Claudesidian: Transform Obsidian into an AI-Powered Second Brain

If you're using both Obsidian for note-taking and Claude Code for coding, here's great news:

An open-source project called Claudesidian has perfectly integrated these two tools. Not just "using them together," but a complete solution with folder structure, workflows, custom commands, and automation scripts.

1300+ Stars, MIT licensed, ready to use out of the box.

This article shows you what Claudesidian is and how to use it to build a true "AI-powered second brain."

What is Claudesidian?

In One Sentence

Claudesidian = Pre-configured Obsidian Vault + Claude Code Integration Kit

It's not a plugin, but a complete Obsidian vault template optimized specifically for Claude Code.

Core Features

1. Folder Structure Based on PARA Method

claudesidian/
├── 00_Inbox/           # Inbox: Quick capture
├── 01_Projects/        # Projects: Time-bound tasks
├── 02_Areas/           # Areas: Ongoing responsibilities
├── 03_Resources/       # Resources: Reference materials
├── 04_Archive/         # Archive: Completed items
├── 05_Attachments/     # Attachments: Images, PDFs, etc.
└── 06_Metadata/        # Metadata: Templates and docs

The PARA method (Projects, Areas, Resources, Archive) is a proven knowledge management system, and Claudesidian has it built in.

2. Pre-configured Claude Code Commands

Run directly in Claude Code:

• /thinking-partner - AI thinking partner that helps you explore ideas through questions
• /inbox-processor - Automatically organize inbox content
• /research-assistant - Deep research assistant
• /daily-review - Daily review and reflection
• /weekly-synthesis - Weekly summary and pattern recognition
• /de-ai-ify - Remove AI writing patterns to make content more natural

3. Interactive Setup Wizard

After running /init-bootstrap, Claude Code will:

• Analyze your existing Obsidian vault structure
• Import your old notes (safely moved to OLD_VAULT/)
• Generate personalized config based on your public work (GitHub, Twitter, etc.)
• Ask about your workflow preferences
• Automatically create a customized CLAUDE.md config file

4. Optional Advanced Integrations

• Gemini Vision MCP: Claude Code can directly "see" images and PDFs

  • No need to describe screenshots, AI sees them directly
  • Batch process documents
  • Auto-generate filenames based on image content

• Firecrawl Web Research: Automatically scrape and save full web content to vault

  • Not summaries, but complete original text
  • Batch scrape multiple URLs
  • Convert to searchable Markdown

5. Automation Scripts

Built-in npm scripts:

npm run attachments:list        # List unprocessed attachments
npm run attachments:orphans     # Find unreferenced files
npm run vault:stats             # Show vault statistics
npm run firecrawl:scrape        # Scrape web pages to vault

Why Do You Need Claudesidian?

The Problem: Great Tools, Hard to Integrate

Using Obsidian Alone:

• Notes are well-written, but execution is manual
• Ideas are recorded, but implementation requires reorganization

Using Claude Code Alone:

• AI is powerful, but lacks structured knowledge input
• Have to re-describe context every time

What Claudesidian Solves:

• ✅ Obsidian notes directly become Claude Code input
• ✅ Claude Code can search and reference your entire knowledge base
• ✅ Complete workflow from idea capture to code implementation
• ✅ Automated daily tasks (organizing, reviewing, archiving)

Core Philosophy: Thinking Mode vs Writing Mode

Claudesidian emphasizes an important distinction:

Thinking Mode:

• AI helps you explore through questions
• Searches existing notes, makes connections
• Records insights and progress
• Goal: Deep understanding, no rush to output

Writing Mode:

• Generates content based on research
• Structures and edits
• Creates final deliverables
• Goal: High-quality output

Many people jump straight to writing mode when using AI, resulting in shallow output. Claudesidian's command system helps you think first, then create.

