GitHub - earlyaidopters/second-brain

An AI that already knows who you are before you type a word.

Obsidian + Claude Code · Local · Private · One command

  Your files (PDFs, docs, notes)
          │
          ▼
  ┌───────────────────┐
  │   Obsidian vault  │  ← plain .md files on your computer
  │  inbox/  daily/   │
  │  projects/  ...   │
  └────────┬──────────┘
           │  Claude Code reads this folder
           ▼
  ┌───────────────────┐
  │   Claude Code     │  ← knows your projects, voice, context
  │   /vault-setup    │     before you type a single word
  │   /daily  /tldr   │
  └───────────────────┘
           │
           ▼
    AI that compounds.
    Session 1: knows your folders.
    Session 20: knows more about
    your work than you consciously remember.

If this saves you hours, drop a ⭐ — it helps others find it.

Quick Start

macOS

Option A — One-liner (paste this into Terminal and hit Enter):

curl -fsSL https://raw.githubusercontent.com/earlyaidopters/second-brain/main/setup.sh -o setup.sh && bash setup.sh

Option B — Clone the repo:

Open Terminal (press ⌘ Space, type Terminal, hit Enter) and run:

git clone https://github.com/earlyaidopters/second-brain.git
cd second-brain
./setup.sh

Don't have git? Run xcode-select --install first, then retry.

Windows

First: do you have git? Open PowerShell (press Win, type powershell, hit Enter) and run:
git --version
If you see a version number, you're good. If not, install git from git-scm.com — use all the default options during install, then reopen PowerShell.

Option A — One-liner (paste this into PowerShell and hit Enter):

Invoke-WebRequest -Uri "https://raw.githubusercontent.com/earlyaidopters/second-brain/main/setup.ps1" -OutFile setup.ps1; powershell -ExecutionPolicy Bypass -File setup.ps1

Option B — Clone the repo:

Once git is ready, run:

git clone https://github.com/earlyaidopters/second-brain.git
cd second-brain
powershell -ExecutionPolicy Bypass -File setup.ps1

"Running scripts is disabled" error? That's a Windows safety setting. The -ExecutionPolicy Bypass part in the command above overrides it just for this one script — it doesn't change anything permanent on your computer.

Errors about Unexpected token '}' or Missing terminator? This was fixed — see Windows Troubleshooting below.

Python not found warning? Download Python from python.org/downloads — on the first screen of the installer, check "Add Python to PATH" before clicking Install. Then close and reopen PowerShell, and rerun the setup script.

The script handles the rest: installs Obsidian, installs Claude Code, creates your vault, and optionally imports your existing files.

Already Have an Obsidian Vault?

The main thing you're getting: 4 slash commands (/vault-setup /daily /tldr /file-intel) and a CLAUDE.md template that makes Claude Code understand your vault from session one. The script adds these without touching your existing notes.

The setup script fully supports existing vaults. When you point it at a folder that already has content, it will:

Add missing folders (inbox/, daily/, projects/, etc.) without touching your existing folders
Back up your existing CLAUDE.md (if present) before installing the new template
Install 4 slash commands into .claude/skills/ (vault + global ~/.claude/skills/)
Copy helper scripts into scripts/
Show you exactly what it will do and ask for confirmation before changing anything
Never touch your existing notes, Obsidian plugins, themes, snippets, or .obsidian/ settings

# macOS — point at your existing vault
./setup.sh
# When prompted: enter your existing vault path, e.g. ~/Documents/MyVault

# Windows — same thing
powershell -ExecutionPolicy Bypass -File setup.ps1
# When prompted: enter your existing vault path, e.g. C:\Users\You\MyVault

After setup, open Claude Code in your vault and run /vault-setup. It will interview you and generate a personalized CLAUDE.md that fits your existing structure.

Already have a CLAUDE.md? The script backs it up as CLAUDE.md.backup-YYYY-MM-DD-HHMMSS before writing the new template. You can always restore it.

