fix(core): keep nested MCP code mode tools direct

packages/cli/test/fixture/standalone-owner.ts

@@ -14,7 +14,7 @@ await Effect.runPromise(
       const response = yield* Effect.promise(() =>
         fetch(new URL("/api/health", endpoint.url), { headers: Service.headers(endpoint) }),
       )
-      console.log(`STANDALONE_READY ${endpoint.pid} ${endpoint.url} ${response.status}`)
+      console.log(`${endpoint.pid} ${endpoint.url} ${response.status}`)
       return yield* Effect.never
     }),
   ),

packages/cli/test/standalone.test.ts

@@ -9,11 +9,8 @@ test("standalone server exits when its owner is killed", async () => {
     stdout: "pipe",
     stderr: "pipe",
   })
-  const line = await Promise.race([
-    readLine(owner.stdout, "STANDALONE_READY "),
-    Bun.sleep(10_000).then(() => undefined),
-  ])
-  const [, rawPID, url, status] = line?.split(" ") ?? []
+  const line = await Promise.race([readLine(owner.stdout), Bun.sleep(10_000).then(() => undefined)])
+  const [rawPID, url, status] = line?.split(" ") ?? []
   const pid = Number(rawPID)
 
   try {
@@ -32,7 +29,7 @@ test("standalone server exits when its owner is killed", async () => {
   }
 })
 
-async function readLine(stream: ReadableStream<Uint8Array>, prefix: string) {
+async function readLine(stream: ReadableStream<Uint8Array>) {
   const reader = stream.getReader()
   const decoder = new TextDecoder()
   const chunks: string[] = []
@@ -41,14 +38,14 @@ async function readLine(stream: ReadableStream<Uint8Array>, prefix: string) {
     if (result.done) break
     chunks.push(decoder.decode(result.value, { stream: true }))
     const output = chunks.join("")
-    const line = output.split("\n").find((line) => line.startsWith(prefix))
-    if (line) {
+    const newline = output.indexOf("\n")
+    if (newline !== -1) {
       reader.releaseLock()
-      return line
+      return output.slice(0, newline)
     }
   }
   reader.releaseLock()
-  return (chunks.join("") + decoder.decode()).split("\n").find((line) => line.startsWith(prefix))
+  return chunks.join("") + decoder.decode()
 }
 
 async function waitForExit(pid: number, attempts = 100): Promise<boolean> {

packages/core/src/plugin/internal.ts

@@ -63,6 +63,7 @@ import { AgentPlugin } from "./agent.js"
 import { CommandPlugin } from "./command.js"
 import { PlanPlugin } from "./plan.js"
 import { ModelsDevPlugin } from "./models-dev.js"
+import { McpCodeModePlugin } from "./mcp-codemode.js"
 import { ProviderPlugins } from "./provider.js"
 import { WebSearchPlugins } from "./websearch/index.js"
 import { PluginRuntime } from "./runtime.js"
@@ -94,6 +95,7 @@ const services = Effect.fn("PluginInternal.services")(function* () {
   const location = yield* Location.Service
   const locationMutation = yield* LocationMutation.Service
   const models = yield* ModelsDev.Service
+  const mcpCodeMode = yield* McpCodeModePlugin.Service
   const npm = yield* Npm.Service
   const permission = yield* Permission.Service
   const runtime = yield* PluginRuntime.Service
@@ -131,6 +133,7 @@ const services = Effect.fn("PluginInternal.services")(function* () {
     Context.make(Location.Service, location),
     Context.make(LocationMutation.Service, locationMutation),
     Context.make(ModelsDev.Service, models),
+    Context.make(McpCodeModePlugin.Service, mcpCodeMode),
     Context.make(Npm.Service, npm),
     Context.make(Permission.Service, permission),
     Context.make(PluginRuntime.Service, runtime),
@@ -175,6 +178,7 @@ export const requirements = LayerNode.group([
   Location.node,
   LocationMutation.node,
   ModelsDev.node,
+  McpCodeModePlugin.node,
   Npm.node,
   Permission.node,
   PluginRuntime.node,
@@ -202,6 +206,7 @@ const pre = [
   SkillPlugin.Plugin,
   ...SystemPromptPlugin.Plugins,
   ModelsDevPlugin,
+  McpCodeModePlugin.Plugin,
   ...ProviderPlugins,
   ...WebSearchPlugins,
   PatchTool.Plugin,

