deer-flow/backend/CLAUDE.md

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

DeerFlow is a LangGraph-based AI agent system with a full-stack architecture. The backend provides a "super agent" with sandbox execution capabilities that can execute code, browse the web, and manage files in isolated environments.

Architecture:

• LangGraph Server (port 2024): Agent runtime and workflow execution
• Gateway API (port 8001): REST API for models, MCP, skills, artifacts, and uploads
• Frontend (port 3000): Next.js web interface
• Nginx (port 2026): Unified reverse proxy entry point

Project Structure:

deer-flow/
├── Makefile                    # Root commands (check, install, dev, stop)
├── nginx.conf                  # Nginx reverse proxy configuration
├── config.yaml                 # Main application configuration
├── extensions_config.json      # MCP servers and skills configuration
├── backend/                    # Backend application (this directory)
│   ├── Makefile               # Backend-only commands (dev, gateway, lint)
│   ├── src/
│   │   ├── agents/            # LangGraph agents and workflows
│   │   ├── gateway/           # FastAPI Gateway API
│   │   ├── sandbox/           # Sandbox execution system
│   │   ├── tools/             # Agent tools
│   │   ├── mcp/               # MCP integration
│   │   ├── models/            # Model factory
│   │   ├── skills/            # Skills loading and management
│   │   ├── config/            # Configuration system
│   │   ├── community/         # Community tools (web search, etc.)
│   │   ├── reflection/        # Dynamic module loading
│   │   └── utils/             # Utilities
│   └── langgraph.json         # LangGraph server configuration
├── frontend/                   # Next.js frontend application
└── skills/                     # Agent skills directory
    ├── public/                # Public skills (committed)
    └── custom/                # Custom skills (gitignored)

Important Development Guidelines

Documentation Update Policy

CRITICAL: Always update README.md and CLAUDE.md after every code change

When making code changes, you MUST update the relevant documentation:

• Update README.md for user-facing changes (features, setup, usage instructions)
• Update CLAUDE.md for development changes (architecture, commands, workflows, internal systems)
• Keep documentation synchronized with the codebase at all times
• Ensure accuracy and timeliness of all documentation

Commands

Root directory (for full application):

# Check system requirements
make check

# Install all dependencies (frontend + backend)
make install

# Start all services (LangGraph + Gateway + Frontend + Nginx)
make dev

# Stop all services
make stop

Backend directory (for backend development only):

# Install backend dependencies
make install

# Run LangGraph server only (port 2024)
make dev

# Run Gateway API only (port 8001)
make gateway

# Lint
make lint

# Format code
make format

Architecture

Configuration System

The app uses a two-tier YAML/JSON-based configuration system.

Main Configuration (config.yaml):

Setup: Copy config.example.yaml to config.yaml in the project root directory.

# From project root (deer-flow/)
cp config.example.yaml config.yaml

Configuration priority:

1. Explicit config_path argument
2. DEER_FLOW_CONFIG_PATH environment variable
3. config.yaml in current directory (backend/)
4. config.yaml in parent directory (project root - recommended location)

Config values starting with $ are resolved as environment variables (e.g., $OPENAI_API_KEY).

Extensions Configuration (extensions_config.json):

MCP servers and skills are configured together in extensions_config.json in project root:

# From project root (deer-flow/)
cp extensions_config.example.json extensions_config.json

Configuration priority:

1. Explicit config_path argument
2. DEER_FLOW_EXTENSIONS_CONFIG_PATH environment variable
3. extensions_config.json in current directory (backend/)
4. extensions_config.json in parent directory (project root - recommended location)
5. For backward compatibility: mcp_config.json (will be deprecated)

Core Components

Gateway API (src/gateway/)

• FastAPI application that provides REST endpoints for frontend integration
• Endpoints:
  • /api/models - List available LLM models from configuration
  • /api/mcp - Manage MCP server configurations (GET, POST)
  • /api/skills - Manage skill configurations (GET, POST)
  • /api/threads/{thread_id}/artifacts/* - Serve agent-generated artifacts
  • /api/threads/{thread_id}/uploads - File upload, list, delete
• Works alongside LangGraph server, handling non-agent HTTP operations
• Proxied through nginx under /api/* routes (except /api/langgraph/*)

