refactor: clean up file names and fix version management

- Renamed files to remove unnecessary suffixes:
  - tools-update.ts → tools.ts
  - server-update.ts → server.ts
  - http-server-fixed.ts → http-server.ts
- Created version utility to read from package.json as single source of truth
- Updated all imports across 21+ files
- Removed legacy files:
  - src/http-server.ts (legacy HTTP server with known issues)
  - src/utils/n8n-client.ts (unused legacy API client)
- Added n8n_diagnostic tool to help troubleshoot management tools visibility
- Added script to sync package.runtime.json version
- Fixed version mismatch issue (was hardcoded 2.4.1, now reads 2.7.0 from package.json)

This addresses GitHub issue #5 regarding version mismatch and provides better diagnostics for users.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/mcp/handlers-n8n-manager.ts

@@ -831,4 +831,108 @@ export async function handleListAvailableTools(): Promise<McpToolResponse> {
       ]
     }
   };
+}
+
+// Handler: n8n_diagnostic
+export async function handleDiagnostic(request: any): Promise<McpToolResponse> {
+  const verbose = request.params?.arguments?.verbose || false;
+  
+  // Check environment variables
+  const envVars = {
+    N8N_API_URL: process.env.N8N_API_URL || null,
+    N8N_API_KEY: process.env.N8N_API_KEY ? '***configured***' : null,
+    NODE_ENV: process.env.NODE_ENV || 'production',
+    MCP_MODE: process.env.MCP_MODE || 'stdio'
+  };
+  
+  // Check API configuration
+  const apiConfigured = n8nApiConfig !== null;
+  const apiClient = getN8nApiClient();
+  
+  // Test API connectivity if configured
+  let apiStatus = {
+    configured: apiConfigured,
+    connected: false,
+    error: null as string | null,
+    version: null as string | null
+  };
+  
+  if (apiClient) {
+    try {
+      const health = await apiClient.healthCheck();
+      apiStatus.connected = true;
+      apiStatus.version = health.n8nVersion || 'unknown';
+    } catch (error) {
+      apiStatus.error = error instanceof Error ? error.message : 'Unknown error';
+    }
+  }
+  
+  // Check which tools are available
+  const documentationTools = 22; // Base documentation tools
+  const managementTools = apiConfigured ? 16 : 0;
+  const totalTools = documentationTools + managementTools;
+  
+  // Build diagnostic report
+  const diagnostic: any = {
+    timestamp: new Date().toISOString(),
+    environment: envVars,
+    apiConfiguration: {
+      configured: apiConfigured,
+      status: apiStatus,
+      config: apiConfigured && n8nApiConfig ? {
+        baseUrl: n8nApiConfig.baseUrl,
+        timeout: n8nApiConfig.timeout,
+        maxRetries: n8nApiConfig.maxRetries
+      } : null
+    },
+    toolsAvailability: {
+      documentationTools: {
+        count: documentationTools,
+        enabled: true,
+        description: 'Always available - node info, search, validation, etc.'
+      },
+      managementTools: {
+        count: managementTools,
+        enabled: apiConfigured,
+        description: apiConfigured ? 
+          'Management tools are ENABLED - create, update, execute workflows' : 
+          'Management tools are DISABLED - configure N8N_API_URL and N8N_API_KEY to enable'
+      },
+      totalAvailable: totalTools
+    },
+    troubleshooting: {
+      steps: apiConfigured ? [
+        'API is configured and should work',
+        'If tools are not showing in Claude Desktop:',
+        '1. Restart Claude Desktop completely',
+        '2. Check if using latest Docker image',
+        '3. Verify environment variables are passed correctly',
+        '4. Try running n8n_health_check to test connectivity'
+      ] : [
+        'To enable management tools:',
+        '1. Set N8N_API_URL environment variable (e.g., https://your-n8n-instance.com)',
+        '2. Set N8N_API_KEY environment variable (get from n8n API settings)',
+        '3. Restart the MCP server',
+        '4. Management tools will automatically appear'
+      ],
+      documentation: 'For detailed setup instructions, see: https://github.com/czlonkowski/n8n-mcp#n8n-management-tools-new-v260---requires-api-configuration'
+    }
+  };
+  
+  // Add verbose debug info if requested
+  if (verbose) {
+    diagnostic['debug'] = {
+      processEnv: Object.keys(process.env).filter(key => 
+        key.startsWith('N8N_') || key.startsWith('MCP_')
+      ),
+      nodeVersion: process.version,
+      platform: process.platform,
+      workingDirectory: process.cwd()
+    };
+  }
+  
+  return {
+    success: true,
+    data: diagnostic
+  };
 }