fix(cli-runtime): replace overlapping user mcp servers

src/agents/cli-runner/bundle-mcp.test.ts

@@ -263,6 +263,7 @@ describe("prepareCliBundleMcpConfig", () => {
     });
 
     const configFlagIndex = prepared.backend.args?.indexOf("--mcp-config") ?? -1;
+    expect(configFlagIndex).toBeGreaterThanOrEqual(0);
     const generatedConfigPath = prepared.backend.args?.[configFlagIndex + 1];
     const raw = JSON.parse(await fs.readFile(generatedConfigPath as string, "utf-8")) as {
       mcpServers?: Record<string, { url?: string }>;
@@ -272,6 +273,90 @@ describe("prepareCliBundleMcpConfig", () => {
     await prepared.cleanup?.();
   });
 
+  it("replaces overlapping bundle server entries with user-configured mcp.servers", async () => {
+    const workspaceDir = await tempHarness.createTempDir(
+      "openclaw-cli-bundle-mcp-user-servers-replace-",
+    );
+    await writeClaudeBundleManifest({
+      homeDir: bundleProbeHomeDir,
+      pluginId: "omi",
+      manifest: { name: "omi" },
+    });
+    const pluginDir = path.join(bundleProbeHomeDir, ".openclaw", "extensions", "omi");
+    await fs.writeFile(
+      path.join(pluginDir, ".mcp.json"),
+      `${JSON.stringify(
+        {
+          mcpServers: {
+            omi: {
+              command: process.execPath,
+              args: [bundleProbeServerPath],
+              env: { BUNDLE_ONLY: "true" },
+            },
+          },
+        },
+        null,
+        2,
+      )}\n`,
+      "utf-8",
+    );
+
+    const env = captureEnv(["HOME"]);
+    try {
+      process.env.HOME = bundleProbeHomeDir;
+      const prepared = await prepareCliBundleMcpConfig({
+        enabled: true,
+        mode: "claude-config-file",
+        backend: {
+          command: "node",
+          args: ["./fake-claude.mjs"],
+        },
+        workspaceDir,
+        config: {
+          plugins: {
+            entries: {
+              omi: { enabled: true, path: pluginDir },
+            },
+          },
+          mcp: {
+            servers: {
+              omi: {
+                type: "sse",
+                url: "https://api.omi.me/v1/mcp/sse",
+                headers: { Authorization: "Bearer test-token" },
+              },
+            },
+          },
+        },
+      });
+
+      const configFlagIndex = prepared.backend.args?.indexOf("--mcp-config") ?? -1;
+      expect(configFlagIndex).toBeGreaterThanOrEqual(0);
+      const generatedConfigPath = prepared.backend.args?.[configFlagIndex + 1];
+      const raw = JSON.parse(await fs.readFile(generatedConfigPath as string, "utf-8")) as {
+        mcpServers?: Record<
+          string,
+          {
+            type?: string;
+            url?: string;
+            command?: string;
+            args?: string[];
+            env?: Record<string, string>;
+          }
+        >;
+      };
+      expect(raw.mcpServers?.omi?.type).toBe("sse");
+      expect(raw.mcpServers?.omi?.url).toBe("https://api.omi.me/v1/mcp/sse");
+      expect(raw.mcpServers?.omi?.command).toBeUndefined();
+      expect(raw.mcpServers?.omi?.args).toBeUndefined();
+      expect(raw.mcpServers?.omi?.env).toBeUndefined();
+
+      await prepared.cleanup?.();
+    } finally {
+      env.restore();
+    }
+  });
+
   it("stabilizes the resume hash when only the OpenClaw loopback port changes", async () => {
     const first = await prepareBundleProbeCliConfig({
       additionalConfig: {

src/agents/cli-runner/bundle-mcp.ts

@@ -2,8 +2,8 @@ import crypto from "node:crypto";
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { applyMergePatch } from "../../config/merge-patch.js";
 import { normalizeConfiguredMcpServers } from "../../config/mcp-config.js";
+import { applyMergePatch } from "../../config/merge-patch.js";
 import type { CliBackendConfig } from "../../config/types.js";
 import type { OpenClawConfig } from "../../config/types.openclaw.js";
 import {
@@ -418,7 +418,13 @@ export async function prepareCliBundleMcpConfig(params: {
   mergedConfig = applyMergePatch(mergedConfig, bundleConfig.config) as BundleMcpConfig;
   const configuredMcp = normalizeConfiguredMcpServers(params.config?.mcp?.servers);
   if (Object.keys(configuredMcp).length > 0) {
-    mergedConfig = applyMergePatch(mergedConfig, { mcpServers: configuredMcp }) as BundleMcpConfig;
+    mergedConfig = {
+      ...mergedConfig,
+      mcpServers: {
+        ...(mergedConfig.mcpServers ?? {}),
+        ...configuredMcp,
+      },
+    } satisfies BundleMcpConfig;
   }
   if (params.additionalConfig) {
     mergedConfig = applyMergePatch(mergedConfig, params.additionalConfig) as BundleMcpConfig;