Codex Desktop sometimes does not inject configured project MCP tools into a thread

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• #23738

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openai/codex #24168: Desktop MCP Tools Not Injected Into Thread

🔍 Root Cause Analysis

Severity: P1 — MCP tools intermittently absent from thread, model cannot call configured tools

Codex Desktop sometimes starts a thread without exposing configured MCP tools to the model, even though the same MCP server is correctly detected by the Codex CLI. The tools are absent from session_meta.dynamic_tools.

Root Cause Chain

1. Desktop vs CLI tool injection divergence: The Desktop app's tool injection pipeline has a race condition or state synchronization gap that the CLI does not have
2. MCP manager state not propagated: The MCP server connection is established (CLI sees it), but the tool definitions are not injected into the thread's dynamic_tools
3. Thread creation timing: The thread may be created before the MCP manager finishes loading/validating the server
4. streamable_http transport specific: The issue occurs with streamable_http MCP servers — possibly a connection timing issue with HTTP-based MCP

🛠️ Proposed Fix

Fix 1: MCP Tool Injection Verification Gate (Critical)

// In ThreadManager — verify MCP tools are injected before thread starts
class ThreadManager {
  async createThread(config: ThreadConfig): Promise<Thread> {
    // Wait for MCP manager to be ready
    await this.mcpManager.waitForReady();

    // Get MCP tool definitions
    const mcpTools = await this.mcpManager.getAllToolDefinitions();

    // NEW: Verify tools are injected into session_meta
    const thread = await this.doCreateThread(config);
    const injectedTools = thread.session_meta.dynamic_tools || [];

    const expectedToolNames = mcpTools.map(t => `mcp__${t.name}`);
    const missingTools = expectedToolNames.filter(
      name => !injectedTools.some(t => t.name === name)
    );

    if (missingTools.length > 0) {
      this.logger.error('MCP tools not injected into thread', {
        threadId: thread.id,
        missingTools,
        injectedTools: injectedTools.map(t => t.name),
        mcpServers: await this.mcpManager.getServerList(),
      });

      // Retry injection
      await this.retryMcpToolInjection(thread, mcpTools);
    }

    return thread;
  }

  private async retryMcpToolInjection(thread: Thread, tools: McpToolDef[]): Promise<void> {
    for (const tool of tools) {
      const toolName = `mcp__${tool.name}`;
      if (!thread.session_meta.dynamic_tools.some(t => t.name === toolName)) {
        thread.session_meta.dynamic_tools.push({
          name: toolName,
          description: tool.description,
          parameters: tool.parameters,
          source: 'mcp',
        });
      }
    }
  }
}

Fix 2: MCP Manager Ready Signal (Important)

// In McpManager — emit ready signal when all servers are loaded
class McpManager {
  private readyPromise: Promise<void> | null = null;
  private servers: Map<string, McpServerConnection> = new Map();

  async waitForReady(): Promise<void> {
    if (!this.readyPromise) {
      this.readyPromise = this.initializeAllServers();
    }
    return this.readyPromise;
  }