hanzo-mcp 0.1.20__tar.gz

hanzo_mcp-0.1.20/LICENSE

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+MIT License
+
+Copyright (c) 2025 hanzoai
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hanzo_mcp-0.1.20/PKG-INFO

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+Metadata-Version: 2.4
+Name: hanzo-mcp
+Version: 0.1.20
+Summary: MCP implementation of Hanzo capabilities
+Author-email: hanzoai <sdglbl.me@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/hanzoai/mcp
+Project-URL: Bug Tracker, https://github.com/hanzoai/mcp/issues
+Project-URL: Documentation, https://github.com/hanzoai/mcp/blob/main/README.md
+Keywords: mcp,claude,hanzo,code,agent
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mcp>=1.3.0
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: uvicorn>=0.23.1
+Requires-Dist: openai>=1.50.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: litellm>=1.40.14
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: black>=23.3.0; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov>=4.1.0; extra == "test"
+Requires-Dist: pytest-mock>=3.10.0; extra == "test"
+Requires-Dist: pytest-asyncio>=0.25.3; extra == "test"
+Requires-Dist: twisted; extra == "test"
+Provides-Extra: performance
+Requires-Dist: ujson>=5.7.0; extra == "performance"
+Requires-Dist: orjson>=3.9.0; extra == "performance"
+Provides-Extra: publish
+Requires-Dist: twine>=4.0.2; extra == "publish"
+Requires-Dist: build>=1.0.3; extra == "publish"
+Dynamic: license-file
+
+# Hanzo MCP
+
+An implementation of Hanzo capabilities using the Model Context Protocol (MCP).
+
+## Overview
+
+This project provides an MCP server that implements Hanzo-like functionality, allowing Claude to directly execute instructions for modifying and improving project files. By leveraging the Model Context Protocol, this implementation enables seamless integration with various MCP clients including Claude Desktop.
+
+![example](./doc/example.gif)
+
+## Features
+
+- **Code Understanding**: Analyze and understand codebases through file access and pattern searching
+- **Code Modification**: Make targeted edits to files with proper permission handling
+- **Enhanced Command Execution**: Run commands and scripts in various languages with improved error handling and shell support
+- **File Operations**: Manage files with proper security controls through shell commands
+- **Code Discovery**: Find relevant files and code patterns across your project
+- **Project Analysis**: Understand project structure, dependencies, and frameworks
+- **Agent Delegation**: Delegate complex tasks to specialized sub-agents that can work concurrently
+- **Multiple LLM Provider Support**: Configure any LiteLLM-compatible model for agent operations
+- **Jupyter Notebook Support**: Read and edit Jupyter notebooks with full cell and output handling
+
+## Tools Implemented
+
+| Tool                   | Description                                                                                   |
+| ---------------------- | --------------------------------------------------------------------------------------------- |
+| `read_files`           | Read one or multiple files with encoding detection                                            |
+| `write_file`           | Create or overwrite files                                                                     |
+| `edit_file`            | Make line-based edits to text files                                                           |
+| `directory_tree`       | Get a recursive tree view of directories                                                      |
+| `get_file_info`        | Get metadata about a file or directory                                                        |
+| `search_content`       | Search for patterns in file contents                                                          |
+| `content_replace`      | Replace patterns in file contents                                                             |
+| `run_command`          | Execute shell commands (also used for directory creation, file moving, and directory listing) |
+| `run_script`           | Execute scripts with specified interpreters                                                   |
+| `script_tool`          | Execute scripts in specific programming languages                                             |
+| `project_analyze_tool` | Analyze project structure and dependencies                                                    |
+| `read_notebook`        | Extract and read source code from all cells in a Jupyter notebook with outputs                |
+| `edit_notebook`        | Edit, insert, or delete cells in a Jupyter notebook                                           |
+| `think`                | Structured space for complex reasoning and analysis without making changes                    |
+| `dispatch_agent`       | Launch one or more agents that can perform tasks using read-only tools concurrently           |
+
+## Getting Started
+
+For detailed installation and configuration instructions, please refer to [INSTALL.md](./doc/INSTALL.md).
+
+Of course, you can also read [USEFUL_PROMPTS](./doc/USEFUL_PROMPTS.md) for some inspiration on how to use hanzo-mcp.
+
+## Security
+
+This implementation follows best practices for securing access to your filesystem:
+
+- Permission prompts for file modifications and command execution
+- Restricted access to specified directories only
+- Input validation and sanitization
+- Proper error handling and reporting
+
+## Development
+
+To contribute to this project:
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Commit your changes (`git commit -m 'Add some amazing feature'`)
+4. Push to the branch (`git push origin feature/amazing-feature`)
+5. Open a Pull Request
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.

