Second Brain Agent Skill

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:

• What was created — directory tree and config files
• 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

• 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:

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