Agent Graph (src/agents/)

• lead_agent is the main entry point registered in langgraph.json
• Uses ThreadState which extends AgentState with:
  • sandbox: Sandbox environment info
  • artifacts: Generated file paths
  • thread_data: Workspace/uploads/outputs paths
  • title: Auto-generated conversation title
  • todos: Task tracking (plan mode)
  • viewed_images: Vision model image data
• Agent is created via make_lead_agent(config) with model, tools, middleware, and system prompt

Sandbox System (src/sandbox/)

• Abstract Sandbox base class defines interface: execute_command, read_file, write_file, list_dir
• SandboxProvider manages sandbox lifecycle: acquire, get, release
• SandboxMiddleware automatically acquires sandbox on agent start and injects into state
• LocalSandboxProvider is a singleton implementation for local execution
• AioSandboxProvider provides Docker-based isolation (in src/community/)
• Sandbox tools (bash, ls, read_file, write_file, str_replace) extract sandbox from tool runtime

Virtual Path System:

• Paths map between virtual and physical locations
• Virtual: /mnt/user-data/{workspace,uploads,outputs} - used by agent
• Physical: backend/.deer-flow/threads/{thread_id}/user-data/{workspace,uploads,outputs}
• Skills path: /mnt/skills maps to deer-flow/skills/

Model Factory (src/models/factory.py)

• create_chat_model() instantiates LLM from config using reflection
• Supports thinking_enabled flag with per-model when_thinking_enabled overrides
• Supports supports_vision flag for image understanding models

Tool System (src/tools/)

• Tools defined in config with use path (e.g., src.sandbox.tools:bash_tool)
• get_available_tools() resolves tool paths via reflection
• Built-in tools in src/tools/builtins/:
  • present_file_tool - Display files to users
  • ask_clarification_tool - Request clarification
  • view_image_tool - Vision model integration (conditional on model capability)
• Community tools in src/community/: Jina AI (web fetch), Tavily (web search), Firecrawl (scraping)
• Supports MCP (Model Context Protocol) for pluggable external tools

MCP System (src/mcp/)

• Integrates with MCP servers to provide pluggable external tools using langchain-mcp-adapters
• Uses MultiServerMCPClient from langchain-mcp-adapters for multi-server management
• Automatic initialization: Tools are loaded on first use with lazy initialization
• Supports both eager loading (FastAPI startup) and lazy loading (LangGraph Studio)
• initialize_mcp_tools() can be called in FastAPI lifespan handler for eager loading
• get_cached_mcp_tools() automatically initializes tools if not already loaded
• Each server can be enabled/disabled independently via enabled flag
• Support types: stdio (command-based), SSE, HTTP
• Built on top of langchain-ai/langchain-mcp-adapters for seamless integration

Reflection System (src/reflection/)

• resolve_variable() imports module and returns variable (e.g., module:variable)
• resolve_class() imports and validates class against base class

Skills System (src/skills/)

• Skills provide specialized workflows for specific tasks (e.g., PDF processing, frontend design)
• Located in deer-flow/skills/{public,custom} directory structure
• Each skill has a SKILL.md file with YAML front matter (name, description, license, allowed-tools)
• Skills are automatically discovered and loaded at runtime
• load_skills() scans directories and parses SKILL.md files
• Skills are injected into agent's system prompt with paths (only enabled skills)
• Path mapping system allows seamless access in both local and Docker sandbox
• Each skill can be enabled/disabled independently via enabled flag in extensions config

Middleware System (src/agents/middlewares/)