hanzo_mcp-0.1.20/README.md

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+# Hanzo MCP
+
+An implementation of Hanzo capabilities using the Model Context Protocol (MCP).
+
+## Overview
+
+This project provides an MCP server that implements Hanzo-like functionality, allowing Claude to directly execute instructions for modifying and improving project files. By leveraging the Model Context Protocol, this implementation enables seamless integration with various MCP clients including Claude Desktop.
+
+![example](./doc/example.gif)
+
+## Features
+
+- **Code Understanding**: Analyze and understand codebases through file access and pattern searching
+- **Code Modification**: Make targeted edits to files with proper permission handling
+- **Enhanced Command Execution**: Run commands and scripts in various languages with improved error handling and shell support
+- **File Operations**: Manage files with proper security controls through shell commands
+- **Code Discovery**: Find relevant files and code patterns across your project
+- **Project Analysis**: Understand project structure, dependencies, and frameworks
+- **Agent Delegation**: Delegate complex tasks to specialized sub-agents that can work concurrently
+- **Multiple LLM Provider Support**: Configure any LiteLLM-compatible model for agent operations
+- **Jupyter Notebook Support**: Read and edit Jupyter notebooks with full cell and output handling
+
+## Tools Implemented
+
+| Tool                   | Description                                                                                   |
+| ---------------------- | --------------------------------------------------------------------------------------------- |
+| `read_files`           | Read one or multiple files with encoding detection                                            |
+| `write_file`           | Create or overwrite files                                                                     |
+| `edit_file`            | Make line-based edits to text files                                                           |
+| `directory_tree`       | Get a recursive tree view of directories                                                      |
+| `get_file_info`        | Get metadata about a file or directory                                                        |
+| `search_content`       | Search for patterns in file contents                                                          |
+| `content_replace`      | Replace patterns in file contents                                                             |
+| `run_command`          | Execute shell commands (also used for directory creation, file moving, and directory listing) |
+| `run_script`           | Execute scripts with specified interpreters                                                   |
+| `script_tool`          | Execute scripts in specific programming languages                                             |
+| `project_analyze_tool` | Analyze project structure and dependencies                                                    |
+| `read_notebook`        | Extract and read source code from all cells in a Jupyter notebook with outputs                |
+| `edit_notebook`        | Edit, insert, or delete cells in a Jupyter notebook                                           |
+| `think`                | Structured space for complex reasoning and analysis without making changes                    |
+| `dispatch_agent`       | Launch one or more agents that can perform tasks using read-only tools concurrently           |
+
+## Getting Started
+
+For detailed installation and configuration instructions, please refer to [INSTALL.md](./doc/INSTALL.md).
+
+Of course, you can also read [USEFUL_PROMPTS](./doc/USEFUL_PROMPTS.md) for some inspiration on how to use hanzo-mcp.
+
+## Security
+
+This implementation follows best practices for securing access to your filesystem:
+
+- Permission prompts for file modifications and command execution
+- Restricted access to specified directories only
+- Input validation and sanitization
+- Proper error handling and reporting
+
+## Development
+
+To contribute to this project:
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Commit your changes (`git commit -m 'Add some amazing feature'`)
+4. Push to the branch (`git push origin feature/amazing-feature`)
+5. Open a Pull Request
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.

