Init Bootstrap

Initialize Bootstrap Configuration

This command helps you create a personalized CLAUDE.md configuration file by asking questions about your Obsidian workflow and preferences.

Task

Read the CLAUDE-BOOTSTRAP.md template and interactively gather information about the user's:

• Existing vault structure (if any)
• Workflow preferences
• Note-taking style
• Organization methods
• Specific requirements

Then generate a customized CLAUDE.md file tailored to their needs.

Process

1. Initial Environment Setup

   • Get current date with date command for timestamps
   • Check current folder name and ask if they want to rename it
   • If yes, guide them through renaming (handle parent directory move)
   • Check for package.json and install dependencies:
     • Try pnpm install first (faster, better)
     • Fall back to npm install if pnpm not available
   • Verify core dependencies are installed
   • Check git status:
     • If no .git folder: Initialize git repository
     • If has remote origin: Ask about development work
       • Personal vault: Remove origin and .github folder
       • Contributing: Keep origin and workflows intact
     • If clean local repo: Ready to go
   • Don't create folders yet - wait until after asking about organization method

2. Check Existing Configuration

   • Look for existing CLAUDE.md
   • If exists, ask if they want to update or start fresh
   • Check for CLAUDE-BOOTSTRAP.md template

3. Gather Vault Information

   • Search common locations for existing Obsidian vaults (.obsidian folder)
   • Check these paths with appropriate depth limits:
     • ~/Documents (maxdepth 3) - all platforms
     • ~/Desktop (maxdepth 3) - all platforms
     • ~/Library/Mobile Documents/iCloud~md~obsidian/Documents (maxdepth 5 - macOS only, iCloud vaults)
     • Home directory ~/ (maxdepth 2) - all platforms
     • Current directory parent (maxdepth 2) - all platforms
   • If found, ask: "Found Obsidian vault at [path]. Is this the vault you want to import?"
   • Count files correctly: find [path] -type f -name "*.md" | wc -l (no depth limit)
   • Show vault size: du -sh [path]
   • If confirmed, analyze vault structure:
     • Run tree -L 3 -d [path] to see folder hierarchy
     • Sample 10-15 random notes to understand content types
     • List 30-50 recent file names to detect naming patterns
     • Check for daily notes folder and format
     • Identify most active folders by file count
     • Detect if using PARA, Zettelkasten, Johnny Decimal, or custom
   • If not the right one or none found:
     • On macOS only: Ask: "Is your vault stored in iCloud Drive? (yes/no)"
     • If yes (macOS): "Please enter the full path to your vault (e.g., /Library/Mobile Documents/iCloudmd~obsidian/Documents/YourVault)"
     • If no, or on Linux/Windows: "Please enter the path to your existing vault, or type 'skip' to start fresh"
     • Validate user-provided paths (see "User Path Validation" section below)
   • If no existing vault or user skips, they're starting fresh

4. Ask Configuration Questions

   • "What's your name?" (for personalization)
   • "Would you like me to research your public work to better understand your context?"
     • If yes: Search for information
     • ALWAYS show findings and ask "Is this correct?" for confirmation
     • If multiple people found, list them numbered for selection
     • If wrong person, offer to search again or skip
     • Save relevant context about their work, writing style, areas of expertise
   • "Do you follow the PARA method or have a different organization system?"
   • "What are your main use cases? (research, writing, project management, knowledge base, daily notes)"

   If using PARA, ask specific setup questions: PARA Method by Tiago Forte

   • "What active projects are you working on?" (Create folders in 01_Projects)
   • "What areas of responsibility do you maintain?" (e.g., Work, Health, Finance, Family)
   • "What topics do you research frequently?" (Set up in 03_Resources)
   • "Any projects you recently completed?" (Can archive with summaries)

   General preferences:

   • Check .obsidian/community-plugins.json to see what plugins they use
   • Analyze existing files to detect naming convention automatically
   • Check for attachments folder to see if they work with media files
   • "Do you use git for version control?"
   • "Any specific websites or resources you reference often?"
   • "Do you have any specific writing style preferences?"
   • "Are there any workflows or patterns you want Claude to follow?"
   • "Would you like a weekly review ritual? (e.g., Thursday project review)"
   • "Do you prefer 'thinking mode' (questions/exploration) vs 'writing mode'?"

