fix: handle project MCP config conflicts

src/CodexAcpClient.ts

@@ -518,11 +518,16 @@ export class CodexAcpClient {
 
     private async getConfigMcpServerNames(projectPath: string): Promise<Set<string>> {
         const response = await this.codexClient.configRead({ includeLayers: true, cwd: projectPath });
-        const mcpServers = response?.config?.["mcp_servers"];
-        if (!mcpServers || typeof mcpServers !== "object" || Array.isArray(mcpServers)) {
+        const effectiveMcpServers = response?.config?.["mcp_servers"];
+        const configLayers = response?.layers ?? [];
+        const layerMcpServers = configLayers.map(layer => {
+            return isJsonObject(layer.config) ? layer.config["mcp_servers"] : undefined;
+        });
+        const configuredMcpServers = [effectiveMcpServers, ...layerMcpServers].filter(isJsonObject);
+        if (configuredMcpServers.length === 0) {
             return new Set();
         }
-        return new Set(Object.keys(mcpServers));
+        return new Set(configuredMcpServers.flatMap(server => Object.keys(server)));
     }
 
     getModelProvider(): string | null {

src/__tests__/CodexACPAgent/mcp-config-merge.test.ts

@@ -8,20 +8,30 @@ import type {McpServerStdio} from "@agentclientprotocol/sdk";
 import {startCodexConnection} from "../../CodexJsonRpcConnection";
 import {createBaseTestFixture, removeDirectoryWithRetry, type TestFixture} from "../acp-test-utils";
 
-describe('MCP config merge across global config and ACP request', { timeout: 40_000 }, () => {
+describe('MCP config merge across configured MCP servers and ACP request', { timeout: 40_000 }, () => {
 
     let codexHome: string;
+    let projectPath: string;
     let fixture: TestFixture;
 
     beforeEach(() => {
         vi.clearAllMocks();
 
-        const configToml = `
+        const globalConfig = `
 [mcp_servers.shared-mcp]
 url = "https://example.com/mcp"
 `;
+
+        const projectConfig = `
+[mcp_servers.project-mcp]
+url = "https://example.com/mcp"
+`;
+
         codexHome = fs.mkdtempSync(path.join(os.tmpdir(), "codex-acp-mcp-merge-"));
-        fs.writeFileSync(path.join(codexHome, "config.toml"), configToml, "utf8");
+        fs.writeFileSync(path.join(codexHome, "config.toml"), globalConfig, "utf8");
+        projectPath = fs.mkdtempSync(path.join(os.tmpdir(), "codex-acp-mcp-project-"));
+        fs.mkdirSync(path.join(projectPath, ".codex"));
+        fs.writeFileSync(path.join(projectPath, ".codex", "config.toml"), projectConfig, "utf8");
 
         const codexConnection = startCodexConnection(undefined, {
             ...process.env,
@@ -37,6 +47,7 @@ url = "https://example.com/mcp"
     afterEach(() => {
         vi.unstubAllEnvs();
         removeDirectoryWithRetry(codexHome);
+        removeDirectoryWithRetry(projectPath);
     });
 
     it('should preserve the global url-based MCP when ACP passes a command-type MCP with the same name', async () => {
@@ -68,6 +79,24 @@ url = "https://example.com/mcp"
         expect(transportDump).contain("- shared-mcp");
     });
 
+    it('should preserve a project url-based MCP when ACP passes a command-type MCP with the same name', async () => {
+        const codexAcpAgent = fixture.getCodexAcpAgent();
+        await codexAcpAgent.initialize({protocolVersion: 1});
+        fixture.getCodexAcpClient().authRequired = vi.fn().mockResolvedValue(false);
+
+        const conflictingMcp = {
+            name: "project-mcp",
+            command: "./node_modules/.bin/mcp-hello-world",
+            args: ["example"],
+            env: [{name: "example", value: "example"}],
+        };
+
+        await expect(codexAcpAgent.newSession({
+            cwd: projectPath,
+            mcpServers: [conflictingMcp],
+        })).resolves.toBeDefined();
+    });
+
     it('should not filter the conflicting ACP MCP when config filtering is disabled', async () => {
         vi.stubEnv("DISABLE_MCP_CONFIG_FILTERING", "true");
         const codexAcpAgent = fixture.getCodexAcpAgent();