diff --git a/backend/packages/harness/deerflow/config/extensions_config.py b/backend/packages/harness/deerflow/config/extensions_config.py
index 425da12b84..18b8cd5e2d 100644
--- a/backend/packages/harness/deerflow/config/extensions_config.py
+++ b/backend/packages/harness/deerflow/config/extensions_config.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 from typing import Any, Literal
 
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import BaseModel, ConfigDict, Field, model_validator
 
 from deerflow.config.runtime_paths import existing_project_file
 
@@ -47,6 +47,24 @@ class McpServerConfig(BaseModel):
     description: str = Field(default="", description="Human-readable description of what this MCP server provides")
     model_config = ConfigDict(extra="allow")
 
+    @model_validator(mode="before")
+    @classmethod
+    def _accept_transport_alias(cls, data: Any) -> Any:
+        """Accept the MCP-spec ``transport`` field as an alias for ``type``.
+
+        The official MCP configuration schema uses ``transport`` to indicate
+        the transport mechanism (``stdio``/``sse``/``http``). Earlier versions
+        of this project only honored ``type``, which caused remote SSE/HTTP
+        servers configured with just ``transport`` to be incorrectly treated as
+        ``stdio`` (the default). This validator normalizes the two so either
+        spelling works, with ``type`` taking precedence when both are provided.
+        """
+        if isinstance(data, dict):
+            transport = data.get("transport")
+            if transport and not data.get("type"):
+                data = {**data, "type": transport}
+        return data
+
 
 class SkillStateConfig(BaseModel):
     """Configuration for a single skill's state."""
diff --git a/backend/tests/test_mcp_client_config.py b/backend/tests/test_mcp_client_config.py
index ca4d0de597..3216b59fa8 100644
--- a/backend/tests/test_mcp_client_config.py
+++ b/backend/tests/test_mcp_client_config.py
@@ -83,6 +83,41 @@ def test_build_server_params_rejects_unsupported_transport():
         build_server_params("bad-transport", config)
 
 
+@pytest.mark.parametrize("transport", ["sse", "http"])
+def test_mcp_server_config_accepts_transport_alias(transport: str):
+    """The MCP-spec ``transport`` field should be accepted as an alias for ``type``.
+
+    Regression test for https://github.com/bytedance/deer-flow/issues/3238 — a
+    remote MCP server configured with only ``transport: sse`` was previously
+    misidentified as ``stdio`` (the default for ``type``).
+    """
+    config = McpServerConfig.model_validate(
+        {
+            "transport": transport,
+            "url": "https://example.com/mcp",
+        }
+    )
+
+    assert config.type == transport
+
+    params = build_server_params("aliased-server", config)
+    assert params["transport"] == transport
+    assert params["url"] == "https://example.com/mcp"
+
+
+def test_mcp_server_config_type_takes_precedence_over_transport():
+    """When both ``type`` and ``transport`` are provided, ``type`` wins."""
+    config = McpServerConfig.model_validate(
+        {
+            "type": "http",
+            "transport": "sse",
+            "url": "https://example.com/mcp",
+        }
+    )
+
+    assert config.type == "http"
+
+
 def test_build_servers_config_returns_empty_when_no_enabled_servers():
     extensions = ExtensionsConfig(
         mcp_servers={
diff --git a/frontend/src/core/threads/hooks.ts b/frontend/src/core/threads/hooks.ts
index 1c927c5ffc..62479061ee 100644
--- a/frontend/src/core/threads/hooks.ts
+++ b/frontend/src/core/threads/hooks.ts
@@ -125,6 +125,24 @@ export function mergeMessages(
   ]);
 }
 
+export function mergeThreadValues(
+  previousValues: Partial<AgentThreadState> | undefined,
+  nextValues: Partial<AgentThreadState> | undefined,
+): Partial<AgentThreadState> | undefined {
+  if (!previousValues) {
+    return nextValues;
+  }
+  if (!nextValues) {
+    return previousValues;
+  }
+
+  return {
+    ...previousValues,
+    ...nextValues,
+    todos: nextValues.todos ?? previousValues.todos,
+  };
+}
+
 function getMessagesAfterBaseline(
   messages: Message[],
   baselineMessageIds: ReadonlySet<string>,
@@ -382,6 +400,8 @@ export function useThreadStream({
   const latestMessageCountsRef = useRef({ humanMessageCount });
   const sendInFlightRef = useRef(false);
   const messagesRef = useRef<Message[]>([]);
+  const valuesRef = useRef<Partial<AgentThreadState> | undefined>(thread.values);
+  const valuesThreadIdRef = useRef<string | null>(threadId ?? null);
   const summarizedRef = useRef<Set<string>>(null);
   // Track human message count before sending to prevent clearing optimistic
   // messages before the server's human message arrives (e.g. when AI messages
@@ -661,9 +681,17 @@ export function useThreadStream({
 
   // Merge history, live stream, and optimistic messages for display
   // History messages may overlap with thread.messages; thread.messages take precedence
+  const activeThreadId = onStreamThreadId ?? threadId ?? null;
+  if (valuesThreadIdRef.current !== activeThreadId) {
+    valuesThreadIdRef.current = activeThreadId;
+    valuesRef.current = thread.values;
+  }
+  const mergedValues = mergeThreadValues(valuesRef.current, thread.values);
+  valuesRef.current = mergedValues;
   const mergedThread = {
     ...thread,
     messages: mergedMessages,
+    values: mergedValues,
   } as typeof thread;
 
   return {
diff --git a/frontend/tests/unit/core/threads/message-merge.test.ts b/frontend/tests/unit/core/threads/message-merge.test.ts
index 2afca1eef8..f560c4632c 100644
--- a/frontend/tests/unit/core/threads/message-merge.test.ts
+++ b/frontend/tests/unit/core/threads/message-merge.test.ts
@@ -4,6 +4,7 @@ import { expect, test } from "vitest";
 import {
   getVisibleOptimisticMessages,
   mergeMessages,
+  mergeThreadValues,
 } from "@/core/threads/hooks";
 
 test("mergeMessages removes duplicate messages already present in history", () => {
@@ -155,3 +156,35 @@ test("getVisibleOptimisticMessages hides optimistic user input after later serve
     optimisticHuman,
   ]);
 });
+
+test("mergeThreadValues preserves todos when a later state omits them", () => {
+  expect(
+    mergeThreadValues(
+      {
+        title: "Thread",
+        todos: [{ content: "Keep me", status: "in_progress" }],
+      },
+      {
+        title: "Thread",
+      },
+    ),
+  ).toEqual({
+    title: "Thread",
+    todos: [{ content: "Keep me", status: "in_progress" }],
+  });
+});
+
+test("mergeThreadValues allows explicit todo clearing", () => {
+  expect(
+    mergeThreadValues(
+      {
+        todos: [{ content: "Done", status: "completed" }],
+      },
+      {
+        todos: [],
+      },
+    ),
+  ).toEqual({
+    todos: [],
+  });
+});