fix: ensure MCP and skills config changes are immediately reflected

- Use ExtensionsConfig.from_file() instead of cached config to always
  read latest configuration from disk in LangGraph Server
- Add mtime-based cache invalidation for MCP tools to detect config
  file changes made through Gateway API
- Call reload_extensions_config() in Gateway API after updates to
  refresh the global cache
- Remove unnecessary MCP initialization from Gateway startup since
  MCP tools are only used by LangGraph Server

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

backend/src/gateway/app.py

@@ -23,13 +23,10 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     config = get_gateway_config()
     logger.info(f"Starting API Gateway on {config.host}:{config.port}")
 
-    # Initialize MCP tools at startup
-    try:
-        from src.mcp import initialize_mcp_tools
-
-        await initialize_mcp_tools()
-    except Exception as e:
-        logger.warning(f"Failed to initialize MCP tools: {e}")
+    # NOTE: MCP tools initialization is NOT done here because:
+    # 1. Gateway doesn't use MCP tools - they are used by Agents in the LangGraph Server
+    # 2. Gateway and LangGraph Server are separate processes with independent caches
+    # MCP tools are lazily initialized in LangGraph Server when first needed
 
     yield
     logger.info("Shutting down API Gateway")