packages/core/src/plugin/mcp-codemode.ts

@@ -0,0 +1,51 @@
+export * as McpCodeModePlugin from "./mcp-codemode.js"
+
+import { define } from "@opencode-ai/plugin/effect/plugin"
+import { ConfigMCP } from "@opencode-ai/schema/config/mcp"
+import { makeLocationNode } from "@opencode-ai/util/effect/app-node"
+import { Context, Effect, Layer, Scope } from "effect"
+
+const directToolHosts = new Set(["mcp.cloudflare.com"])
+type Resolver = (config: typeof ConfigMCP.Server.Type) => boolean | undefined
+
+export interface Interface {
+  register: (resolver: Resolver) => Effect.Effect<void, never, Scope.Scope>
+  resolve: (config: typeof ConfigMCP.Server.Type) => boolean | undefined
+}
+
+export class Service extends Context.Service<Service, Interface>()("@opencode/McpCodeModePlugin") {}
+
+export const layer = Layer.effect(
+  Service,
+  Effect.sync(() => {
+    let resolvers: Resolver[] = []
+    return Service.of({
+      register: Effect.fn("McpCodeModePlugin.register")(function* (resolver) {
+        resolvers = [...resolvers, resolver]
+        yield* Effect.addFinalizer(() => Effect.sync(() => (resolvers = resolvers.filter((item) => item !== resolver))))
+      }),
+      resolve: (config) =>
+        resolvers
+          .toReversed()
+          .map((resolver) => resolver(config))
+          .find((value) => value !== undefined),
+    })
+  }),
+)
+
+export const node = makeLocationNode({ service: Service, layer, deps: [] })
+
+export const Plugin = define({
+  id: "opencode.mcp.codemode-compatibility",
+  effect: Effect.fn(function* () {
+    const defaults = yield* Service
+    yield* defaults.register(codeModeCompatibilityDefault)
+  }),
+})
+
+export function codeModeCompatibilityDefault(config: typeof ConfigMCP.Server.Type) {
+  if (config.type !== "remote") return
+  const url = URL.parse(config.url)
+  if (!url || !directToolHosts.has(url.hostname.toLowerCase())) return
+  return false
+}

packages/core/src/tool/mcp.ts

@@ -2,12 +2,17 @@ export * as McpTool from "./mcp.js"
 
 import { ToolFailure } from "@opencode-ai/ai"
 import { McpEvent } from "@opencode-ai/schema/mcp-event"
+import { Document } from "@opencode-ai/schema/config"
 import { Context, Effect, Exit, Fiber, type JsonSchema, Layer, Scope, Semaphore, Stream } from "effect"
 import { makeLocationNode } from "@opencode-ai/util/effect/app-node"
 import { Bus } from "../bus.js"
 
 import { MCP } from "../mcp/index.js"
+import { Config } from "../config.js"
 import { Permission } from "../permission.js"
+import { Plugin } from "../plugin.js"
+import { McpCodeModePlugin } from "../plugin/mcp-codemode.js"
+import { PluginSupervisor } from "../plugin/supervisor.js"
 import { Tool } from "../tool.js"
 
 /**
@@ -27,6 +32,8 @@ export const layer = Layer.effect(
   Service,
   Effect.gen(function* () {
     const mcp = yield* MCP.Service
+    const config = yield* Config.Service
+    const codemode = yield* McpCodeModePlugin.Service
     const tools = yield* Tool.Service
     const bus = yield* Bus.Service
     const permission = yield* Permission.Service
@@ -39,14 +46,23 @@ export const layer = Layer.effect(
     const reconcile = lock.withPermit(
       Effect.gen(function* () {
         const discovered = yield* mcp.tools()
+        const servers = new Map(
+          (yield* config.entries())
+            .filter((entry): entry is Document => entry.type === "document")
+            .flatMap((entry) => Object.entries(entry.info.mcp?.servers ?? {})),
+        )
         const next = yield* Scope.fork(scope)
         yield* tools
           .transform((draft) => {
             for (const tool of discovered) {
               const schema = (tool.inputSchema ?? {}) as JsonSchema.JsonSchema
+              const server = servers.get(tool.server)
               draft.add({
                 name: tool.name,
-                options: { namespace: namespace(tool.server), codemode: tool.codemode !== false },
+                options: {
+                  namespace: namespace(tool.server),
+                  codemode: (tool.codemode ?? (server ? codemode.resolve(server) : undefined)) !== false,
+                },
                 description: tool.description ?? "",
                 input: {
                   ...schema,
@@ -122,7 +138,7 @@ export const layer = Layer.effect(
     )
 
