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
+  };
 }

src/mcp/index.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 
-import { N8NDocumentationMCPServer } from './server-update';
+import { N8NDocumentationMCPServer } from './server';
 import { logger } from '../utils/logger';
 
 // Add error details to stderr for Claude Desktop debugging
@@ -35,7 +35,7 @@ async function main() {
       // Check if we should use the fixed implementation
       if (process.env.USE_FIXED_HTTP === 'true') {
         // Use the fixed HTTP implementation that bypasses StreamableHTTPServerTransport issues
-        const { startFixedHTTPServer } = await import('../http-server-fixed');
+        const { startFixedHTTPServer } = await import('../http-server');
         await startFixedHTTPServer();
       } else {
         // HTTP mode - for remote deployment with single-session architecture

src/mcp/server.ts

@@ -7,7 +7,7 @@ import {
 } from '@modelcontextprotocol/sdk/types.js';
 import { existsSync } from 'fs';
 import path from 'path';
-import { n8nDocumentationToolsFinal } from './tools-update';
+import { n8nDocumentationToolsFinal } from './tools';
 import { n8nManagementTools } from './tools-n8n-manager';
 import { logger } from '../utils/logger';
 import { NodeRepository } from '../database/node-repository';
@@ -24,6 +24,7 @@ import { WorkflowValidator } from '../services/workflow-validator';
 import { isN8nApiConfigured } from '../config/n8n-api';
 import * as n8nHandlers from './handlers-n8n-manager';
 import { handleUpdatePartialWorkflow } from './handlers-workflow-diff';
+import { PROJECT_VERSION } from '../utils/version';
 
 interface NodeRow {
   node_type: string;
@@ -121,7 +122,7 @@ export class N8NDocumentationMCPServer {
         },
         serverInfo: {
           name: 'n8n-documentation-mcp',
-          version: '2.4.1',
+          version: PROJECT_VERSION,
         },
       };
       
@@ -261,6 +262,8 @@ export class N8NDocumentationMCPServer {
         return n8nHandlers.handleHealthCheck();
       case 'n8n_list_available_tools':
         return n8nHandlers.handleListAvailableTools();
+      case 'n8n_diagnostic':
+        return n8nHandlers.handleDiagnostic({ params: { arguments: args } });
         
       default:
         throw new Error(`Unknown tool: ${name}`);

src/mcp/stdio-wrapper.ts

@@ -40,7 +40,7 @@ console.count = () => {};
 console.countReset = () => {};
 
 // Import and run the server AFTER suppressing output
-import { N8NDocumentationMCPServer } from './server-update';
+import { N8NDocumentationMCPServer } from './server';
 
 async function main() {
   try {

src/mcp/tools-n8n-manager.ts

@@ -484,5 +484,18 @@ Validation example:
       type: 'object',
       properties: {}
     }
+  },
+  {
+    name: 'n8n_diagnostic',
+    description: `Diagnose n8n API configuration and management tools availability. Shows current configuration status, which tools are enabled/disabled, and helps troubleshoot why management tools might not be appearing. Returns detailed diagnostic information including environment variables, API connectivity, and tool registration status.`,
+    inputSchema: {
+      type: 'object',
+      properties: {
+        verbose: {
+          type: 'boolean',
+          description: 'Include detailed debug information (default: false)'
+        }
+      }
+    }
   }
 ];