Codex bug: MCP servers load successfully but their tools aren't exposed to the model

Suggested title for the issue:

MCP servers configured in [mcp_servers.X] load successfully but their tools are not surfaced to the model in the session

Suggested repo: openai/codex

Description

A user-defined MCP server configured under [mcp_servers.<name>] in ~/.codex/config.toml is spawned correctly and completes the MCP handshake (verified in logs), but the Codex session's tool list shown to the model contains only Codex-managed plugins (github, vercel, google-calendar, notion). The user-defined server's tools never appear, so the model can't invoke them.

Environment

• codex-cli: 0.128.0
• macOS: 14.x

Configuration

[mcp_servers.agent-state]
command = "bash"
args = ["/Users/<user>/.codex/mcp-wrappers/agent-state.sh"]

The wrapper resolves credentials from 1Password and execs a Node.js MCP server. Both work standalone — running the wrapper from a Terminal produces the expected agent-state-mcp ready stderr line and the server accepts tools/list requests.

Evidence the server loads + responds

From ~/.codex/logs_2.sqlite:

level=TRACE target=rmcp::service
serve_inner: new event evt=PeerMessage(Response(JsonRpcResponse {
  jsonrpc: JsonRpcVersion2_0,
  id: Number(1),
  result: ListToolsResult(ListToolsResult {
    meta: None,
    next_cursor: None,
    tools: [
      Tool { name: "event_log", title: None, description: Some("..."), ... },
      // ...13 more tools
    ]
  })
}))

So at the protocol layer, Codex received the catalog of 14 tools.

What the model sees

When prompted "list all available tools", the model reports only github, vercel, google-calendar, notion — the four [plugins.*] entries from config.toml. It does not mention the agent-state server or any of its 14 tools, and direct invocations like "call the tool named event_log" return "no such tool."

Expected behavior

Tools from [mcp_servers.X] entries should be visible alongside [plugins.X] tools in the model's tool registry.

Reproduction

1. Configure any MCP server under [mcp_servers.X] in ~/.codex/config.toml (a public stdio MCP like the GitHub MCP or a tiny local hello-world MCP works for repro)
2. Launch codex
3. Verify in ~/.codex/logs_2.sqlite that rmcp::service recorded ListToolsResult for the server (proves it loaded)
4. Inside the Codex session, ask the model to list available tools
5. The user-defined server's tools are absent from the model's response

Hypothesis

Looks like there's a registration step between rmcp receiving the tool list and the session tool-registry being populated for the model. Either the registration call is missing, or the session's tool-list serialisation is filtering out non-plugin entries.

Workaround

None found. [plugins.*] entries work; [mcp_servers.*] entries connect but are unusable from the agent's perspective.