Quick Start

1. Get Claudesidian

Option A: Clone with Git

git clone https://github.com/heyitsnoah/claudesidian.git my-vault
cd my-vault

Option B: Download ZIP

1. Visit the GitHub repository
2. Click "Code" → "Download ZIP"
3. Extract to your desired location

2. Run Setup Wizard

# Start Claude Code
claude

# Run setup wizard in Claude Code
/init-bootstrap

What the wizard does:

1. Install dependencies - Auto npm install
2. Disconnect from origin - Detach from claudesidian repo, make it yours
3. Analyze existing structure - If you have an old Obsidian vault, analyzes patterns
4. Safely import old notes - Moved to OLD_VAULT/ for reference
5. Research your public work - With permission, analyzes your GitHub, Twitter, etc.
6. Ask workflow preferences - How do you use notes? What type of work?
7. Generate personalized config - Creates CLAUDE.md tailored to you
8. Configure optional integrations - Gemini Vision, Firecrawl
9. Initialize Git - Prepare for version control

3. Open in Obsidian (Optional but Recommended)

1. Download Obsidian
2. "Open folder as vault" → Select claudesidian directory
3. Now you have both visual interface + CLI experience

4. First Session

Try in Claude Code:

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

Or use pre-configured commands:

/thinking-partner    # Start thinking dialogue
/inbox-processor     # Organize inbox
/daily-review        # Daily review

Real-World Scenarios

Scenario 1: Explore Ideas with /thinking-partner

You quickly note in Obsidian:

# 00_Inbox/Idea - User Recommendation System.md

Want to add recommendation feature to product
- Based on user behavior
- Real-time recommendations
- Unsure: collaborative filtering or deep learning

Run in Claude Code:

/thinking-partner

Claude Code will:

1. Search your vault - Look for relevant notes

   • Finds 03_Resources/Machine-Learning/collaborative-filtering-notes.md
   • Finds 01_Projects/last-year-recommendation/summary.md

2. Start asking questions

   • "What format is your user behavior data currently in?"
   • "What's the response time requirement for real-time recommendations?"
   • "Does the team have machine learning experience?"

3. Make connections

   • "I see you did a similar project last year, what problems did you encounter?"
   • "Your collaborative filtering notes mention cold start issues, is that a concern this time?"

4. Record progress

   • Creates thinking log in 00_Inbox/
   • Extracts key decision points
   • Marks areas needing further research

Not giving direct answers, but helping you think deeply.

Scenario 2: Auto-organize with /inbox-processor

Your inbox is messy:

00_Inbox/
├── random-note.md
├── api-doc-links.md
├── bug-idea.md
├── book-notes-design-patterns.md
└── weekend-todos.md

Run:

/inbox-processor

Claude Code will:

1. Read all inbox content

2. Analyze each note's nature

   • "api-doc-links" → Project resource
   • "bug-idea" → Task to handle
   • "book-notes" → Knowledge resource
   • "weekend-todos" → Personal area todo

3. Suggest organization

   Suggested moves:
   - api-doc-links.md → 01_Projects/current-project/Resources/
   - bug-idea.md → 01_Projects/product-dev/Issues/
   - book-notes-design-patterns.md → 03_Resources/Programming/Design-Patterns/
   - weekend-todos.md → 02_Areas/Personal-Life/
   

4. Auto-move with consent

5. Clear inbox, keep it clean

Scenario 3: Deep Research with /research-assistant

You're doing technical selection:

# 01_Projects/new-project/tech-selection.md

Need to choose frontend framework
- React?
- Vue?
- Svelte?

Consider: team familiarity, ecosystem, performance, learning curve

Run:

/research-assistant

Topic: Frontend framework selection
Reference: 01_Projects/new-project/tech-selection.md

Claude Code will:

1. Search vault internal knowledge

   • Find previous framework usage experience
   • Find team skill records
   • Find performance test results

2. Propose research plan

   • Create comparison table framework
   • List research points
   • Provide information source suggestions

3. Assist information collection

   • If Firecrawl configured, can scrape official docs
   • Compare actual data from existing projects
   • Summarize pros and cons

4. Generate research report

   • Save to 01_Projects/new-project/research-reports/
   • Include data, analysis, recommendations
   • Facilitate future decisions

Scenario 4: Process Screenshots with Gemini Vision

You have a bunch of UI screenshots to organize:

05_Attachments/
├── screenshot-1.png
├── screenshot-2.png
├── screenshot-3.png
└── ...

After configuring Gemini Vision, in Claude Code:

Please analyze all screenshots in 05_Attachments/
and auto-rename and categorize based on content.

Claude Code will:

1. Directly "see" each image

   • screenshot-1.png → "Login page error message"
   • screenshot-2.png → "Dashboard performance chart"
   • screenshot-3.png → "Mobile responsive layout"

2. Auto-rename

   screenshot-1.png → login-error-message.png
   screenshot-2.png → dashboard-performance-chart.png
   screenshot-3.png → mobile-responsive-layout.png
   

3. Categorize

   05_Attachments/
   ├── UI-Bugs/
   │   └── login-error-message.png
   ├── Performance/
   │   └── dashboard-performance-chart.png
   └── Mobile/
       └── mobile-responsive-layout.png
   

4. Generate documentation

   • Create 03_Resources/UI-Issues.md
   • Auto-insert image references
   • Add issue descriptions

No manual description needed, AI sees and understands images directly.

