Document Organizer MCP Server

A powerful Model Context Protocol (MCP) server for systematic document organization, PDF-to-Markdown conversion, and Universal Project Documentation Standard implementation.

Features

🔄 PDF Conversion Engine

• Dual Engine Support: marker (recommended) and pymupdf4llm
• Intelligent Table Preservation: Advanced table-aware cleaning
• Image Extraction: Optional embedded image extraction
• Memory Efficient: Configurable processing for large documents
• Auto-Cleaning: Removes marker formatting artifacts automatically

📊 Document Organization

• Recursive PDF Discovery: Comprehensive file system scanning
• Conversion Status Auditing: Track converted vs unconverted documents
• Intelligent Categorization: Keyword-based content analysis
• Automated Folder Organization: Category-based directory structures
• Full Workflow Automation: End-to-end document processing pipeline

📋 Universal Project Documentation Standard

• Standardized Structure: Consistent documentation across all projects
• Status-Driven Plans: ACTIVE, ARCHIVED, SUPERSEDED, BLOCKED statuses
• Weekly Progress Tracking: Automated handoff documentation
• Compliance Validation: Ensure adherence to documentation standards
• Template Generation: Project-specific documentation templates

Installation

npm install -g document-organizer-mcp

Dependencies

For PDF conversion functionality, install one or both engines:

# Marker (recommended for complex documents)
pip install marker-pdf

# pymupdf4llm (lightweight alternative)
pip install pymupdf4llm

Usage

MCP Configuration

Add to your MCP client configuration:

{
  "mcpServers": {
    "document-organizer": {
      "command": "document-organizer-mcp",
      "args": []
    }
  }
}

Available Tools

PDF Conversion Tools

• convert_pdf - Convert PDF to Markdown with configurable options
• check_dependency - Verify and optionally install conversion engines

Document Organization Tools

• document_organizer__discover_pdfs - Recursively find all PDF files
• document_organizer__check_conversions - Audit conversion status
• document_organizer__convert_missing - Convert only unconverted PDFs
• document_organizer__analyze_content - Categorize documents by content
• document_organizer__organize_structure - Create organized folder hierarchies
• document_organizer__full_workflow - Complete automation pipeline

Documentation Standard Tools

• document_organizer__init_project_docs - Initialize standard documentation structure
• document_organizer__validate_doc_structure - Validate compliance
• document_organizer__archive_plan - Archive development plans
• document_organizer__create_weekly_handoff - Generate progress reports

Examples

Basic PDF Conversion

// Convert a single PDF using marker engine
await client.callTool("convert_pdf", {
  pdf_path: "/path/to/document.pdf",
  output_path: "/path/to/output.md",
  options: {
    engine: "marker",
    auto_clean: true
  }
});

Full Document Organization Workflow

// Discover, convert, and organize all documents
await client.callTool("document_organizer__full_workflow", {
  directory_path: "/path/to/documents",
  analyze_content: true
});

Initialize Project Documentation

// Set up Universal Project Documentation Standard
await client.callTool("document_organizer__init_project_docs", {
  directory_path: "/path/to/project",
  project_name: "My Project",
  project_type: "web-app"
});

Configuration Options

PDF Conversion Options

interface ConversionOptions {
  engine?: "marker" | "pymupdf4llm";     // Conversion engine
  auto_clean?: boolean;                  // Auto-clean marker output
  page_chunks?: boolean;                 // Process as individual pages
  write_images?: boolean;                // Extract embedded images
  image_path?: string;                   // Image extraction directory
  table_strategy?: "fast" | "accurate";  // Table extraction strategy
  extract_content?: "text" | "figures" | "both"; // Content types
}

Document Categories

Automatic categorization supports:

• Research: Analysis, studies, investigations
• Planning: Strategies, roadmaps, discussions
• Documentation: Guides, manuals, references
• Technical: Implementation, architecture, APIs
• Business: Market analysis, commercial strategies
• General: Uncategorized content

Universal Project Documentation Standard

Required Files

• CURRENT_STATUS.md - Real-time project status
• ACTIVE_PLAN.md - Currently executing plan
• .claude-instructions.md - AI assistant instructions

Directory Structure

/docs/
├── plans/
│   ├── archived/     # Completed plans
│   └── superseded/   # Replaced plans
├── progress/YYYY-MM/ # Monthly progress logs
└── reference/        # Technical documentation
    ├── 01-architecture/
    ├── 02-apis/
    ├── 03-development/
    └── ...

Status Management

• ACTIVE: Currently executing plan
• ARCHIVED: Historical/completed plan
• SUPERSEDED: Replaced by newer plan
• BLOCKED: Waiting for external input

Development

# Clone repository
git clone https://github.com/cordlesssteve/document-organizer-mcp.git
cd document-organizer-mcp

# Install dependencies
npm install

# Build project
npm run build

# Run development mode
npm run dev

# Run tests
npm test

# Lint code
npm run lint

Performance Considerations

• Memory Efficiency: Use page_chunks: true for large PDFs
• Processing Speed: marker is slower but higher quality than pymupdf4llm
• Batch Processing: convert_missing tool optimizes bulk conversions
• Table Preservation: marker with auto-cleaning provides best table formatting

Error Handling

The server provides comprehensive error handling:

• Dependency validation before operations
• Graceful fallback between conversion engines
• Detailed error messages with context
• Progress tracking for long-running operations

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests for new functionality
5. Ensure all tests pass
6. Submit a pull request

License

MIT License - see LICENSE file for details.

Support

• Issues
• Discussions
• Wiki