What can you do with this server?

The All-in-MCP server provides academic paper search, PDF processing, and GitHub repository access through a modular FastMCP architecture. Academic Paper Search - Search across IACR ePrint Archive, CryptoBib, Google Scholar, Crossref, and DBLP with filtering by year, conference, and other parameters PDF Management - Download PDFs from IACR ePrint Archive, extract text content from local or online PDFs with customizable page ranges GitHub Repository Tools - Retrieve directory structures, navigate specific paths, and read file contents from any GitHub repository Configuration & Integration - Configure modular backends through environment variables (APaper, GitHub-Repo-MCP), run as standalone servers or through a proxy, integrate with MCP clients like VSCode and Claude Code, and debug using MCP Inspector

Which integrations are available for this server?

Provides tools for accessing GitHub repository contents, including retrieving directory structures and file contents from repositories. Enables searching academic papers through Google Scholar with citation data across multiple disciplines.

How do I use All-in-MCP?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@All-in-MCP search for recent papers about post-quantum cryptography on IACR" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

All-in-MCP

A FastMCP-based Model Context Protocol (MCP) server providing academic paper search, web search, and PDF processing utilities. Features a modular architecture with both proxy and standalone server capabilities.

Paper Tools overview
Overview PDF

APaper Research Direction

Architecture

All-in-MCP uses a modern FastMCP architecture with three main components:

🔄 All-in-MCP Proxy Server: Main server that routes requests to academic tools and web search
📚 APaper Module: Isolated academic research server with specialized paper search tools
🔍 Qwen Search Module: Web search server powered by Qwen/Dashscope API with SSE-based MCP

This design provides better modularity, performance, and scalability.

Features

All servers expose search tools as FastMCP endpoints with automatic tool registration:

Available Tools

Category	Tool Name	Description	Backend
Academic Research	`apaper_search_iacr_papers`	Search academic papers from IACR ePrint Archive	APaper
	`apaper_download_iacr_paper`	Download PDF of an IACR ePrint paper	APaper
	`apaper_read_iacr_paper`	Read and extract text content from an IACR ePrint paper PDF	APaper
Bibliography Search	`apaper_search_dblp_papers`	Search DBLP computer science bibliography database	APaper
Cross-platform Search	`apaper_search_google_scholar_papers`	Search academic papers across disciplines with citation data	APaper
Web Search	`qwen_search_web_search`	Search the web using Qwen/Dashscope API	Qwen Search
GitHub Repository	`github-repo-mcp_getRepoAllDirectories`	Get all directories from a GitHub repository	GitHub-Repo-MCP
	`github-repo-mcp_getRepoDirectories`	Get directories from a specific path in GitHub repository	GitHub-Repo-MCP
	`github-repo-mcp_getRepoFile`	Get file content from GitHub repository	GitHub-Repo-MCP

All tools are implemented using FastMCP decorators with automatic registration, built-in validation, and enhanced error handling.

Quick Start

Video for Env Setup Video for Claude code
Overview PDF PDF for Claude code

Prerequisites

Python 3.10 or higher
pipx for Python package installation
npx for MCP Inspector (Node.js required)

Integration with MCP Clients

Add the servers to your MCP client configuration:

VSCode Configuration (.vscode/mcp.json)

{
  "servers": {
    "all-in-mcp": {
      "type": "stdio",
      "command": "pipx",
      "args": ["run", "all-in-mcp"],
      "env": {
        "APAPER": "true",
        "QWEN_SEARCH": "true",
        "DASHSCOPE_API_KEY": "your_api_key_here",
        "GITHUB_REPO_MCP": "true"
      }
    }
  }
}

Claude Code Configuration (.mcp.json)

{
  "mcpServers": {
    "all-in-mcp": {
      "type": "stdio",
      "command": "pipx",
      "args": ["run", "all-in-mcp"],
      "env": {
        "APAPER": "true",
        "QWEN_SEARCH": "true",
        "DASHSCOPE_API_KEY": "your_api_key_here",
        "GITHUB_REPO_MCP": "true"
      }
    }
  }
}

Server Options

The main proxy server supports multiple MCP backends through environment variables:

# Run with APaper academic tools enabled
APAPER=true pipx run all-in-mcp

# Run with Qwen Search web search enabled
QWEN_SEARCH=true DASHSCOPE_API_KEY=your_api_key_here pipx run all-in-mcp

# Run with GitHub repository tools enabled
GITHUB_REPO_MCP=true pipx run all-in-mcp

# Run with all backends enabled
APAPER=true QWEN_SEARCH=true DASHSCOPE_API_KEY=your_api_key_here GITHUB_REPO_MCP=true pipx run all-in-mcp

# Run standalone APaper server (academic tools only)
pipx run apaper

# Run standalone Qwen Search server (web search only)
DASHSCOPE_API_KEY=your_api_key_here pipx run qwen-search

Note: If you have the package installed globally, you can also run directly: all-in-mcp or qwen-search

Debugging & Testing

MCP Inspector

Use the official MCP Inspector to debug and test server functionality:

# Debug the main proxy server with APaper tools
APAPER=true npx @modelcontextprotocol/inspector pipx run all-in-mcp

# Debug with all backends enabled
APAPER=true GITHUB_REPO_MCP=true npx @modelcontextprotocol/inspector pipx run all-in-mcp

# Debug standalone APaper server
npx @modelcontextprotocol/inspector pipx run apaper

Local Development with uv

When developing locally, use uv run to debug specific MCP functions:

# Debug APaper server (academic tools)
npx @modelcontextprotocol/inspector uv run apaper

# Debug all-in-mcp proxy with APaper enabled
APAPER=true npx @modelcontextprotocol/inspector uv run all-in-mcp

# Debug all-in-mcp proxy with GitHub repo tools enabled
GITHUB_REPO_MCP=true npx @modelcontextprotocol/inspector uv run all-in-mcp

# Debug all-in-mcp with all backends enabled
APAPER=true QWEN_SEARCH=true DASHSCOPE_API_KEY=your_api_key_here GITHUB_REPO_MCP=true npx @modelcontextprotocol/inspector uv run all-in-mcp

# Debug Qwen Search server
DASHSCOPE_API_KEY=your_api_key_here npx @modelcontextprotocol/inspector uv run qwen-search

The MCP Inspector provides:

🔍 Interactive Tool Testing: Test all available tools with real parameters
📊 Server Information: View server capabilities and tool schemas
🐛 Debug Messages: Monitor server communication and error messages
⚡ Real-time Testing: Execute tools and see results immediately

Perfect for development, debugging, and understanding how the FastMCP tools work.

For development setup and contribution guidelines, see the Development Guide.

Quick Development Setup

# Clone the repository
git clone https://github.com/jiahaoxiang2000/all-in-mcp.git
cd all-in-mcp

# Install with development dependencies
uv sync --extra dev

# Run tests (now using unittest)
uv run python tests/test_fastmcp_server.py
uv run python tests/test_apaper_iacr.py
uv run python tests/test_apaper_pdf.py
uv run python tests/test_qwen_search.py

All-in-MCP

All-in-MCP

Architecture

Features

Available Tools

Quick Start

Prerequisites

Integration with MCP Clients

VSCode Configuration (.vscode/mcp.json)

Claude Code Configuration (.mcp.json)

Server Options

Debugging & Testing

MCP Inspector

Local Development with uv

Quick Development Setup

Resources

Tools

Latest Blog Posts

MCP directory API