From 43a47771221b695994803f5b7275cb47bafe7881 Mon Sep 17 00:00:00 2001
From: Aiden Cline <aidenpcline@gmail.com>
Date: Wed, 4 Nov 2026 16:33:51 -0600
Subject: [PATCH 1/2] fix(core): fall back to legacy for stdio MCP servers that
 ignore the version probe

---
 packages/core/src/mcp/stdio.ts                |  9 ++++++-
 .../core/test/fixture/mcp-legacy-silent.ts    | 22 ++++++++++++++++
 packages/core/test/mcp.test.ts                | 26 +++++++++++++++++++
 3 files changed, 56 insertions(+), 1 deletion(-)
 create mode 100644 packages/core/test/fixture/mcp-legacy-silent.ts

diff --git a/packages/core/src/mcp/stdio.ts b/packages/core/src/mcp/stdio.ts
index 569f78f1aaff..ceb6e3c6bf6d 100644
--- a/packages/core/src/mcp/stdio.ts
+++ b/packages/core/src/mcp/stdio.ts
@@ -87,7 +87,14 @@ export const make = Effect.fnUntraced(function* (options: Options) {
       }).pipe(Effect.ensuring(Queue.shutdown(outgoing))),
     ))
 
-  const transport: Transport = {
+  // `pid` and `stderr` match the SDK's StdioClientTransport accessors. The SDK detects stdio by their
+  // presence, and only for stdio does it treat an unanswered server/discover probe as a legacy server.
+  // stderr is drained into the debug log, so no stream is handed out.
+  const transport: Transport & { readonly pid: number | null; readonly stderr: null } = {
+    get pid() {
+      return state.handle?.pid ?? null
+    },
+    stderr: null,
     start: () => {
       if (state.phase !== "ready") return Promise.reject(new Error("Stdio transport already started"))
       state.phase = "starting"
diff --git a/packages/core/test/fixture/mcp-legacy-silent.ts b/packages/core/test/fixture/mcp-legacy-silent.ts
new file mode 100644
index 000000000000..7c3370d3dd2f
--- /dev/null
+++ b/packages/core/test/fixture/mcp-legacy-silent.ts
@@ -0,0 +1,22 @@
+import { createInterface } from "node:readline"
+
+// A 2025-11-25 stdio server that never answers requests it doesn't know, such as server/discover.
+const send = (message: unknown) => process.stdout.write(JSON.stringify(message) + "\n")
+
+for await (const line of createInterface({ input: process.stdin })) {
+  if (!line.trim()) continue
+  const message = JSON.parse(line)
+  if (message.id === undefined || message.method === undefined) continue
+  if (message.method === "initialize")
+    send({
+      jsonrpc: "2.0",
+      id: message.id,
+      result: {
+        protocolVersion: "2025-11-25",
+        capabilities: { tools: {} },
+        serverInfo: { name: "legacy-silent", version: "1.0.0" },
+      },
+    })
+  if (message.method === "tools/list")
+    send({ jsonrpc: "2.0", id: message.id, result: { tools: [{ name: "echo", inputSchema: { type: "object" } }] } })
+}
diff --git a/packages/core/test/mcp.test.ts b/packages/core/test/mcp.test.ts
index 2d6044a7f0c4..2db8616dda45 100644
--- a/packages/core/test/mcp.test.ts
+++ b/packages/core/test/mcp.test.ts
@@ -984,6 +984,32 @@ test("closes a stdio process that finishes spawning after close", async () => {
   expect(signals).toEqual(["SIGTERM"])
 })
 
+test("falls back to legacy when a stdio server ignores the version probe", async () => {
+  const started = performance.now()
+  const result = await Effect.runPromise(
+    Effect.scoped(
+      Effect.gen(function* () {
+        const connection = yield* connect(
+          "legacy-silent",
+          new ConfigMCP.Local({
+            type: "local",
+            command: [process.execPath, path.join(import.meta.dir, "fixture/mcp-legacy-silent.ts")],
+            protocol: "auto",
+            // The probe waits out the startup timeout before falling back.
+            timeout: new ConfigMCP.Timeout({ startup: 300 }),
+          }),
+          import.meta.dir,
+        )
+        return { modern: connection.modern, tools: yield* connection.tools() }
+      }),
+    ),
+  )
+
+  expect(result.modern).toBe(false)
+  expect(result.tools.map((tool) => tool.name)).toEqual(["echo"])
+  expect(performance.now() - started).toBeLessThan(2_000)
+})
+
 test("applies the configured MCP catalog timeout", async () => {
   const result = Effect.runPromise(
     Effect.scoped(

From ec2a91e5591717f780f220aca2dc0ded1aa8774c Mon Sep 17 00:00:00 2001
From: Aiden Cline <aidenpcline@gmail.com>
Date: Wed, 4 Nov 2026 16:45:32 -0600
Subject: [PATCH 2/2] test(core): drop wall-clock assertion from probe fallback
 test

---
 packages/core/test/mcp.test.ts | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/packages/core/test/mcp.test.ts b/packages/core/test/mcp.test.ts
index 2db8616dda45..3363b0f57cc1 100644
--- a/packages/core/test/mcp.test.ts
+++ b/packages/core/test/mcp.test.ts
@@ -985,7 +985,6 @@ test("closes a stdio process that finishes spawning after close", async () => {
 })
 
 test("falls back to legacy when a stdio server ignores the version probe", async () => {
-  const started = performance.now()
   const result = await Effect.runPromise(
     Effect.scoped(
       Effect.gen(function* () {
@@ -995,8 +994,8 @@ test("falls back to legacy when a stdio server ignores the version probe", async
             type: "local",
             command: [process.execPath, path.join(import.meta.dir, "fixture/mcp-legacy-silent.ts")],
             protocol: "auto",
-            // The probe waits out the startup timeout before falling back.
-            timeout: new ConfigMCP.Timeout({ startup: 300 }),
+            // The probe waits out the startup timeout before falling back; Windows needs room to start Bun.
+            timeout: new ConfigMCP.Timeout({ startup: 1_000 }),
           }),
           import.meta.dir,
         )
@@ -1007,7 +1006,6 @@ test("falls back to legacy when a stdio server ignores the version probe", async
 
   expect(result.modern).toBe(false)
   expect(result.tools.map((tool) => tool.name)).toEqual(["echo"])
-  expect(performance.now() - started).toBeLessThan(2_000)
 })
 
 test("applies the configured MCP catalog timeout", async () => {