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/tools/builtins/present_file_tool.py

@@ -33,7 +33,7 @@ def _normalize_presented_filepath(
     if runtime.state is None:
         raise ValueError("Thread runtime state is not available")
 
-    thread_id = runtime.context.get("thread_id")
+    thread_id = runtime.context.get("thread_id") if runtime.context else None
     if not thread_id:
         raise ValueError("Thread ID is not available in runtime context")