# Clone with your preferred folder name (replace 'my-vault' with any name you like)
git clone https://github.com/heyitsnoah/claudesidian.git my-vault
cd my-vault

# Examples:
# git clone https://github.com/heyitsnoah/claudesidian.git obsidian-notes
# git clone https://github.com/heyitsnoah/claudesidian.git knowledge-base
# git clone https://github.com/heyitsnoah/claudesidian.git second-brain

Option B: Download ZIP (no Git required)

Click "Code" → "Download ZIP" on GitHub
Extract to your desired location
Open the folder in Claude Code

2. Run the Setup Wizard

# Start Claude Code in the directory
claude

# Run the interactive setup wizard (in Claude Code)
/init-bootstrap

This will:

Install dependencies automatically
Disconnect from the original claudesidian repository
Intelligently analyze your existing vault structure and patterns
Import your existing Obsidian vault safely to OLD_VAULT/ (if you have one)
Research your public work for personalized context (with your permission)
Ask you about your workflow preferences
Create a personalized CLAUDE.md configuration
Set up your folder structure
Optionally configure Gemini Vision for image/video analysis
Optionally configure Firecrawl for web research
Initialize Git for version control

3. Open in Obsidian (Optional but Recommended)

Download Obsidian
Open vault from the claudesidian folder
This gives you a visual interface alongside Claude Code

4. Your First Session

Tell Claude Code:

I'm starting a new project about [topic].
I'm in thinking mode, not writing mode.
Please search my vault for any relevant existing notes,
then help me explore this topic by asking questions.

Or use one of the pre-configured commands (in Claude Code):

/thinking-partner   # For collaborative exploration
/daily-review       # For end-of-day reflection
/research-assistant # For deep dives into topics

Folder Structure

claudesidian/
├── 00_Inbox/           # Temporary capture point for new ideas
├── 01_Projects/        # Active, time-bound initiatives
├── 02_Areas/           # Ongoing responsibilities
├── 03_Resources/       # Reference materials and knowledge base
├── 04_Archive/         # Completed projects and inactive items
├── 05_Attachments/     # Images, PDFs, and other files
├── 06_Metadata/        # Vault configuration and templates
│   ├── Reference/      # Documentation and guides
│   └── Templates/      # Reusable note templates
└── .scripts/           # Helper scripts for automation

Key Concepts

Thinking Mode vs Writing Mode

Thinking Mode (Research & Exploration):

Claude asks questions to understand your goals
Searches existing notes for relevant content
Helps make connections between ideas
Maintains a log of insights and progress

Writing Mode (Content Creation):

Generates drafts based on your research
Helps structure and edit content
Creates final deliverables

The PARA Method

Projects: Have a deadline and specific outcome

Example: "Q4 2025 Marketing Strategy"
Create a folder in 01_Projects/

Areas: Ongoing without an end date

Example: "Health", "Finances", "Team Management"
Lives in 02_Areas/

Resources: Topics of ongoing interest

Example: "AI Research", "Writing Tips"
Store in 03_Resources/

Archive: Inactive items

Completed projects with their outputs
Old notes no longer relevant

Essential Workflows

Starting a Research Project

Create project folder:

mkdir -p "01_Projects/My_New_Project/{Research,Chats,Daily_Progress}"

Tell Claude Code:

I'm starting a project on [topic] in 01_Projects/My_New_Project.
I'm in thinking mode. Help me explore this topic.

Let Claude search your vault and ask clarifying questions

Daily Capture

Create a daily note in 00_Inbox/
Dump thoughts, links, ideas throughout the day
Weekly: Process inbox items to appropriate folders

Synthesizing Research

Ask Claude Code:

Can you review all notes in [project folder] 
and create a synthesis of the key themes and insights?

Claude Code Commands

Pre-configured AI assistants ready to use:

thinking-partner - Explore ideas through questions
inbox-processor - Organize your captures
research-assistant - Deep dive into topics
daily-review - End of day reflection
weekly-synthesis - Find patterns in your week
create-command - Build new custom commands
de-ai-ify - Remove AI writing patterns from text
upgrade - Update to the latest claudesidian version
init-bootstrap - Re-run the setup wizard

Run with: /[command-name] in Claude Code

Staying Updated with `/upgrade`

Claudesidian automatically checks for updates when you start Claude Code and will remind you to run /upgrade when new features are available.