Want to undo everything? Delete .claude/skills/, scripts/, CLAUDE.md, and memory.md from your vault. Your original notes are untouched. To remove global skills: delete ~/.claude/skills/ (Mac) or %USERPROFILE%\.claude\skills\ (Windows).

This script is safe to re-run. It detects your existing vault, backs up CLAUDE.md, and only adds what's missing.

Why This Exists

You've tried to build a second brain before.

Maybe Notion. Maybe Apple Notes. Maybe a folder of markdown files you swore you'd organize.

Every time, the same outcome: you'd set it up, use it for a week, and then completely forget it existed.

The problem was never the tool. It was that you had to remember to use it.

This wires Obsidian (your local knowledge vault) to Claude Code (your AI agent) so that:

Claude Code reads your notes before answering — it knows your projects, your clients, your voice
Claude Code writes your notes after working — your vault builds itself from your sessions
Your existing files (PDFs, docs, slides) get synthesized and imported automatically via Gemini 3 Flash
Everything stays local, private, and yours — no cloud lock-in, no subscription creep

The result: an AI that knows who you are from the first prompt of every session. Not because you told it. Because it read your vault.

What Gets Installed

Tool	What it is	Why
Obsidian	Free note-taking app	Your notes live as plain `.md` files on your computer — no cloud, no subscription, yours forever
Claude Code	Anthropic's AI terminal	Reads and writes files directly in your vault — no copy-pasting, no switching tabs
Python packages	Background libraries	Used by Gemini 3 Flash to read and synthesize your existing files (PDFs, docs, slides)
Vault skills	Slash commands	`/vault-setup` `/daily` `/tldr` `/file-intel` — teach Claude how to work with your vault
Obsidian Skills (optional)	Official skills by Kepano (Obsidian CEO)	Lets Claude navigate, read, and write your vault natively using the Obsidian CLI

Nothing is uploaded. Your vault is a folder on your computer. Claude Code reads it locally. The only optional network call is Gemini file processing — and that's fully skippable.

What the Setup Script Does

Step 1 — Check dependencies       (Homebrew on Mac / winget on Windows)
Step 2 — Install Obsidian         (free, local note-taking app)
Step 3 — Install Claude Code CLI  (Anthropic's AI terminal)
Step 4 — Install Python packages  (for Gemini file processing)
Step 5 — Create your vault        (inbox, daily, projects, research, archive + skills)
         └─> Skills installed both locally AND globally (~/.claude/skills/)
         └─> API key input is masked (hidden) for security
Step 6 — Import existing files    (optional — Gemini reads and synthesizes them)
Step 7 — Obsidian Skills          (optional — official skills by Kepano, Obsidian CEO)
         └─> Opens Obsidian pointed at your new vault

After Setup

1. Enable the Obsidian CLI

Obsidian → Settings → General → Enable Command Line Interface

This adds the obsidian command to your PATH so you can open your vault from the terminal. (CLI docs)

2. Open Claude Code in your vault

cd ~/second-brain
claude

3. Run your first command

/vault-setup

Claude Code will interview you about your role and work, then generate a personalized CLAUDE.md and suggest slash commands for your specific workflow. Business owner gets different folders than a developer. Creator gets different slash commands than a consultant.

Slash Commands

Four commands come pre-installed. More get added as you use the system.

Command	What it does
`/vault-setup`	Interviews you (role, projects, goals) and generates your personalized vault structure + CLAUDE.md + custom slash commands
`/daily`	Starts your day — reads today's note or creates one, surfaces your top priorities, asks what you're working on
`/tldr`	At the end of any session, saves a structured summary to the right folder in your vault automatically
`/file-intel`	Point it at any folder — Gemini reads every file and generates Obsidian-ready summaries into your inbox

Good news: The setup script automatically installs skills both locally (in your vault) and globally (~/.claude/skills/), so slash commands work from any folder — not just inside the vault.

If you set up manually without the script, cd into your vault before running claude, or ask Claude Code to "Make these slash commands global so they work in any folder."

