Codex Desktop does not expose custom MCP tools although codex mcp list sees the server.

What version of the Codex App are you using (From “About Codex” dialog)?

Версия 26.527.60818 (3437)

What subscription do you have?

pro

What platform is your computer?

macOS

What issue are you seeing?

Codex Desktop on macOS does not expose my custom MCP server tools inside new threads.

The MCP server is registered and visible through Codex CLI:

codex mcp list
shows:

obsidian_rag  /Users/.../node  /Users/.../mcp-server.mjs  enabled
The MCP server itself works. A local framed MCP smoke-test returns tools/list with:

status
search
read_note
However, in Codex Desktop threads, these tools never become callable. tool_search only finds built-in tools such as:

multi_agent_v1.close_agent
multi_agent_v1.wait_agent
codex_app.read_thread
codex_app.automation_update
It does not expose:

mcp__obsidian_rag__status
mcp__obsidian_rag__search
mcp__obsidian_rag__read_note
I also tested with Provider: OpenAI and Model: GPT-5/Codex, so this does not appear to be a custom gateway/proxy issue like #19649.

The MCP server is stdio-based, uses an absolute Node path, and is configured in ~/.codex/config.toml.


**What steps can reproduce the bug?**
```markdown
1. Configure a custom MCP server in `~/.codex/config.toml`:

```toml
[mcp_servers.obsidian_rag]
command = "/Users/shamilabdullaev/.cache/codex-runtimes/codex-primary-runtime/dependencies/node/bin/node"
args = ["/Users/shamilabdullaev/plugins/obsidian-rag/scripts/mcp-server.mjs"]
startup_timeout_sec = 120

[mcp_servers.obsidian_rag.env]
OBSIDIAN_VAULT_PATH = "/Users/shamilabdullaev/muwahhid_obsidian/muwahhid_obsidian"
OBSIDIAN_RAG_URL = "http://192.168.1.24:5055"
OBSIDIAN_RAG_TOKEN_FILE = "/Users/shamilabdullaev/.config/obsidian-rag/token"
Verify the MCP server is registered:
codex mcp list
Expected/observed CLI result: the server appears as enabled.

Verify the MCP server responds locally using MCP framing.
Observed: tools/list returns:

status
search
read_note
Fully quit Codex Desktop with Cmd+Q.

Reopen Codex Desktop and create a new thread.

Use Provider: OpenAI and Model: GPT-5/Codex.

Ask Codex Desktop:

Try to call:
- mcp__obsidian_rag__status
- mcp__obsidian_rag__search
- mcp__obsidian_rag__read_note

Do not use shell commands or direct file reads.

### What steps can reproduce the bug?

odex Desktop says those MCP tools are not available. tool_search does not expose them. Only built-in tools are available.

Expected result:

The MCP tools from obsidian_rag should be injected/exposed to the Desktop thread and callable as tools.


**Дополнительно, если есть поле version/platform:**

Для platform можно точнее вставить вывод команды:

```bash
uname -mprs

### What is the expected behavior?

_No response_

### Additional information

_No response_