5. Optional Tool Setup

   Gemini Vision (already included)

   • Ask: "Gemini Vision is already included for analyzing images, PDFs, and videos. Would you like to activate it? (yes/no/later)"
   • Explain: "You just need a free API key from Google. This lets Claude analyze any visual content in your vault."
   • If later: "No problem! You can set it up anytime by getting an API key from https://aistudio.google.com/apikey and adding GEMINI_API_KEY to your shell profile, then running claude mcp add --scope project gemini-vision node .claude/mcp-servers/gemini-vision.mjs."
   • If yes:
     • Guide to get API key from https://aistudio.google.com/apikey (free, takes 30 seconds)
     • Help add to shell profile (.zshrc, .bashrc, etc.)
     • Run claude mcp add --scope project gemini-vision node .claude/mcp-servers/gemini-vision.mjs
     • Configure .mcp.json with API key
     • Test the connection with a sample command

   Firecrawl (already included)

   • Ask: "Firecrawl is included for web research. Would you like to set it up? (yes/no/later)"
   • Explain: "This is a game-changer for research! When you find an article or website, you can save it directly to your vault as markdown - preserving the content forever, making it searchable, and letting Claude analyze it. Perfect for building a research library."
   • Example: "Just tell Claude: 'Save this article to my vault: [URL]' and it's done!"
   • If later: "You can set it up anytime by getting an API key from https://firecrawl.dev and configuring the scripts in .scripts/."
   • If yes:
     • Guide to get API key from https://firecrawl.dev (free tier available)
     • Help configure the scripts in .scripts/
     • Show example usage: .scripts/firecrawl-scrape.sh https://example.com

6. Generate Custom Configuration

   • Get current date: date +"%B %d, %Y" for the CLAUDE.md header
   • Save preferences to .claude/vault-config.json:

     {
       "user": {
         "name": "Jane Smith",
         "background": {
           "companies": ["Variance", "Percolate"],
           "roles": ["Co-founder", "Writer"],
           "publications": ["Why Is This Interesting?", "every.to"],
           "expertise": [
             "Developer tools",
             "Marketing tech",
             "Systems thinking"
           ],
           "interests": ["AI for thinking", "Note-taking systems", "Creativity"]
         },
         "profileSources": [
           "https://whyisthisinteresting.com/about",
           "https://every.to/@username"
         ],
         "customContext": "Focuses on AI as thinking augmentation, not just writing",
         "publicProfile": true
       },
       "vaultPath": "/path/to/existing/vault",
       "fileNamingPattern": "detected-pattern",
       "organizationMethod": "PARA",
       "primaryUses": ["research", "writing", "projects"],
       "tools": {
         "geminiVision": true,
         "firecrawl": false
       },
       "projects": ["Book - Productivity", "SaaS App"],
       "areas": ["Newsletter", "Health"],
       "importedAt": "2025-01-13",
       "lastUpdated": "2025-01-13"
     }

   • Start with CLAUDE-BOOTSTRAP.md as base
   • Add user-specific sections:
     • Custom folder structure with their actual projects/areas
     • Personal workflows
     • Preferred tools and scripts
     • Specific guidelines
     • MCP configuration if set up
   • Include their websites/resources if provided
   • Add any custom naming conventions
   • Pre-populate with their projects and areas:
     • Create project folders in 01_Projects/
     • Create area folders in 02_Areas/
     • Create resource topics in 03_Resources/
     • Add README files explaining each project/area

7. Import Existing Vault (if applicable)

   • If user has existing vault:
     • Create OLD_VAULT folder: mkdir OLD_VAULT
     • Copy entire vault preserving structure: cp -r [vault-path]/* ./OLD_VAULT/
     • Copy Obsidian configuration: cp -r [vault-path]/.obsidian ./
     • Check for and copy other important files:
       • .trash/ (Obsidian's trash folder)
       • .smart-connections/ (if using that plugin)
       • Any workspace files: .obsidian.vimrc, etc.
     • Skip copying: .git/ (they'll have their own), .claude/ (using ours)
     • Show summary: "Imported your vault to OLD_VAULT/ (X files, Y folders)"
     • Explain: "Your original structure is preserved in OLD_VAULT. You can gradually migrate files to the PARA folders as needed."

8. Create Supporting Files

   • Generate initial folder structure if new vault
   • Create README files for main folders
   • For each project folder, create subfolders:
     • Research/ (source materials)
     • Chats/ (AI conversations)
     • Daily Progress/ (running log)
   • Create 05_Attachments/Organized/ directory
   • Set up .gitignore if using git (include .mcp.json, node_modules)
   • Create initial templates if requested
   • Create WEEKLY_REVIEW.md if user wants review ritual
   • Remove FIRST_RUN marker file if it exists
   • Make initial git commit if repository was initialized

9. Run Test Commands

   • Execute pnpm vault:stats to verify scripts work
   • Test attachment commands if folders exist
   • Test MCP tools if configured
   • Verify git is tracking files correctly

10. Provide Next Steps

• Summary of what was created and configured
• Quick start guide specific to their setup
• List of available commands they can use
• Test commands to verify everything works
• Suggestions for first tasks based on their use cases
• How to modify configuration later