Importing Existing Files

Have years of PDFs, Word docs, and slide decks sitting in folders? Don't manually convert them.

python3 scripts/process_docs_to_obsidian.py ~/your-files ~/second-brain/inbox

What happens:

Every file gets read by Gemini 3 Flash (gemini-3-flash-preview)
Signal is extracted, noise is discarded (legal boilerplate, headers, filler)
A clean compressed Markdown note is saved to your inbox/ (300–600 words max)

Then open Claude Code and say: "Sort everything in inbox/ into the right folders."

It reads your CLAUDE.md, understands your vault structure, and routes every note to where it belongs.

Supported formats: .pdf .docx .pptx .txt .md

Have Excel, CSV, or JSON files too? Use the broader script instead:
python3 scripts/process_files_with_gemini.py ~/your-files
This handles .xlsx .csv .json .xml .py .js .html and most text-based files. Results land in outputs/file_summaries/ with a MASTER_SUMMARY.md digest of everything.

How the Memory Works

Your vault is structured so Claude Code can find the right context for any task:

~/second-brain/
├── CLAUDE.md        ← The brain of the brain. Read at every session start.
├── memory.md        ← Session log. Updated by Claude Code after each conversation.
├── inbox/           ← Drop zone. Anything new lands here first.
├── daily/           ← Daily notes (YYYY-MM-DD.md). Your running log.
├── projects/        ← Active projects. Claude reads the relevant one before helping.
├── research/        ← Synthesized knowledge. Sources, notes, ideas.
└── archive/         ← Completed work. Never delete — just archive.

The compounding effect:

Session 1: Claude knows your folder structure
Session 5: Claude knows your projects, your voice, your preferences
Session 20: Claude is your personalized operating system — it knows more about your knowledge base than you consciously remember

Requirements

Tool	Platform	How to get it
Obsidian	macOS / Windows / Linux	`brew install --cask obsidian` or `winget install Obsidian.Obsidian`
Claude Code	macOS / Linux	`curl -fsSL https://claude.ai/install.sh \| sh`
Claude Code	Windows	`winget install Anthropic.ClaudeCode`
Python 3.8+	All	python.org
Google API key	All	aistudio.google.com/apikey — free
Claude account	All	claude.ai — Pro recommended for heavy use

Repository Structure

second-brain/
├── setup.sh                              ← macOS/Linux one-command setup
├── setup.ps1                             ← Windows one-command setup
├── CLAUDE.md                             ← Vault system file (personalized by /vault-setup)
├── memory.md                             ← Session memory (auto-updated by Claude Code)
├── requirements.txt                      ← Python dependencies
├── .env.example                          ← Copy to .env, add your Google API key
├── .gitignore                            ← Keeps .env and .venv out of git
├── scripts/
│   ├── process_docs_to_obsidian.py      ← Gemini 3 Flash file synthesizer
│   └── process_files_with_gemini.py     ← Batch Gemini file processor
├── skills/
│   ├── vault-setup/SKILL.md             ← Interactive vault configurator
│   ├── daily/SKILL.md                   ← Daily standup command
│   ├── tldr/SKILL.md                    ← Session summary command
│   └── file-intel/SKILL.md              ← Process any folder via Gemini
└── vault-template/
    ├── inbox/   daily/   projects/
    ├── research/   archive/

Manual Setup

Prefer to install each piece yourself? Click to expand the full step-by-step for both platforms.

macOS — Manual Steps

1. Install Homebrew (macOS app installer — skip if you have it)

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

2. Install Obsidian

brew install --cask obsidian

3. Install Claude Code

curl -fsSL https://claude.ai/install.sh | sh

4. Install Python dependencies

python3 -m venv ~/.second-brain-venv
~/.second-brain-venv/bin/pip install -r second-brain/requirements.txt