     const initial = yield* reconcile.pipe(Effect.forkScoped)
-    yield* bus.subscribe(McpEvent.ToolsChanged).pipe(
+    yield* bus.subscribe([McpEvent.ToolsChanged, Plugin.Event.Updated]).pipe(
       Stream.runForEach(() => reconcile),
       Effect.forkScoped({ startImmediately: true }),
     )
@@ -133,5 +149,5 @@ export const layer = Layer.effect(
 export const node = makeLocationNode({
   service: Service,
   layer,
-  deps: [Tool.node, MCP.node, Bus.node, Permission.node],
+  deps: [Tool.node, MCP.node, McpCodeModePlugin.node, Config.node, Bus.node, Permission.node, PluginSupervisor.node],
 })

packages/core/test/mcp.test.ts

@@ -29,6 +29,8 @@ import { MCP } from "@opencode-ai/core/mcp/index"
 import { MCPClient } from "@opencode-ai/core/mcp/client"
 import { MCPStdio } from "@opencode-ai/core/mcp/stdio"
 import { Permission } from "@opencode-ai/core/permission"
+import { McpCodeModePlugin } from "@opencode-ai/core/plugin/mcp-codemode"
+import { PluginSupervisor } from "@opencode-ai/core/plugin/supervisor"
 import { AbsolutePath } from "@opencode-ai/core/schema"
 import { Session } from "@opencode-ai/core/session"
 import { McpTool } from "@opencode-ai/core/tool/mcp"
@@ -336,12 +338,16 @@ const permissions = Layer.mock(Permission.Service, {
     }),
 })
 const events = Layer.mock(Bus.Service, { subscribe: () => Stream.never })
+const plugins = Layer.succeed(PluginSupervisor.Service, PluginSupervisor.Service.of({ flush: Effect.void }))
 const it = testEffect(
   AppNodeBuilder.build(LayerNode.group([Tool.node, McpTool.node]), [
     [MCP.node, mcp],
+    [McpCodeModePlugin.node, McpCodeModePlugin.layer],
+    [Config.node, Config.testLayer()],
     [Permission.node, permissions],
     [Bus.node, events],
     [Image.node, imagePassthrough],
+    [PluginSupervisor.node, plugins],
   ]),
 )
 

packages/core/test/plugin/mcp-codemode.test.ts

@@ -0,0 +1,36 @@
+import { ConfigMCP } from "@opencode-ai/schema/config/mcp"
+import { codeModeCompatibilityDefault, McpCodeModePlugin } from "@opencode-ai/core/plugin/mcp-codemode"
+import { describe, expect, it } from "bun:test"
+import { Effect } from "effect"
+
+describe("MCP Code Mode compatibility defaults", () => {
+  it("keeps Cloudflare's Code Mode MCP server direct by default", () => {
+    const config = new ConfigMCP.Remote({ type: "remote", url: "https://mcp.cloudflare.com/mcp" })
+    expect(codeModeCompatibilityDefault(config)).toBe(false)
+  })
+
+  it("does not change Cloudflare's product-specific MCP servers", () => {
+    const config = new ConfigMCP.Remote({ type: "remote", url: "https://docs.mcp.cloudflare.com/mcp" })
+    expect(codeModeCompatibilityDefault(config)).toBeUndefined()
+  })
+
+  it("does not change local or unrelated remote servers", () => {
+    const local = new ConfigMCP.Local({ type: "local", command: ["server"] })
+    const remote = new ConfigMCP.Remote({ type: "remote", url: "https://example.com/mcp" })
+    expect(codeModeCompatibilityDefault(local)).toBeUndefined()
+    expect(codeModeCompatibilityDefault(remote)).toBeUndefined()
+  })
+
+  it("retains a registered direct-tool default", async () => {
+    await Effect.runPromise(
+      Effect.scoped(
+        Effect.gen(function* () {
+          const defaults = yield* McpCodeModePlugin.Service
+          yield* defaults.register(codeModeCompatibilityDefault)
+          const config = new ConfigMCP.Remote({ type: "remote", url: "https://mcp.cloudflare.com/mcp" })
+          expect(defaults.resolve(config)).toBe(false)
+        }).pipe(Effect.provide(McpCodeModePlugin.layer)),
+      ),
+    )
+  })
+})