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/http-server-single-session.ts

@@ -6,7 +6,7 @@
  */
 import express from 'express';
 import { StreamableHTTPServerTransport } from '@modelcontextprotocol/sdk/server/streamableHttp.js';
-import { N8NDocumentationMCPServer } from './mcp/server-update';
+import { N8NDocumentationMCPServer } from './mcp/server';
 import { ConsoleManager } from './utils/console-manager';
 import { logger } from './utils/logger';
 import dotenv from 'dotenv';