5. Download and set up the vault

git clone https://github.com/earlyaidopters/second-brain.git
mkdir -p ~/second-brain/{inbox,daily,projects,research,archive,.claude/skills/vault-setup,.claude/skills/daily,.claude/skills/tldr,.claude/skills/file-intel,scripts}
cp second-brain/CLAUDE.md second-brain/memory.md ~/second-brain/
cp second-brain/skills/vault-setup/SKILL.md ~/second-brain/.claude/skills/vault-setup/
cp second-brain/skills/daily/SKILL.md ~/second-brain/.claude/skills/daily/
cp second-brain/skills/tldr/SKILL.md ~/second-brain/.claude/skills/tldr/
cp second-brain/skills/file-intel/SKILL.md ~/second-brain/.claude/skills/file-intel/
cp second-brain/scripts/* ~/second-brain/scripts/
cp second-brain/.env.example ~/second-brain/.env
# Also install skills globally (so they work in any folder):
mkdir -p ~/.claude/skills/{vault-setup,daily,tldr,file-intel}
cp second-brain/skills/vault-setup/SKILL.md ~/.claude/skills/vault-setup/
cp second-brain/skills/daily/SKILL.md ~/.claude/skills/daily/
cp second-brain/skills/tldr/SKILL.md ~/.claude/skills/tldr/
cp second-brain/skills/file-intel/SKILL.md ~/.claude/skills/file-intel/

6. Add your Google API key

Open ~/second-brain/.env in any text editor and replace your_key_here with your key from aistudio.google.com/apikey.

7. (Optional) Install Kepano's Obsidian Skills

git clone --depth=1 https://github.com/kepano/obsidian-skills.git /tmp/obs-skills
for d in /tmp/obs-skills/skills/*/; do
  name=$(basename "$d")
  mkdir -p ~/second-brain/.claude/skills/$name
  cp "$d/SKILL.md" ~/second-brain/.claude/skills/$name/
done
rm -rf /tmp/obs-skills

8. Open Claude Code in your vault

cd ~/second-brain && claude

Windows — Manual Steps

Open PowerShell for all commands below.

1. Install Obsidian

winget install Obsidian.Obsidian

2. Install Claude Code

winget install Anthropic.ClaudeCode

Close and reopen PowerShell after this step.

3. Install Python (if you don't have it)

Download from python.org/downloads. On the installer's first screen, check "Add Python to PATH" before clicking Install.

4. Download and set up the vault

git clone https://github.com/earlyaidopters/second-brain.git
$vault = "$env:USERPROFILE\second-brain"
New-Item -ItemType Directory -Force -Path "$vault\inbox","$vault\daily","$vault\projects","$vault\research","$vault\archive","$vault\scripts","$vault\.claude\skills\vault-setup","$vault\.claude\skills\daily","$vault\.claude\skills\tldr","$vault\.claude\skills\file-intel" | Out-Null
Copy-Item "second-brain\CLAUDE.md","second-brain\memory.md" $vault
Copy-Item "second-brain\skills\vault-setup\SKILL.md" "$vault\.claude\skills\vault-setup\"
Copy-Item "second-brain\skills\daily\SKILL.md" "$vault\.claude\skills\daily\"
Copy-Item "second-brain\skills\tldr\SKILL.md" "$vault\.claude\skills\tldr\"
Copy-Item "second-brain\skills\file-intel\SKILL.md" "$vault\.claude\skills\file-intel\"
Copy-Item "second-brain\scripts\*" "$vault\scripts\"
Copy-Item "second-brain\.env.example" "$vault\.env"
# Also install skills globally (so they work in any folder):
$global = "$env:USERPROFILE\.claude\skills"
New-Item -ItemType Directory -Force -Path "$global\vault-setup","$global\daily","$global\tldr","$global\file-intel" | Out-Null
Copy-Item "second-brain\skills\vault-setup\SKILL.md" "$global\vault-setup\"
Copy-Item "second-brain\skills\daily\SKILL.md" "$global\daily\"
Copy-Item "second-brain\skills\tldr\SKILL.md" "$global\tldr\"
Copy-Item "second-brain\skills\file-intel\SKILL.md" "$global\file-intel\"

5. Install Python dependencies

pip install -r second-brain\requirements.txt

6. Add your Google API key

Open %USERPROFILE%\second-brain\.env in Notepad and replace your_key_here with your key from aistudio.google.com/apikey.