Example Output

# Your Obsidian Vault Configuration

Generated on: [Run `date +"%B %d, %Y"` to get current date] Last updated: [Same
date] Based on your preferences for: [main use cases] Setup completed with: ✅
Dependencies ✅ Folder structure ✅ Git initialized

## Your Custom Folder Structure

[Their specific structure with explanations]

## Your Workflows

### Daily Routine

[Based on their answers]

### Project Management

[Their specific approach]

### Research Method (Noah Brier Style)

- Capture everything you read
- Let important ideas naturally resurface
- Start with writing to test understanding
- Use search, not tags, to find things
- [Learn more from Noah's system](https://every.to/superorganizers/ceo-by-day-internet-sleuth-by-night-267452)

### Weekly Review Ritual

[If enabled: Every Thursday at 4pm, review all projects]

## Your Preferences

### File Naming

- Pattern: [their convention]
- Examples: [specific examples]

### Tools & Scripts

[Relevant scripts for their workflow]

## MCP Servers (if configured)

### Gemini Vision

- Status: ✅ Configured and tested
- API Key: Set in .mcp.json
- Test with: `Use gemini-vision to analyze [image path]`

## Available Commands

### Vault Management

- `pnpm vault:stats` - Show vault statistics
- `pnpm attachments:list` - List unprocessed attachments
- `pnpm attachments:organized` - Count organized files

### Claude Skills

Skills auto-discover when you describe the task. Examples:

- "Help me think through X" → `thinking-partner`
- "Wrap up my day" / "daily review" → `daily-review`
- "Process my inbox" → `inbox-processor`
- "Re-run the setup wizard" → `init-bootstrap`

Skills live in `.agents/skills/` (canonical) with symlinks in `.claude/skills/`
and `.pi/skills/`. They work in Claude Code, OpenCode, Codex, Cursor, and Pi.

## Quick Start

1. [Personalized first step]
2. [Next action based on their goals]
3. [Specific to their workflow]

## Pro Tips from Research Masters

- **Be a token maximalist**: Provide lots of context to Claude
- **Writing scales**: Document everything for future reference
  ([Noah Brier](https://every.to/superorganizers/ceo-by-day-internet-sleuth-by-night-267452))
- **Trust emergence**: Important ideas will keep surfacing
- **Start with writing**: Always begin projects in text form
- **Review regularly**: Set aside time weekly to prune and update
- **PARA Method**: Projects, Areas, Resources, Archive
  ([Tiago Forte](https://fortelabs.com/blog/para/))

## Setup Summary

✅ Dependencies installed (pnpm/npm) ✅ Folder structure created ✅ Git
repository initialized and disconnected from original ✅ CLAUDE.md personalized
✅ First-run setup completed [✅ MCP Gemini Vision configured - if set up] [✅
First commit made - if git was initialized]

Important Implementation Notes

Handling Multiple Vaults

When multiple vaults are detected:

1. Always list all vaults found with clear numbering and details
2. Require explicit selection - don't assume which vault to use
3. Confirm the selection before proceeding with import
4. Handle ambiguous responses - if user provides unclear input (like pasting a screenshot), ask for clarification:
   • "I see you've shared a screenshot. Could you please type the number (1-3) of the vault you'd like to import?"
   • "I need a clear selection. Please type '1', '2', or '3' to choose a vault, or 'skip' to start fresh."

Never Proceed Without Clear Confirmation

If the user's response is unclear:

• Don't guess or assume
• Ask for explicit confirmation
• Provide clear options again
• Example: "I want to make sure I import the right vault. Please type the number of your choice (1, 2, or 3)."

Platform Compatibility

This command is designed to work across Linux, macOS, and Windows (WSL/Git Bash), with platform-specific features:

All Platforms:

• Search ~/Documents, ~/Desktop, home directory
• Standard Obsidian vault detection
• Full vault import and setup

macOS Only:

• iCloud Drive vault detection and import
• Obsidian's iCloud sync is macOS-only, so iCloud features are disabled on other platforms

Platform Detection:

# Check platform
if [[ "$OSTYPE" == "darwin"* ]]; then
  # macOS - enable iCloud features
  PLATFORM="macOS"
  ICLOUD_SUPPORTED=true
elif [[ "$OSTYPE" == "linux-gnu"* ]]; then
  # Linux
  PLATFORM="Linux"
  ICLOUD_SUPPORTED=false
elif [[ "$OSTYPE" == "msys" || "$OSTYPE" == "cygwin" ]]; then
  # Windows (Git Bash or WSL)
  PLATFORM="Windows"
  ICLOUD_SUPPORTED=false
fi

iCloud Vault Search Implementation

When searching for vaults, use this find command pattern:

# Standard locations (shallow search)
# Note: 2>/dev/null suppresses expected permission errors from system directories
# If no vaults are found, we'll ask the user for their vault path
find ~/Documents ~/Desktop -maxdepth 3 -type d -name ".obsidian" 2>/dev/null

