fix: add null checks for runtime.context in middlewares and tools (#1269)

Add defensive null checks before accessing runtime.context.get() to
prevent AttributeError when runtime.context is None. This affects:
- UploadsMiddleware
- MemoryMiddleware
- LoopDetectionMiddleware
- SandboxMiddleware
- sandbox tools
- setup_agent_tool
- present_file_tool
- task_tool

Also adds .env loading in serve.sh for environment variable support.

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

backend/packages/harness/deerflow/agents/middlewares/loop_detection_middleware.py

@@ -106,7 +106,7 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
 
     def _get_thread_id(self, runtime: Runtime) -> str:
         """Extract thread_id from runtime context for per-thread tracking."""
-        thread_id = runtime.context.get("thread_id")
+        thread_id = runtime.context.get("thread_id") if runtime.context else None
         if thread_id:
             return thread_id
         return "default"