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>

package.json

@@ -12,7 +12,6 @@
     "start": "node dist/mcp/index.js",
     "start:http": "MCP_MODE=http node dist/mcp/index.js",
     "start:http:fixed": "MCP_MODE=http USE_FIXED_HTTP=true node dist/mcp/index.js",
-    "start:http:legacy": "MCP_MODE=http node dist/http-server.js",
     "http": "npm run build && npm run start:http:fixed",
     "dev": "npm run build && npm run rebuild && npm run validate",
     "dev:http": "MCP_MODE=http nodemon --watch src --ext ts --exec 'npm run build && npm run start:http'",
@@ -40,7 +39,8 @@
     "test:update-partial:debug": "node dist/scripts/test-update-partial-debug.js",
     "db:rebuild": "node dist/scripts/rebuild-database.js",
     "db:init": "node -e \"new (require('./dist/services/sqlite-storage-service').SQLiteStorageService)(); console.log('Database initialized')\"",
-    "docs:rebuild": "ts-node src/scripts/rebuild-database.ts"
+    "docs:rebuild": "ts-node src/scripts/rebuild-database.ts",
+    "sync:runtime-version": "node scripts/sync-runtime-version.js"
   },
   "repository": {
     "type": "git",