second-brain

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass, no license.

Audit 0.4.1 · source sha f7a1cdab60be · 20 Oct 2026Report an issue or request a re-scan

• Publishernicholasspisak GitHub userOwner of the repository this skill is read from
• Source foldernicholasspisak/second-brain/skills/second-brainThe exact folder we audited
• LicenceNot declaredAs the repository states it
• Commit pinned for this verdictf7a1cdab60beA new audit runs when the source changes
• Repository statusNot archivedLast push 196 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its 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…

---
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

Excerpt, first 5,938 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

1. 2026-10-20
   ✓SAFE B 89 / 100

   first audit · source f7a1cdab60be

Questions about second-brain

• github.com/nicholasspisak/second-brain/tree/main/skills/second-b — the audited source at commit f7a1cdab60be and every finding aboveObserved · 20 Oct 2026

Spotted something wrong? Report a correction · Methodology