Scenario 5: Batch Save Research with Firecrawl

You're researching a tech topic and found 10 good articles:

Create URL list:

# urls.txt
https://example.com/article-1
https://example.com/article-2
https://example.com/article-3
...

Run batch scrape:

npm run firecrawl:batch -- urls.txt "03_Resources/Tech-Research"

Result:

1. Full text scrape - Not summaries, complete articles
2. Convert to Markdown - Searchable, editable

3. Auto-save

   03_Resources/Tech-Research/
   ├── article-1.md
   ├── article-2.md
   └── article-3.md
   

4. Permanent archive - Even if webpage deleted, you have full backup in vault

Then in Claude Code:

Please analyze all articles in 03_Resources/Tech-Research/
and summarize key points and common patterns.

Claude Code can search and analyze thousands of saved articles without context limits.

Customize Your Workflow

Create Custom Commands

Claudesidian provides /create-command for quick command creation.

Example: Create /code-reviewer command

/create-command

Claude Code asks:

• Command name? code-reviewer
• Command purpose? Review code, find potential issues
• How it works? Check code style, performance, security

Generated command file:

.claude/commands/code-reviewer.md:

You are a professional code reviewer.

## Tasks
- Check code style and best practices
- Identify potential performance issues
- Recognize security vulnerabilities
- Provide improvement suggestions

## Workflow
1. Read user-specified code files
2. Check item by item: functionality, performance, security, maintainability
3. Generate review report, save to project's Reviews/ directory
4. List priority-sorted improvement suggestions

Usage:

/code-reviewer

Please review: src/auth/login.ts

Upgrades and Maintenance

Get Latest Features

Claudesidian continuously updates with community contributions.

Check updates:

/upgrade check

Run upgrade:

/upgrade

Upgrade process:

1. Create backup - Timestamped backup to .backup/upgrade-[timestamp]/
2. Show changes - Display diff file by file
3. Confirm updates - You decide whether to accept each change
4. Protect content - Never touches your notes (00-04 folders)
5. Update system only - Commands, scripts, configs, etc.

Safety features:

• Complete backup
• Rollback capability
• File-level confirmation
• Progress tracking (.upgrade-checklist.md)

Summary

Core Value of Claudesidian

1. Zero-Config Start

• No need to design folder structure from scratch
• No need to write Claude Code commands yourself
• Download and use, quick start

2. Best Practices Integrated

• PARA method (proven knowledge management system)
• Thinking mode vs writing mode (avoid shallow AI use)
• Automated workflows (reduce repetitive work)

3. Community-Driven

• 1300+ Stars, continuous updates
• Community contributes new commands and workflows
• /upgrade one-click to get new features

4. Full Control

• MIT open source, modify as you wish
• Local-first, data on your hard drive
• Git version control, never lose anything

Who Is It For?

Best for:

• Developers, researchers, knowledge workers
• Already using or want to use Obsidian
• Want AI to truly understand your knowledge base
• Need structured workflows

May not suit:

• Complete note-taking beginners (may need to familiarize with basics first)
• Those who dislike command-line tools
• Only need simple memos

Next Steps

Start today:

1. Clone Claudesidian

   git clone https://github.com/heyitsnoah/claudesidian.git my-vault
   cd my-vault
   

2. Run setup wizard

   claude
   /init-bootstrap
   

3. Try a command

   /thinking-partner
   
   Help me think through: [your question]
   

4. Build habits gradually

   • Week 1: Get used to inbox for idea capture
   • Week 2: Try /inbox-processor for organizing
   • Week 3: Establish daily/weekly reviews
   • Ongoing: Customize commands as needed

Remember: Tools assist thinking, not replace it.

Claudesidian's goal isn't to have AI complete all work for you, but to make AI a powerful partner in your thinking process—questioning, connecting, deepening, recording.

The distance from "I have an idea" to "I implemented it" should be as short as possible.

That's what Claudesidian is all about.

Related Resources:

• Claudesidian GitHub
• Obsidian Official
• Claude Code Documentation
• PARA Method Introduction
• How to Use Claude Code as a Thinking Partner (Podcast)