VS Code extension: project-scoped Streamable HTTP MCP resources load but tools are not injected

What version of the IDE extension are you using?

openai.chatgpt@26.707.91948

What subscription do you have?

other

Which IDE are you using?

VS Code

What platform is your computer?

Darwin 25.5.0 arm64 arm

What issue are you seeing?

A project-scoped Streamable HTTP MCP server appears to be partially loaded in the Codex VS Code extension: the server is enabled and its MCP resources are visible/readable, but its callable tools are not injected into the active Codex agent session.

This makes notebooks under the VS Code VFS workspace unusable from Codex even though the project guidance and MCP resource both say to use notebook MCP tools.

The server is expected to expose notebook discovery, notebook content/editing, resource, and runtime tools for the VS Code notebook integration.

None of the server-provided callable tools are available in the active agent tool surface.

Current evidence:

Project-scoped .codex/config.toml contains the MCP server entry:

[mcp_servers.example-notebook-mcp]
url = "http://127.0.0.1:<port>/mcp"
http_headers = { Authorization = "Bearer <redacted>" }

codex mcp get example-notebook-mcp reports:

example-notebook-mcp
  enabled: true
  transport: streamable_http
  url: http://127.0.0.1:<port>/mcp
  bearer_token_env_var: -
  http_headers: Authorization=*****
  env_http_headers: -

The active agent session can list MCP resources and sees the notebook integration resource:

server: example-notebook-mcp
uri: example://guidance/notebook-workflow
name: notebook-workflow
title: Notebook workflow guidance
mimeType: text/markdown

The active agent session can also read that MCP resource. It returns guidance saying to use server-provided notebook MCP tools for notebook content, editing, resource, and runtime operations. For example, the guidance says these tools should be used to inspect notebook cells, edit notebook cells/metadata, manage notebook resources, and control notebook kernel execution.

<redacted: guidance names specific server-provided notebook MCP tools>

However, those tools are not present as callable MCP tools in the session. The only MCP-like tool surface visible to the agent is generic resource access (list_mcp_resources, read_mcp_resource, etc.), not the server-provided notebook tools.

What steps can reproduce the bug?

1. Install/use the ChatGPT/Codex VS Code extension.
2. Open a VS Code workspace whose project root is a notebook VFS anchor.
3. Configure a project-scoped Streamable HTTP MCP server in .codex/config.toml, for example:

``toml
[mcp_servers.example-notebook-mcp]
url = "http://127.0.0.1:<port>/mcp"
http_headers = { Authorization = "Bearer <token>" }
``

1. Ensure the project is trusted.
2. Reload VS Code and start a new Codex chat/session.
3. Observe that codex mcp get example-notebook-mcp reports the server as enabled.
4. Observe that MCP resources from example-notebook-mcp are visible/readable in the active agent session.
5. Ask Codex to use one of the server-provided notebook MCP tools.

Actual behavior:

• The MCP server is configured and enabled.
• MCP resources from the server are visible/readable.
• The server guidance refers to expected notebook tools.
• The expected MCP tools are not injected into the active Codex agent tool surface.
• Notebook operations cannot be performed from Codex.

What is the expected behavior?

After the Streamable HTTP MCP server is enabled and its resources are visible, Codex should also complete tool discovery for that MCP server and expose its tools in the active agent session, e.g. as callable mcp__... tools or equivalent tool names.

At minimum, if resources can load but tools cannot be discovered or injected, the extension should surface a diagnostic explaining which phase failed (initialize, tools/list, caching, tool filtering, policy/allowlist, or thread injection).

Additional information

Local validation already tried:

• Reloaded VS Code / started a fresh Codex session.
• Confirmed codex mcp list and codex mcp get example-notebook-mcp show the server as enabled.
• Confirmed the MCP resource example://guidance/notebook-workflow is visible/readable.
• Confirmed the expected notebook callable tools are still absent from the agent session.
• codex doctor shows no proxy environment variables.
• Codex CLI version: codex-cli 0.144.5.

Possibly related issues:

• #34496: Streamable HTTP MCP initializes successfully but tools never become available in VS Code
• #6465: MCP servers not detected in Codex VS Code extension but working in Codex CLI
• #14242: Codex stops at list_mcp_resources and fails to discover/use tool-only MCP servers
• #19425 / #34018: MCP discovery succeeds but tools are not exposed to Codex threads/tool surface