Second Brain
A personal knowledge management and productivity system for Obsidian, combining:
- GTD (Getting Things Done) - Task and project management
- Zettelkasten - Atomic note-taking for knowledge building
- PARA Method - Folder organization (Projects, Areas, Resources, Archives)
Configuration (MEMORY-BASED)
CRITICAL FIRST STEP: Before any operation, check for configuration in Claude's Memory.
How Configuration Works
Configuration is stored in Claude's Memory feature and persists across all sessions automatically.
Why Memory? Skills in Claude Desktop run in a sandboxed environment with no file system access. Memory is the only way to persist configuration across sessions.
Once set up, Claude remembers:
- Your vault path
- Your name
- Whether setup is complete
- Your preferences
Configuration Check Flow
- Check Claude Memory for "Second Brain vault path"
- If found in Memory: Use the remembered vault path for all operations
- If NOT found in Memory: This is first-time setup - ask user for vault path
Checking Memory
At the start of ANY Second Brain operation, check if you remember the vault path:
Do I have the user's Second Brain vault path in my memory?
- If YES: Use that path for all operations
- If NO: Ask the user and save to memoryIf No Configuration Found (First Time)
Ask the user for their vault path:
Welcome to Second Brain!
I need to know where your Obsidian vault is located so I can save and organize your notes.
Please provide the full path to your Obsidian vault folder.
Examples:
- macOS: /Users/yourname/Documents/MyVault
- Windows: C:\Users\yourname\Documents\MyVault
- Linux: /home/yourname/Documents/MyVault
What's the path to your vault?Once you have the path:
- Save to Claude Memory: Remember the vault path for future sessions
- Run the full setup workflow to complete onboarding
- Save setup completion status to Memory
Claude Memory persists across ALL sessions automatically.
What Gets Saved to Memory
After setup, Claude should remember:
- Second Brain vault path: The absolute path to the user's Obsidian vault
- Second Brain user name: The user's name
- Second Brain setup complete: Whether full setup has been done
- Second Brain preferences: User preferences (proactive capture, inbox threshold)
If Configuration Exists in Memory
Use the remembered vault path for ALL file operations.
Claude Code Fallback
For Claude Code users only: If Memory is empty, you may also check for a legacy config file at ~/.second-brain/config.json. If found, migrate that configuration to Memory for future use.
Environment Variable Override
Environment variable SECOND_BRAIN_VAULT_PATH can override Memory (useful for testing).
Core Capabilities
1. Quick Capture
Trigger phrases: "capture this", "save this thought", "remember this", "note this down", "add to my inbox"
What it does: Instantly captures thoughts, tasks, or ideas to today's inbox without categorization.
GTD Principle: "Capture first, clarify later."
See: Capture Workflow
2. Daily Planning
Trigger phrases: "plan my day", "what should I work on", "daily planning", "morning planning"
What it does:
- Checks inbox (prompts to process if 5+ items)
- Scans all projects for next actions
- Asks about energy, context, time available
- Generates prioritized task list (must-do, should-do, quick-wins)
See: Daily Plan Workflow
3. Inbox Processing
Trigger phrases: "process my inbox", "organize my captures", "clarify my tasks", "GTD processing"
What it does:
- Asks clarifying questions for vague items (batched, not one-by-one)
- Routes actionable items to Projects/Areas
- Routes knowledge items to Permanent Notes
- Reviews all active projects
- Archives completed projects
4. Daily Closeout
Trigger phrases: "daily closeout", "review my day", "end of day review", "evening reflection"
What it does:
- Reads today's plan
- Asks what was accomplished
- Marks completed/partial/deferred items
- Asks about tomorrow's priorities
- Creates tomorrow's DRAFT plan
5. Setup & Configuration
Trigger phrases: "set up my second brain", "configure my vault", "second brain setup", "reconfigure"
What it does:
- First-time: Full interactive setup (goals, relationships, first project)
- Re-run: Update existing configuration
See: Setup Workflow
6. Excalidraw Diagrams
Trigger phrases: "create a diagram", "draw a flowchart", "make an excalidraw", "visualize this", "sketch this out", "diagram showing"
What it does:
- Creates
.excalidraw.mdfiles compatible with Obsidian Excalidraw plugin - Generates flowcharts, concept maps, system diagrams, mind maps
- Supports shapes (rectangles, ellipses, diamonds), arrows, lines, and text
- Full JSON structure with proper element properties
Output location: {{vaultPath}}/ (user specifies location or defaults to appropriate folder)
See: Excalidraw Reference
Proactive Capture
IMPORTANT: When you notice the user:
- Discovering valuable information during research
- Having insights or realizations
- Discussing ideas worth preserving
- Solving problems in interesting ways
Offer to capture:
That's an interesting insight about [topic]. Would you like me to capture this to your Second Brain?If they agree:
- Use the capture workflow
- Add context about where the insight came from
- Suggest relevant tags or connections
Vault Structure
The system uses PARA + Zettelkasten organization:
{{vaultPath}}/
├── 00-Inbox/
│ ├── Daily/ # Captures go here (YYYY-MM-DD.md)
│ └── Fleeting-Notes/ # Knowledge items during processing
├── 01-Projects/ # Multi-step outcomes with deadlines
