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

~

{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

wiki/log.md

2. Generate agent config file(s)

For each selected agent, read the corresponding template from

<skill-directory>/references/agent-configs/

claude-code.md

CLAUDE.md

codex.md

AGENTS.md

cursor.md

second-brain.mdc

<vault>/.cursor/rules/

gemini.md

GEMINI.md

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

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