The upgrade command intelligently merges new features while preserving your customizations:

# Preview what would be updated (recommended first)
/upgrade check

# Run the interactive upgrade
/upgrade

# Skip confirmations for safe updates (advanced)
/upgrade force

What the upgrade does:

Creates a timestamped backup before making any changes
Shows you diffs for each file before updating
Preserves your personal notes and customizations
Only updates system files (commands, agents, scripts)
Never touches your content folders (00_Inbox, 01_Projects, etc.)
Provides rollback capability if needed

Safety features:

All your personal content is protected
Complete backup created in .backup/upgrade-[timestamp]/
File-by-file review and confirmation
Progress tracked in .upgrade-checklist.md
Can be stopped and resumed at any time

Vision & Document Analysis (Optional)

With Gemini MCP configured, you can:

Analyze images and screenshots
Extract text from PDFs
Compare multiple images
Generate smart filenames
Process documents

See .claude/mcp-servers/README.md for setup

Web Research (Optional)

With Firecrawl configured, you can save web content directly to your vault:

Save entire articles as markdown
Preserve content permanently
Make web research searchable
Build a research library

Tell Claude: "Save this article to my vault: [URL]" and it's done!

Helper Scripts

Run these with pnpm:

attachments:list - Show unprocessed attachments
attachments:organized - Count organized files
attachments:sizes - Find large files
attachments:orphans - Find unreferenced attachments
vault:stats - Show vault statistics

Advanced Setup

Git Integration

Initialize Git for version control:

git init
git add .
git commit -m "Initial vault setup"
git remote add origin your-repo-url
git push -u origin main

Best practices:

Commit after each work session
Use descriptive commit messages
Pull before starting work

Mobile Access

Set up a small server (mini PC, cloud VPS, or home server)
Install Tailscale for secure VPN access
Clone your vault to the server
Use Termius or similar SSH client on mobile
Run Claude Code remotely

Custom Commands

Create specialized commands by saving instructions in .claude/commands/:

Research Assistant (06_Metadata/Agents/research-assistant.md):

You are a research assistant.
- Search the vault for relevant information
- Synthesize findings from multiple sources
- Identify gaps in knowledge
- Suggest areas for further exploration

Tips & Best Practices

From Experience

Start in thinking mode: Resist the urge to generate content immediately
Be a token maximalist: More context = better results
Save everything: Capture chats, fragments, partial thoughts
Trust but verify: Always read AI-generated content
Break your flow: AI helps you resume easily

Common Patterns

The Daily Review:

What new notes were created today?
What connections can you see between today's work and my existing notes?

The Weekly Synthesis:

Review all notes from this week.
What are the key themes and insights?
What questions remain unanswered?

The Project Retrospective:

This project is complete.
Create a summary of what was learned and accomplished.
What should be archived vs kept accessible?

Troubleshooting

Claude Code can't find my notes

Make sure you're running Claude Code from the vault root directory
Check file permissions
Verify markdown files have .md extension

Git conflicts

Always pull before starting work
Commit frequently with clear messages
Use branches for experimental changes

Attachment management

Run npm run attachments:create-organized to set up folders
Use helper scripts to find orphaned files
Keep attachments under 10MB for Git

Philosophy

This setup is based on key principles:

AI amplifies thinking, not just writing
Local files = full control
Structure enables creativity
Iteration beats perfection
The goal is insight, not just information

Contributing

We welcome contributions from the community! This is a living template that gets better with everyone's input.

How to Contribute

Fork the repository on GitHub
Create a feature branch (git checkout -b feature/amazing-feature)
Make your changes
Test your changes to ensure everything works
Commit your changes (git commit -m 'Add amazing feature')
Push to the branch (git push origin feature/amazing-feature)
Open a Pull Request with a clear description of what you've done

What We're Looking For

New commands: Useful Claude Code commands for common workflows
New agents: Specialized agents for specific tasks
Documentation improvements: Better explanations, examples, or guides
Bug fixes: Found something broken? Fix it!
Workflow templates: Share your productive workflows
Helper scripts: Automation tools that make vault management easier
Integration guides: Connect Claudesidian with other tools
Core updates: Improvements to the upgrade system, setup wizard, or other core features

Guidelines

Keep commands focused and single-purpose
Write clear documentation with examples
Test thoroughly before submitting
Follow existing code style and structure
Update the CHANGELOG.md with your changes

Getting Updates

When new features are contributed and merged, users can easily get them with:

/upgrade

The upgrade command intelligently merges new features while preserving your personal customizations, making it easy to benefit from community contributions without losing your work.

Questions or Ideas?

Open an issue to discuss major changes before starting work
Join discussions in existing issues
Share your use cases - they help us understand needs better

Remember: best practices emerge from use, not theory. Your real-world experience makes this better for everyone!

Resources

Inspiration

This starter kit was inspired by the workflows discussed in:

How to Use Claude Code as a Second Brain - Noah Brier's interview with Dan Shipper
Built by the team at Alephic - an AI-first strategy and software partner that helps organizations solve complex challenges through custom AI systems

License

MIT - Use this however you want. Make it your own.

Remember: The bicycle feels wobbly at first, then you forget it was ever hard.

README.md

Claudesidian: Claude Code + Obsidian Starter Kit

What is this?

Quick Start

1. Get the Starter Kit