7. (Optional) Install Kepano's Obsidian Skills

$tmp = "$env:TEMP\obs-skills"
git clone --depth=1 https://github.com/kepano/obsidian-skills.git $tmp
Get-ChildItem "$tmp\skills" -Directory | ForEach-Object {
    $dest = "$env:USERPROFILE\second-brain\.claude\skills\$($_.Name)"
    New-Item -ItemType Directory -Force -Path $dest | Out-Null
    Copy-Item "$($_.FullName)\SKILL.md" "$dest\" -Force
}
Remove-Item $tmp -Recurse -Force

8. Open Claude Code in your vault

cd "$env:USERPROFILE\second-brain"
claude

Important Warnings

Obsidian Sync / Cloud Sync Users

If you use Obsidian Sync, iCloud, OneDrive, Dropbox, or any other cloud sync with your vault, you MUST exclude these folders from sync:

Exclude from sync	Why
`.claude/`	Contains Claude Code's skills, logs, and internal state. Syncing this can create a recursive feedback loop where Claude reads its own logs as vault content, causing massive file bloat and corrupted context.
`scripts/`	Python scripts that don't need to sync across devices
`.env`	Contains your API key — never sync credentials

How to exclude in Obsidian Sync:

Obsidian → Settings → Sync → Excluded folders → Add: .claude, scripts

How to exclude in iCloud/OneDrive/Dropbox: Add a .nosync file or move the folders to your sync tool's ignore list.

Real-world horror story: One community member synced their vault with their global .claude folder. It created a recursive loop where Claude replicated everything within that folder back into itself — corrupting the vault so badly it was unusable for three months. Keep your Obsidian vault and Claude configuration folders completely separate.

Vault vs Global Claude Config

These are two different things:

Path	What it is	Should Obsidian see it?
`~/second-brain/` (or wherever your vault is)	Your Obsidian vault + Second Brain	Yes — this is your vault
`~/.claude/` (or `%USERPROFILE%\.claude`)	Claude Code's global config, skills, memory	No — never point Obsidian or any sync tool here

Windows Troubleshooting

Errors like "Unexpected token '}'" or "Missing terminator"

This was a known issue with an earlier version of setup.ps1 that used PowerShell 7+ syntax. Windows ships with PowerShell 5.1 by default, which doesn't support certain escape codes. The latest version is fully compatible with PowerShell 5.1+.

The script is safe to re-run. Any steps that already completed (Obsidian installed, etc.) will be detected and skipped. Your existing vault files won't be touched.

Check your PowerShell version (optional):

$PSVersionTable.PSVersion

If you used the one-liner (most common), download the fixed script:

Invoke-WebRequest -Uri "https://raw.githubusercontent.com/earlyaidopters/second-brain/main/setup.ps1" -OutFile setup.ps1
powershell -ExecutionPolicy Bypass -File setup.ps1

This downloads the updated script — it replaces the broken one you downloaded before.

If you cloned the repo, pull the latest and re-run:

cd second-brain
git pull
powershell -ExecutionPolicy Bypass -File setup.ps1

After running, you should see Step 1/7 -- Checking winget with no errors. If you see that, the fix worked.

Python not found / pip not found

Windows can report Python as "installed" when only the Python Install Manager (py.exe) exists — which is just a launcher, not Python itself.

How to fix:

Download Python from python.org/downloads
On the very first screen of the installer, check "Add Python to PATH"
Complete the install
Close and reopen PowerShell (required for PATH changes to take effect)
Re-run the setup script

WSL gotcha: If Python is installed inside WSL (Windows Subsystem for Linux) but not as a native Windows app, PowerShell can't use it. You need native Windows Python.

py.exe shortcut: If you have the Python Install Manager, you can run py install 3.13 to install Python 3.13 through it. But if py isn't recognized either, go the python.org route.