├── 02-Areas/ # Ongoing responsibilities
│ ├── Career-Development.md
│ ├── Health-Fitness.md
│ ├── Personal-Development.md
│ ├── Errands.md
│ ├── Personal-Todos.md
│ └── Relationships/ # Individual notes per person
├── 03-Resources/
│ └── Reference-Notes/ # Summaries of external sources
├── 04-Archives/ # Completed/inactive projects
├── Daily Plans/ # Generated daily plans
├── Meeting Notes/ # Meeting documentation
├── Permanent Notes/ # Zettelkasten - synthesized insights
│ └── Assisting-User-Context.md # User's goals & context
└── Templates/ # Reusable templatesSee: PARA + Zettelkasten Guide
Unified Task Structure
ALL Projects, Areas, and Relationship notes use identical priority sections:
## High Priority / Critical
- Urgent/important items (scanned FIRST by daily planning)
## Next Actions / Current Tasks
- Regular priority items (scanned SECOND)
## Someday/Maybe
- Lower priority/exploratory (SKIPPED by daily planning)
## Waiting On
- Blocked by external dependencies
## Completed
- Finished tasks with datesTemplates
Use these templates when creating new notes:
| Template | Use When |
|---|---|
| project.md | Creating a new project (multi-step outcome) |
| area.md | Creating a new area of responsibility |
| permanent-note.md | Creating a Zettelkasten permanent note |
| fleeting-note.md | Quick knowledge capture for later processing |
| relationship.md | Tracking an important person |
| meeting-note.md | Meeting documentation |
| daily-plan.md | Daily execution plan |
| daily-inbox.md | Daily capture file |
| user-context.md | User goals and preferences |
| excalidraw-diagram.md | Visual diagrams and flowcharts |
Key References
- GTD Methodology - David Allen's Getting Things Done
- PARA + Zettelkasten - Folder organization
- Obsidian Mastery - Obsidian conventions
- Tagging Strategy - Tag taxonomy
- Excalidraw Diagrams - Visual diagrams and flowcharts
ADHD-Friendly Principles
The system is designed for users who may have ADHD:
- Read entire documents first - Understand existing structure
- Make targeted edits - Update specific sections, don't append
- Never just add to bottom - Unless explicitly asked
- Keep it concise - Remove redundancy
- One plan, not many - Replace old plans, don't add "revised" sections
Bad: Adding "REVISED PLAN" below "TODAY'S PLAN" Good: Replacing "TODAY'S PLAN" content with updated tasks
Daily Workflow Summary
The Complete Loop:
- Throughout day: Capture thoughts (30 sec each)
- 3x per week: Process inbox - Clarify + Organize (15 min)
- Every morning: Daily plan - Choose what to work on (5 min)
- Every evening: Daily closeout - Reflect + Prep tomorrow (5 min)
Total time: ~20-25 min/day + 45 min/week processing = Sustainable!
Examples
Example 1: Quick Capture
User: "Capture: Need to call the dentist and also research new project management tools"
You:
- Read config to get vault path
- Find/create today's inbox file at
{{vaultPath}}/00-Inbox/Daily/YYYY-MM-DD.md - Append the capture with timestamp
- Confirm: "Captured at 14:32. You have 3 captures today."
Example 2: Daily Planning
User: "What should I work on today?"
You:
- Check inbox count (process if 5+ items)
- Scan all projects in
01-Projects/for next actions - Ask: "How's your energy today? Any context constraints?"
- Generate prioritized list based on goals from user context
- Create/update
Daily Plans/YYYY-MM-DD.md
Example 3: Proactive Capture
During conversation about a topic:
You: "That insight about [topic] seems valuable. Would you like me to capture it to your Second Brain? I can add it to your inbox for later processing, or create a permanent note if it's already well-formed."
Tool Usage
Always use the vault path from Claude Memory for all operations.
Claude Desktop (with Filesystem Extension)
Claude Desktop requires the Filesystem Desktop Extension to read/write files. Once installed, these tools are available:
| Skill Operation | Filesystem Extension Tool |
|---|---|
| Read files | read_file |
| Write new files | write_file |
| Edit existing files | edit_file |
| Find files by pattern | list_directory + search_files |
| Create directories | create_directory |
Prerequisites for Claude Desktop:
- Install the Filesystem extension from the built-in extension store
- Grant access to your Obsidian vault folder when prompted
- Claude will then be able to read/write files in your vault
Claude Code
Claude Code has built-in file system access. These tools are available:
- Read - Check files, load context
- Write - Create new files
- Edit - Update existing files
- Glob - Find files by pattern
- Bash - Create directories, run commands
Capability Comparison
| Capability | Claude Desktop | Claude Code |
|---|---|---|
| File operations in vault | ✅ Yes (with extension) | ✅ Yes (built-in) |
| Claude Memory | ✅ Yes | ✅ Yes |
| Config file fallback | ❌ No | ✅ Yes |
| Bash commands | ❌ No | ✅ Yes |
Important: The skill is designed to work in BOTH environments:
- Configuration is stored in Claude Memory (works everywhere)
- File operations use the filesystem extension (Desktop) or built-in tools (Code)
Version History
Version 4.1 (2025-12-11)
- Switched to Claude Memory for configuration persistence
- Added Claude Desktop compatibility (sandboxed skills)
- Legacy config file fallback for Claude Code
Version 4.0 (2025-10-15)
- Unified skill architecture (single skill replaces multiple commands)
- Natural language triggers instead of slash commands
- Intelligent handling of existing Obsidian vaults
- Works in both Claude Code and Claude Desktop