Successfully reorganized the AWS MCP Server codebase from a flat structure into a clean, modular nested folder architecture without altering any functionality.

src/
├── auth/                    # Authentication components
├── aws/                     # AWS client utilities  
├── mcp/                     # MCP protocol handlers
├── storage/                 # Storage abstractions
└── tools/                   # Tool definitions and handlers
    └── handlers/            # Individual tool handler implementations

• Moved AuthManager to src/auth/auth-manager.ts
• Handles token-to-namespace resolution and access control

• Extracted AWS client creation logic to src/aws/clients.ts
• Centralized credential management and client configuration

• Moved NamespacedKVStore to src/storage/kv-store.ts
• Moved NamespacedFilesStore to src/storage/files-store.ts
• Maintained all namespace isolation and multi-tenancy features

• Split MCP handler into two files:
  • src/mcp/handler.ts - Main request routing and tool orchestration
  • src/mcp/protocol-handlers.ts - Protocol-specific handlers (prompts, resources)

• Extracted tool definitions to src/tools/definitions.ts
• Created individual tool handler classes:
  • src/tools/handlers/kv-tools.ts - Key-value store operations
  • src/tools/handlers/files-tools.ts - File store operations
  • src/tools/handlers/code-tools.ts - Code execution functionality
• Added unified export in src/tools/handlers/index.ts

• Updated index.ts to use new import paths
• All internal imports now use relative paths within the src/ structure

• Deleted original flat structure files after confirming functionality
• Cleaned up temporary files

• Each component has a single, clear responsibility
• Related functionality is grouped together
• Easier to locate and modify specific features

• Individual components can be tested in isolation
• Clear interfaces between components
• Reduced coupling between modules

• New tools can be easily added to src/tools/handlers/
• New storage backends can be added to src/storage/
• New authentication methods can be added to src/auth/

• Logical grouping of related functionality
• Clear separation between protocol handling and business logic
• Consistent naming conventions and structure

✅ Server Functionality: All endpoints continue to work exactly as before ✅ Tool Operations: KV store, files store, and code execution all functional
✅ Authentication: Namespace isolation and bearer token auth working ✅ MCP Protocol: JSON-RPC requests and responses unchanged ✅ Error Handling: All error handling preserved

• All API endpoints remain identical
• All tool schemas and behaviors unchanged
• All authentication mechanisms preserved
• All namespace isolation maintained
• All AWS integrations continue to work

The refactoring was purely structural - improving code organization without affecting any external interfaces or functionality.