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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:"
summarize — summarize links, files, and media from the CLI
qmd — local search engine for your wiki (helpful as it grows)
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 monthlydon't have the plugin yet? install it then click "run inline in claude" again.