feat: Add MCP support for enhanced code assistance

[yunusgungor]

This PR introduces comprehensive MCP (Model
Context Protocol) support to enhance Codebuff's
code assistance capabilities. The implementation
includes:

Key Features Added

1. MCP Server Management System:

   • Implemented McpServerManager to handle MCP
     server lifecycle (initialization, startup,
     shutdown)
   • Added configuration loading from both
     workspace and global settings
   • Created server process management with
     proper error handling and cleanup

2. New Specialized Agents:

   • Context7 Documentation Expert Agent:
     Provides up-to-date, version-specific
     documentation and code examples by directly
     accessing library sources
   • Sequential Deep Thinker Agent: Uses MCP
     Sequential Thinking protocol for
     step-by-step analysis, revision, and
     synthesis of complex problems

3. MCP Tool Integration:

   • Added support for various MCP tools
     including Context7 library resolution and
     documentation fetching
   • Implemented filesystem operations through
     MCP protocol
   • Integrated sequential thinking capabilities
     for complex problem solving

4. CLI Enhancements:

   • Added MCP status command to show connected
     servers and available tools
   • Improved agent spawning with MCP tool
     awareness

Technical Implementation

The MCP support enables Codebuff to:

• Access real-time, accurate documentation
  directly from library sources
• Perform deep, step-by-step analysis of complex
  coding problems
• Maintain context across multiple tool
  interactions
• Provide more precise code suggestions and error
  resolution

This enhancement significantly improves the
development experience by offering more accurate,
context-aware assistance while reducing
hallucinations and outdated information issues
commonly found in AI coding assistants.

Benefits

• Enhanced Accuracy: Direct source documentation
  access eliminates outdated or incorrect
  information
• Improved Problem Solving: Sequential thinking
  capabilities for complex multi-step problems
• Better Context Understanding: Maintains
  conversation and code context across tool
  interactions
• Extensibility: Modular design allows for easy
  addition of new MCP servers and tools

This contribution aligns with Codebuff's goal of
providing deep customizability and leveraging the
latest AI capabilities to deliver superior
coding assistance.

[codebuff-team]

Thanks for contributing!

A few questions: Do you have an overview of how this works? How would a user use this?

Some preliminary notes:

The agents in the .agents directory are standalone (not integrated with our base agent).. Instead of uploading them to the repo, you should run codebuff publish [agent-name] to publish them to the agent store under your name.

Also, try to run the formatter on all the files, it looks like there are quite a few whitespace changes that don't conform to our formatter.