hanzo_mcp-0.1.20/hanzo_mcp/__init__.py

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+"""Hanzo MCP - Implementation of Hanzo capabilities using MCP."""
+
+__version__ = "0.1.8"

hanzo_mcp-0.1.20/hanzo_mcp/cli.py

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+"""Command-line interface for the Hanzo MCP server."""
+
+import argparse
+import json
+import os
+import sys
+from pathlib import Path
+from typing import Any, cast
+
+from hanzo_mcp.server import HanzoServer
+
+
+def main() -> None:
+    """Run the CLI for the Hanzo MCP server."""
+    parser = argparse.ArgumentParser(
+        description="MCP server implementing Hanzo capabilities"
+    )
+
+    _ = parser.add_argument(
+        "--transport",
+        choices=["stdio", "sse"],
+        default="stdio",
+        help="Transport protocol to use (default: stdio)",
+    )
+
+    _ = parser.add_argument(
+        "--name",
+        default="claude-code",
+        help="Name of the MCP server (default: claude-code)",
+    )
+
+    _ = parser.add_argument(
+        "--allow-path",
+        action="append",
+        dest="allowed_paths",
+        help="Add an allowed path (can be specified multiple times)",
+    )
+
+    _ = parser.add_argument(
+        "--project-dir", dest="project_dir", help="Set the project directory to analyze"
+    )
+    
+    _ = parser.add_argument(
+        "--agent-model",
+        dest="agent_model",
+        help="Specify the model name in LiteLLM format (e.g., 'openai/gpt-4o', 'anthropic/claude-3-sonnet')"
+    )
+    
+    _ = parser.add_argument(
+        "--agent-max-tokens",
+        dest="agent_max_tokens",
+        type=int,
+        help="Specify the maximum tokens for agent responses"
+    )
+    
+    _ = parser.add_argument(
+        "--agent-api-key",
+        dest="agent_api_key",
+        help="Specify the API key for the LLM provider (for development/testing only)"
+    )
+    
+    _ = parser.add_argument(
+        "--agent-max-iterations",
+        dest="agent_max_iterations",
+        type=int,
+        default=10,
+        help="Maximum number of iterations for agent (default: 10)"
+    )
+    
+    _ = parser.add_argument(
+        "--agent-max-tool-uses",
+        dest="agent_max_tool_uses",
+        type=int,
+        default=30,
+        help="Maximum number of total tool uses for agent (default: 30)"
+    )
+    
+    _ = parser.add_argument(
+        "--enable-agent-tool",
+        dest="enable_agent_tool",
+        action="store_true",
+        default=False,
+        help="Enable the agent tool (disabled by default)"
+    )
+
+    _ = parser.add_argument(
+        "--install",
+        action="store_true",
+        help="Install server configuration in Claude Desktop",
+    )
+
+    args = parser.parse_args()
+
+    # Cast args attributes to appropriate types to avoid 'Any' warnings
+    name: str = cast(str, args.name)
+    install: bool = cast(bool, args.install)
+    transport: str = cast(str, args.transport)
+    project_dir: str | None = cast(str | None, args.project_dir)
+    agent_model: str | None = cast(str | None, args.agent_model)
+    agent_max_tokens: int | None = cast(int | None, args.agent_max_tokens)
+    agent_api_key: str | None = cast(str | None, args.agent_api_key)
+    agent_max_iterations: int = cast(int, args.agent_max_iterations)
+    agent_max_tool_uses: int = cast(int, args.agent_max_tool_uses)
+    enable_agent_tool: bool = cast(bool, args.enable_agent_tool)
+    allowed_paths: list[str] = (
+        cast(list[str], args.allowed_paths) if args.allowed_paths else []
