from Step 3
- `{{WIKI_SCHEMA}}` → read `<skill-directory>/references/wiki-schema.md` and insert everything from `## Architecture` onward

Write the generated config to the vault.

### 3. Update wiki/log.md

Append the setup entry:

```
## [YYYY-MM-DD] setup | Vault initialized
Created vault "{{VAULT_NAME}}" for {{DOMAIN_DESCRIPTION}}.
Agent configs: {{list of generated config files}}.
```

### 4. Install CLI tools (if selected)

For each tool the user selected in Step 5, run the install command:

- summarize: `npm i -g @steipete/summarize`
- qmd: `npm i -g @tobilu/qmd`
- agent-browser: `npm i -g agent-browser && agent-browser install`

After each install, verify with `<tool> --version`. Report success or failure for each.

### 5. Print summary

Show the user:

1. **What was created** — directory tree and config files
2. **Required next step** — install the Obsidian Web Clipper browser extension:
   > Install the Obsidian Web Clipper to easily save web articles into your vault:
   > https://chromewebstore.google.com/detail/obsidian-web-clipper/cnjifjpddelmedmihgijeibhnjfabmlf
3. **How to start** — open the vault folder in Obsidian, clip an article to `raw/`, then run `/second-brain-ingest`

## Reference Files

These files are bundled with this skill and available at `<skill-directory>/references/`:

- `wiki-schema.md` — canonical wiki rules (single source of truth for all agent configs)
- `tooling.md` — CLI tool details, install commands, and verification steps
- `agent-configs/claude-code.md` — CLAUDE.md template
- `agent-configs/codex.md` — AGENTS.md template
- `agent-configs/cursor.md` — Cursor rules template
- `agent-configs/gemini.md` — GEMINI.md template

## Next Steps

After setup is complete, the user's workflow is:

1. **Clip articles** to `raw/` using the Obsidian Web Clipper
2. **Ingest sources** with `/second-brain-ingest` — processes raw files into wiki pages
3. **Ask questions** with `/second-brain-query` — searches and synthesizes from the wiki
4. **Health-check** with `/second-brain-lint` — run after every 10 ingests or monthly