• Custom middlewares handle cross-cutting concerns
• Middlewares are registered in src/agents/lead_agent/agent.py with execution order:
  1. ThreadDataMiddleware - Initializes thread context (workspace, uploads, outputs paths)
  2. UploadsMiddleware - Processes uploaded files, injects file list into state
  3. SandboxMiddleware - Manages sandbox lifecycle, acquires on start
  4. SummarizationMiddleware - Reduces context when token limits approached (if enabled)
  5. TitleMiddleware - Generates conversation titles
  6. TodoListMiddleware - Tracks multi-step tasks (if plan_mode enabled)
  7. ViewImageMiddleware - Injects image details for vision models
  8. MemoryMiddleware - Automatic context retention and personalization (if enabled)
  9. ClarificationMiddleware - Handles clarification requests (must be last)

Memory System (src/agents/memory/)

• LLM-powered personalization layer that automatically extracts and stores user context across conversations
• Components:
  • updater.py - LLM-based memory updates with fact extraction and file I/O
  • queue.py - Debounced update queue for batching and performance optimization
  • prompt.py - Prompt templates and formatting utilities for memory updates
• MemoryMiddleware (src/agents/middlewares/memory_middleware.py) - Queues conversations for memory updates
• Gateway API (src/gateway/routers/memory.py) - REST endpoints for memory management
• Storage: JSON file at backend/.deer-flow/memory.json

Memory Data Structure:

• User Context (current state):
  • workContext - Work-related information (job, projects, technologies)
  • personalContext - Preferences, communication style, background
  • topOfMind - Current focus areas and immediate priorities
• History (temporal context):
  • recentMonths - Recent activities and discussions
  • earlierContext - Important historical context
  • longTermBackground - Persistent background information
• Facts (structured knowledge):
  • Discrete facts with categories: preference, knowledge, context, behavior, goal
  • Each fact includes: id, content, category, confidence (0-1), createdAt, source (thread ID)
  • Confidence threshold (default 0.7) filters low-quality facts
  • Max facts limit (default 100) keeps highest-confidence facts

Memory Workflow:

1. Post-Interaction: MemoryMiddleware filters messages (user inputs + final AI responses only) and queues conversation
2. Debounced Processing: Queue waits 30s (configurable), batches multiple updates, resets timer on new updates
3. LLM-Based Update: Background thread loads memory, formats conversation, invokes LLM to extract:
   • Updated context summaries (1-3 sentences each)
   • New facts with confidence scores and categories
   • Facts to remove (contradictions)
4. Storage: Applies updates atomically to memory.json with cache invalidation (mtime-based)
5. Injection: Next interaction loads memory, formats top 15 facts + context, injects into <memory> tags in system prompt

Memory API Endpoints (/api/memory):

• GET /api/memory - Retrieve current memory data
• POST /api/memory/reload - Force reload from file (invalidates cache)
• GET /api/memory/config - Get memory configuration
• GET /api/memory/status - Get both config and data

Config Schema

Models, tools, sandbox providers, skills, and middleware settings are configured in config.yaml:

• models[]: LLM configurations with use class path, supports_thinking, supports_vision
• tools[]: Tool configurations with use variable path and group
• tool_groups[]: Logical groupings for tools
• sandbox.use: Sandbox provider class path
• skills.path: Host path to skills directory (optional, default: ../skills)
• skills.container_path: Container mount path (default: /mnt/skills)
• title: Automatic thread title generation configuration
• summarization: Automatic conversation summarization configuration
• memory: Memory system configuration
  • enabled: Master switch (boolean)
  • storage_path: Path to memory.json file (relative to backend/)
  • debounce_seconds: Wait time before processing updates (default: 30)
  • model_name: LLM model for memory updates (null = use default model)
  • max_facts: Maximum facts to store (default: 100)
  • fact_confidence_threshold: Minimum confidence to store fact (default: 0.7)
  • injection_enabled: Inject memory into system prompt (boolean)
  • max_injection_tokens: Token limit for memory injection (default: 2000)

Extensions Configuration Schema (extensions_config.json):

• mcpServers: Map of MCP server name to configuration
  • enabled: Whether the server is enabled (boolean)
  • type: Transport type (stdio, sse, http)
  • command: Command to execute (for stdio type)
  • args: Arguments to pass to the command (array)
  • env: Environment variables (object with $VAR support)
  • description: Human-readable description
• skills: Map of skill name to state configuration
  • enabled: Whether the skill is enabled (boolean, default: true if not specified)

Both MCP servers and skills can be modified at runtime via API endpoints.