+    )
+
+    if install:
+        install_claude_desktop_config(name, allowed_paths)
+        return
+
+    # If no allowed paths are specified, use the current directory
+    if not allowed_paths:
+        allowed_paths = [os.getcwd()]
+
+    # If project directory is specified, add it to allowed paths
+    if project_dir and project_dir not in allowed_paths:
+        allowed_paths.append(project_dir)
+
+    # Run the server
+    server = HanzoServer(
+        name=name, 
+        allowed_paths=allowed_paths,
+        agent_model=agent_model,
+        agent_max_tokens=agent_max_tokens,
+        agent_api_key=agent_api_key,
+        agent_max_iterations=agent_max_iterations,
+        agent_max_tool_uses=agent_max_tool_uses,
+        enable_agent_tool=enable_agent_tool
+    )
+    # Transport will be automatically cast to Literal['stdio', 'sse'] by the server
+    server.run(transport=transport)
+
+
+def install_claude_desktop_config(
+    name: str = "claude-code", allowed_paths: list[str] | None = None
+) -> None:
+    """Install the server configuration in Claude Desktop.
+
+    Args:
+        name: The name to use for the server in the config
+        allowed_paths: Optional list of paths to allow
+    """
+    # Find the Claude Desktop config directory
+    home: Path = Path.home()
+
+    if sys.platform == "darwin":  # macOS
+        config_dir: Path = home / "Library" / "Application Support" / "Claude"
+    elif sys.platform == "win32":  # Windows
+        config_dir = Path(os.environ.get("APPDATA", "")) / "Claude"
+    else:  # Linux and others
+        config_dir = home / ".config" / "claude"
+
+    config_file: Path = config_dir / "claude_desktop_config.json"
+
+    # Create directory if it doesn't exist
+    config_dir.mkdir(parents=True, exist_ok=True)
+
+    # Get current script path
+    script_path: Path = Path(sys.executable)
+
+    # Create args array
+    args: list[str] = ["-m", "hanzo_mcp.cli"]
+
+    # Add allowed paths if specified
+    if allowed_paths:
+        for path in allowed_paths:
+            args.extend(["--allow-path", path])
+    else:
+        # Allow home directory by default
+        args.extend(["--allow-path", str(home)])
+
+    # Create config object
+    config: dict[str, Any] = {
+        "mcpServers": {name: {"command": str(script_path), "args": args}}
+    }
+
+    # Check if the file already exists
+    if config_file.exists():
+        try:
+            with open(config_file, "r") as f:
+                existing_config: dict[str, Any] = json.load(f)
+
+            # Update the existing config
+            if "mcpServers" not in existing_config:
+                existing_config["mcpServers"] = {}
+
+            existing_config["mcpServers"][name] = config["mcpServers"][name]
+            config = existing_config
+        except Exception as e:
+            print(f"Error reading existing config: {e}")
+            print("Creating new config file.")
+
+    # Write the config file
+    with open(config_file, mode="w") as f:
+        json.dump(config, f, indent=2)
+
+    print(f"Successfully installed {name} in Claude Desktop configuration.")
+    print(f"Config file: {config_file}")
+
+    if allowed_paths:
+        print("\nAllowed paths:")
+        for path in allowed_paths:
+            print(f"- {path}")
+    else:
+        print(f"\nDefault allowed path: {home}")
+    print("\nYou can modify allowed paths in the config file directly.")
+    print("Restart Claude Desktop for changes to take effect.")
+
+
+if __name__ == "__main__":
+    main()