'claude' is not recognized after installing Claude Code

After winget install Anthropic.ClaudeCode, the claude command won't be available in your current terminal session.

Fix: Close PowerShell completely and open a new window. The PATH update only takes effect in new sessions.

Script downloaded to wrong location

The one-liner downloads setup.ps1 to whatever folder PowerShell is currently in. If you get errors about missing files:

# Check where you are
Get-Location

# Option 1: clone the repo properly
git clone https://github.com/earlyaidopters/second-brain.git
cd second-brain
powershell -ExecutionPolicy Bypass -File setup.ps1

# Option 2: run from the folder where setup.ps1 was downloaded
cd C:\Users\YourName\wherever-you-downloaded-it
powershell -ExecutionPolicy Bypass -File setup.ps1

FAQ

Is my data private? Yes. Obsidian stores everything as local markdown files on your computer. Nothing is uploaded to any server. Claude Code processes your files locally in the folder you open it in. The only time anything leaves your machine is when you call the Gemini API to process existing files — and that's optional.

Do I need a paid Claude account? The free tier works for light use. For daily use with long sessions, Claude Pro ($20/month) gives substantially more usage than equivalent API costs in other tools.

What if I already have an Obsidian vault? Fully supported. See Already Have an Obsidian Vault? above. The script detects your existing vault, asks for confirmation, backs up your CLAUDE.md if present, and only adds the Second Brain components (skills, scripts, folder structure) without touching your existing notes, plugins, or themes.

Can I use this without the file processing? Absolutely. The Gemini API key and file processing are optional. The core system (Obsidian + Claude Code + CLAUDE.md + slash commands) works without it.

I use Obsidian Sync / iCloud / OneDrive — is that safe? Yes, but you must exclude .claude/, scripts/, and .env from sync. See Important Warnings above. Syncing the .claude/ folder can create a recursive loop that corrupts your vault.

I'm on Windows and get parsing errors when running the script This was a known issue with an earlier version. Pull the latest script (git pull) or download it fresh. See Windows Troubleshooting for details.

Can I use this from WSL? Yes. After setting up the vault on Windows, access it from WSL at /mnt/c/Users/YOUR_WINDOWS_USERNAME/second-brain. Obsidian (Windows app) and Claude Code (WSL) work on the same files — no sync needed.

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Repository files navigation

Quick Start

macOS

Windows

Already Have an Obsidian Vault?

Why This Exists

What Gets Installed

What the Setup Script Does

After Setup

1. Enable the Obsidian CLI

2. Open Claude Code in your vault

3. Run your first command

Slash Commands

Importing Existing Files

How the Memory Works

Requirements

Repository Structure

Manual Setup

macOS — Manual Steps

Windows — Manual Steps

Important Warnings

Obsidian Sync / Cloud Sync Users

Vault vs Global Claude Config

Windows Troubleshooting

FAQ

About

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Packages

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Contributors 2

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Name		Name	Last commit message	Last commit date
Latest commit History 25 Commits
scripts		scripts
skills		skills
vault-template		vault-template
.env.example		.env.example
.gitignore		.gitignore
CLAUDE.md		CLAUDE.md
README.md		README.md
banner.svg		banner.svg
memory.md		memory.md
requirements.txt		requirements.txt
setup.ps1		setup.ps1
setup.sh		setup.sh

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Quick Start

macOS

Windows

Already Have an Obsidian Vault?

Why This Exists

What Gets Installed

What the Setup Script Does

After Setup

1. Enable the Obsidian CLI

2. Open Claude Code in your vault

3. Run your first command

Slash Commands

Importing Existing Files

How the Memory Works

Requirements

Repository Structure

Manual Setup

macOS — Manual Steps

Windows — Manual Steps

Important Warnings

Obsidian Sync / Cloud Sync Users

Vault vs Global Claude Config

Windows Troubleshooting

FAQ

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