Development Workflow

Running the Full Application

From the project root directory:

make dev

This starts all services and makes the application available at http://localhost:2026.

Nginx routing:

• /api/langgraph/* → LangGraph Server (2024) - Agent interactions, threads, streaming
• /api/* (other) → Gateway API (8001) - Models, MCP, skills, artifacts, uploads
• / (non-API) → Frontend (3000) - Web interface

Running Backend Services Separately

For backend-only development, from the backend directory:

# Terminal 1: LangGraph server
make dev

# Terminal 2: Gateway API
make gateway

Direct access (without nginx):

• LangGraph: http://localhost:2024
• Gateway: http://localhost:8001

Frontend Configuration

The frontend uses environment variables to connect to backend services:

• NEXT_PUBLIC_LANGGRAPH_BASE_URL - Defaults to /api/langgraph (through nginx)
• NEXT_PUBLIC_BACKEND_BASE_URL - Defaults to empty string (through nginx)

When using make dev from root, the frontend automatically connects through nginx.

Key Features

File Upload

The backend supports multi-file upload with automatic document conversion:

• Endpoint: POST /api/threads/{thread_id}/uploads
• Supports: PDF, PPT, Excel, Word documents
• Auto-converts documents to Markdown using markitdown
• Files stored in thread-isolated directories
• Agent automatically receives uploaded file list via UploadsMiddleware

See docs/FILE_UPLOAD.md for details.

Plan Mode

Enable TodoList middleware for complex multi-step tasks:

• Controlled via runtime config: config.configurable.is_plan_mode = True
• Provides write_todos tool for task tracking
• Agent can break down complex tasks and track progress

See docs/plan_mode_usage.md for details.

Context Summarization

Automatic conversation summarization when approaching token limits:

• Configured in config.yaml under summarization key
• Trigger types: tokens, messages, or fraction of max input
• Keeps recent messages while summarizing older ones

See docs/summarization.md for details.

Vision Support

For models with supports_vision: true:

• ViewImageMiddleware processes images in conversation
• view_image_tool added to agent's toolset
• Images automatically converted and injected into state

Memory System

Persistent context retention and personalization across conversations:

• Automatic Extraction: LLM analyzes conversations to extract user context, facts, and preferences
• Structured Storage: Maintains user context, history, and confidence-scored facts in JSON format
• Smart Filtering: Only processes meaningful messages (user inputs + final AI responses)
• Debounced Updates: Batches updates to minimize LLM calls (configurable wait time)
• System Prompt Injection: Automatically injects relevant memory context into agent prompts
• Cache Optimization: File modification time-based cache invalidation for external edits
• Thread Safety: Locks protect queue and cache for concurrent access
• REST API: Full CRUD operations via /api/memory endpoints
• Frontend Integration: Memory settings page for viewing and managing memory data

Configuration: Controlled via memory section in config.yaml

• Enable/disable memory system
• Configure storage path, debounce timing, fact limits
• Control system prompt injection and token limits
• Set confidence thresholds for fact storage

Storage Location: backend/.deer-flow/memory.json

See configuration section for detailed settings.

Code Style

• Uses ruff for linting and formatting
• Line length: 240 characters
• Python 3.12+ with type hints
• Double quotes, space indentation

Documentation

See docs/ directory for detailed documentation:

• CONFIGURATION.md - Configuration options
• SETUP.md - Setup guide
• FILE_UPLOAD.md - File upload feature
• PATH_EXAMPLES.md - Path types and usage
• summarization.md - Context summarization
• plan_mode_usage.md - Plan mode with TodoList