hanzo_mcp-0.1.20/hanzo_mcp/server.py

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+"""MCP server implementing Hanzo capabilities."""
+
+from typing import Literal, cast, final
+
+from mcp.server.fastmcp import FastMCP
+
+from hanzo_mcp.tools import register_all_tools
+from hanzo_mcp.tools.common.context import DocumentContext
+from hanzo_mcp.tools.common.permissions import PermissionManager
+from hanzo_mcp.tools.project.analysis import ProjectAnalyzer, ProjectManager
+from hanzo_mcp.tools.shell.command_executor import CommandExecutor
+
+
+@final
+class HanzoServer:
+    """MCP server implementing Hanzo capabilities."""
+
+    def __init__(
+        self,
+        name: str = "claude-code",
+        allowed_paths: list[str] | None = None,
+        mcp_instance: FastMCP | None = None,
+        agent_model: str | None = None,
+        agent_max_tokens: int | None = None,
+        agent_api_key: str | None = None,
+        agent_max_iterations: int = 10,
+        agent_max_tool_uses: int = 30,
+        enable_agent_tool: bool = False,
+    ):
+        """Initialize the Hanzo server.
+
+        Args:
+            name: The name of the server
+            allowed_paths: list of paths that the server is allowed to access
+            mcp_instance: Optional FastMCP instance for testing
+            agent_model: Optional model name for agent tool in LiteLLM format
+            agent_max_tokens: Optional maximum tokens for agent responses
+            agent_api_key: Optional API key for the LLM provider
+            agent_max_iterations: Maximum number of iterations for agent (default: 10)
+            agent_max_tool_uses: Maximum number of total tool uses for agent (default: 30)
+            enable_agent_tool: Whether to enable the agent tool (default: False)
+        """
+        self.mcp = mcp_instance if mcp_instance is not None else FastMCP(name)
+
+        # Initialize context, permissions, and command executor
+        self.document_context = DocumentContext()
+        self.permission_manager = PermissionManager()
+
+        # Initialize command executor
+        self.command_executor = CommandExecutor(
+            permission_manager=self.permission_manager,
+            verbose=False,  # Set to True for debugging
+        )
+
+        # Initialize project analyzer
+        self.project_analyzer = ProjectAnalyzer(self.command_executor)
+
+        # Initialize project manager
+        self.project_manager = ProjectManager(
+            self.document_context, self.permission_manager, self.project_analyzer
+        )
+
+        # Add allowed paths
+        if allowed_paths:
+            for path in allowed_paths:
+                self.permission_manager.add_allowed_path(path)
+                self.document_context.add_allowed_path(path)
+
+        # Store agent options
+        self.agent_model = agent_model
+        self.agent_max_tokens = agent_max_tokens
+        self.agent_api_key = agent_api_key
+        self.agent_max_iterations = agent_max_iterations
+        self.agent_max_tool_uses = agent_max_tool_uses
+        self.enable_agent_tool = enable_agent_tool
+        
+        # Register all tools
+        register_all_tools(
+            mcp_server=self.mcp,
+            document_context=self.document_context,
+            permission_manager=self.permission_manager,
+            agent_model=self.agent_model,
+            agent_max_tokens=self.agent_max_tokens,
+            agent_api_key=self.agent_api_key,
+            agent_max_iterations=self.agent_max_iterations,
+            agent_max_tool_uses=self.agent_max_tool_uses,
+            enable_agent_tool=self.enable_agent_tool,
+        )
+
+    def run(self, transport: str = "stdio", allowed_paths: list[str] | None = None):
+        """Run the MCP server.
+
+        Args:
+            transport: The transport to use (stdio or sse)
+            allowed_paths: list of paths that the server is allowed to access
+        """
+        # Add allowed paths if provided
+        allowed_paths_list = allowed_paths or []
+        for path in allowed_paths_list:
+            self.permission_manager.add_allowed_path(path)
+            self.document_context.add_allowed_path(path)
+
+        # Run the server
+        transport_type = cast(Literal["stdio", "sse"], transport)
+        self.mcp.run(transport=transport_type)
+
+
+def main():
+    """Run the Hanzo MCP server."""
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description="MCP server implementing Hanzo capabilities"
+    )
+
+    _ = parser.add_argument(
+        "--name",
+        default="claude-code",
+        help="Name of the MCP server (default: claude-code)",
+    )
+
+    _ = parser.add_argument(
+        "--transport",
+        choices=["stdio", "sse"],
+        default="stdio",
+        help="Transport protocol to use (default: stdio)",
+    )
+
+    _ = parser.add_argument(
+        "--allow-path",
+        action="append",
+        dest="allowed_paths",
+        help="Add an allowed path (can be specified multiple times)",
+    )
+
+    args = parser.parse_args()
+
+    # Type annotations for args to avoid Any warnings
+    name: str = args.name
+    transport: str = args.transport
+    allowed_paths: list[str] | None = args.allowed_paths
+
+    # Create and run the server
+    server = HanzoServer(name=name, allowed_paths=allowed_paths)
+    server.run(transport=transport, allowed_paths=allowed_paths or [])
+
+
+if __name__ == "__main__":
+    main()

