Add working directory support for stdio MCP servers

[Dumbris]

Summary

• Add working_dir field to ServerConfig for stdio servers
• Implement working directory validation with proper error handling
• Extend upstream_servers tool to accept working_dir parameter for add/update operations
• Add comprehensive tests and documentation

Background

Resolves the issue where file-based MCP servers (like ast-grep-mcp, filesystem-mcp, git-mcp) operate from mcpproxy's directory instead of project directories when mcpproxy runs as a global daemon.

Changes Made

• Config: Added WorkingDir field to ServerConfig struct
• Validation: Added validateWorkingDir() function with directory existence checking
• Transport: Custom CommandFunc using mcp-go's WithCommandFunc option
• Management: Extended upstream_servers tool operations (add/update/patch)
• Testing: Comprehensive test suite in workingdir_test.go
• Documentation: Updated README.md and CLAUDE.md with examples

Example Usage

{
  "mcpServers": [
    {
      "name": "ast-grep-project-a",
      "command": "npx", 
      "args": ["ast-grep-mcp"],
      "working_dir": "/home/user/projects/project-a",
      "enabled": true
    }
  ]
}

Test Plan

• Unit tests for working directory validation
• Integration tests with Docker isolation
• Error handling for non-existent directories
• Backwards compatibility (empty working_dir)
• Tool management operations
• Linter and formatting checks

Backwards Compatibility

✅ Fully backwards compatible - empty/unspecified working_dir uses current directory (existing behavior)