# iCloud location (deeper search needed due to nested structure)
# Only search on macOS
if [[ "$OSTYPE" == "darwin"* ]]; then
  find ~/Library/Mobile\ Documents/iCloud~md~obsidian/Documents -maxdepth 5 -type d -name ".obsidian" 2>/dev/null
fi

# Home directory (shallow to avoid deep recursion)
find ~ -maxdepth 2 -type d -name ".obsidian" 2>/dev/null

The iCloud path requires:

• Higher maxdepth (5) due to nested folder structure
• Escaped spaces in path name
• Silent error handling (2>/dev/null) as many users won't have iCloud
• Platform check (macOS only)

Error Handling Note: Permission errors are suppressed (2>/dev/null) because they're expected when searching system directories. If no vaults are found, the script gracefully prompts the user for their vault path.

User Path Validation

When users manually provide a vault path, validate it thoroughly with helpful error messages:

# User provided path
USER_PATH="$1"

# Expand tilde and resolve to absolute path
USER_PATH="${USER_PATH/#\~/$HOME}"
REAL_PATH=$(realpath "$USER_PATH" 2>/dev/null)

# Validation 1: Path exists
if [ -z "$REAL_PATH" ]; then
  echo "❌ Error: Path does not exist: $USER_PATH"
  echo ""
  echo "💡 Suggestions:"
  echo "   • Check for typos in the path"
  echo "   • Make sure you're using the full path (e.g., /Users/name/vault)"
  echo "   • You can use ~ for your home directory (e.g., ~/Documents/vault)"
  exit 1
fi

# Validation 2: Is a directory
if [ ! -d "$REAL_PATH" ]; then
  echo "❌ Error: Not a directory: $REAL_PATH"
  echo ""
  echo "💡 The path exists but points to a file, not a folder."
  exit 1
fi

# Validation 3: Contains .obsidian folder
if [ ! -d "$REAL_PATH/.obsidian" ]; then
  echo "❌ Error: Not a valid Obsidian vault (no .obsidian folder)"
  echo "   Looking in: $REAL_PATH"
  echo ""
  echo "💡 Suggestions:"
  echo "   • Make sure the path points to your vault root (not a subfolder)"
  echo "   • Check that you've opened this vault in Obsidian at least once"
  echo "   • Try the path without trailing slash"
  echo "   • For iCloud: ~/Library/Mobile Documents/iCloud~md~obsidian/Documents/YourVault"
  exit 1
fi

# Validation 4: Readable permissions
if [ ! -r "$REAL_PATH/.obsidian" ]; then
  echo "❌ Error: Cannot read vault directory (permission denied)"
  echo "   Path: $REAL_PATH"
  echo ""
  echo "💡 You may need to:"
  echo "   • Check file permissions with: ls -la \"$REAL_PATH\""
  echo "   • Make sure you own this directory"
  exit 1
fi

# Show resolved path if different from input
if [ "$USER_PATH" != "$REAL_PATH" ]; then
  echo "✓ Resolved path: $REAL_PATH"
fi

# Valid vault path
VAULT_PATH="$REAL_PATH"
echo "✓ Valid Obsidian vault found"

This validation:

• Expands ~ to home directory properly
• Resolves symlinks and relative paths to absolute paths
• Checks all essential requirements (exists, is directory, has .obsidian, readable)
• Provides helpful, actionable error messages with suggestions
• Shows the resolved path so users understand what's being checked
• Trusts users (allows symlinks, paths outside home directory)
• Cross-platform compatible (works on Linux, macOS, Windows/WSL)

iCloud Sync State Checking

When a user selects an iCloud vault, check sync state and warn if needed:

# After user confirms vault selection
if [[ "$OSTYPE" == "darwin"* ]] && [[ "$vault_path" == *"iCloud"* ]]; then
  # Check for common iCloud sync indicators
  if [ -f "$vault_path/.icloud" ] || [ -f "$vault_path/.obsidian/.icloud" ]; then
    echo ""
    echo "📱 iCloud Sync Notice:"
    echo "   This vault appears to be still downloading from iCloud."
    echo "   For best results, open it in Obsidian first to ensure files are synced."
    echo ""
    read -p "Continue anyway? (yes/no): " sync_answer
    if [[ ! "$sync_answer" =~ ^[Yy] ]]; then
      echo "No problem! Open the vault in Obsidian, then re-run /init-bootstrap"
      exit 0
    fi
  else
    echo ""
    echo "📱 iCloud vault detected. If import seems incomplete, make sure sync is complete."
    echo ""
  fi
fi

This provides a soft warning that:

• Only runs on macOS for iCloud paths
• Checks for placeholder files that indicate incomplete download
• Asks for confirmation if sync issues detected
• Gives gentle reminder even when no issues found
• Lets users proceed if they choose