hanzo_mcp-0.1.20/hanzo_mcp/tools/__init__.py

@@ -0,0 +1,81 @@
+"""Tools package for Hanzo MCP.
+
+This package contains all the tools for the Hanzo MCP server.
+It provides a unified interface for registering all tools with an MCP server.
+
+This includes a "think" tool implementation based on Anthropic's research showing
+improved performance for complex tool-based interactions when Claude has a dedicated
+space for structured thinking. It also includes an "agent" tool that enables Claude
+to delegate tasks to sub-agents for concurrent execution and specialized processing.
+"""
+
+from mcp.server.fastmcp import FastMCP
+
+from hanzo_mcp.tools.agent import register_agent_tools
+from hanzo_mcp.tools.common import register_thinking_tool
+from hanzo_mcp.tools.common.context import DocumentContext
+from hanzo_mcp.tools.common.permissions import PermissionManager
+from hanzo_mcp.tools.filesystem import register_filesystem_tools
+from hanzo_mcp.tools.jupyter import register_jupyter_tools
+from hanzo_mcp.tools.project import register_project_tools
+from hanzo_mcp.tools.shell import register_shell_tools
+from hanzo_mcp.tools.shell.command_executor import CommandExecutor
+
+
+def register_all_tools(
+    mcp_server: FastMCP,
+    document_context: DocumentContext,
+    permission_manager: PermissionManager,
+    agent_model: str | None = None,
+    agent_max_tokens: int | None = None,
+    agent_api_key: str | None = None,
+    agent_max_iterations: int = 10,
+    agent_max_tool_uses: int = 30,
+    enable_agent_tool: bool = False,
+) -> None:
+    """Register all Hanzo tools with the MCP server.
+
+    Args:
+        mcp_server: The FastMCP server instance
+        document_context: Document context for tracking file contents
+        permission_manager: Permission manager for access control
+        agent_model: Optional model name for agent tool in LiteLLM format
+        agent_max_tokens: Optional maximum tokens for agent responses
+        agent_api_key: Optional API key for the LLM provider
+        agent_max_iterations: Maximum number of iterations for agent (default: 10)
+        agent_max_tool_uses: Maximum number of total tool uses for agent (default: 30)
+        enable_agent_tool: Whether to enable the agent tool (default: False)
+    """
+    # Register all filesystem tools
+    register_filesystem_tools(mcp_server, document_context, permission_manager)
+
+    # Register all jupyter tools
+    register_jupyter_tools(mcp_server, document_context, permission_manager)
+
+    # Register shell tools
+    register_shell_tools(mcp_server, permission_manager)
+
+    # Register project analysis tools
+    register_project_tools(
+        mcp_server, 
+        permission_manager, 
+        document_context, 
+        CommandExecutor(permission_manager)
+    )
+
+    # Register agent tools only if enabled
+    if enable_agent_tool:
+        register_agent_tools(
+            mcp_server, 
+            document_context, 
+            permission_manager,
+            CommandExecutor(permission_manager),
+            agent_model=agent_model,
+            agent_max_tokens=agent_max_tokens,
+            agent_api_key=agent_api_key,
+            agent_max_iterations=agent_max_iterations,
+            agent_max_tool_uses=agent_max_tool_uses
+        )
+    
+    # Initialize and register thinking tool
+    register_thinking_tool(mcp_server)