Custom STDIO MCP server enabled and tools/list works, but tools are not exposed in Codex Desktop thread

[ilkerfatih44]

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

Version 26.602.40724 • Released 5 Haz 2026

What subscription do you have?

Plus

What platform is your computer?

Microsoft Windows NT 10.0.26200.0 x64

What issue are you seeing?

A custom STDIO MCP server is enabled in Codex Desktop and works correctly at the MCP protocol level, but its tools are not exposed to the active Codex Desktop thread.

The MCP server appears enabled in Codex Desktop Settings → MCP servers. It also appears in /mcp as enabled.

Local protocol probe succeeds:

• initialize: OK

• serverInfo: kuponcu-context-mcp v0.2.0

• tools/list returns 7 tools:

  • get_current_baseline
  • get_task_policy
  • get_forbidden_surfaces
  • get_validation_profile
  • search_project_sources
  • verify_hash_only
  • get_report_contract

However, inside a Codex Desktop thread opened in the correct workspace, tool_search cannot find any of these tools.

Relevant session evidence:

• cwd: C:\Users\QQ\Desktop\altin-starter
• originator: Codex Desktop
• cli_version shown in logs: 0.137.0-alpha.4
• The prompt asked Codex to check for these exact MCP tools:
  get_current_baseline, get_task_policy, get_forbidden_surfaces, get_validation_profile, search_project_sources, verify_hash_only, get_report_contract
• Codex performed a tool_search_call with these tool names.
• tool_search_output returned:
  tools: []
• Final result:
  MCP_TOOLS_NOT_VISIBLE

The issue is not that the MCP server is missing or failing to start. The server is enabled, visible in settings, and protocol-valid, but the active Codex thread does not expose its tools.

What steps can reproduce the bug?

1. On Windows, create a custom STDIO MCP server and add it in Codex Desktop Settings → MCP servers.

2. Configure it with:

   • command: C:\Users\QQ\Desktop\altin-starter.venv\Scripts\python.exe

   • args:

     • -B
     • C:\Users\QQ\Desktop\altin-starter\mcp_servers\kuponcu_context_mcp\kuponcu_context_mcp\server.py
     • --repo-root
     • C:\Users\QQ\Desktop\altin-starter
     • --source-root
     • C:\Users\QQ\Desktop\kuponcu-context-sources\PR69_K1U_K1S_GA

   • cwd: C:\Users\QQ\Desktop\altin-starter

3. Confirm the server is enabled in Codex Desktop Settings.

4. Confirm /mcp shows the server as enabled.

5. Verify locally outside Codex that the MCP protocol works:

   • initialize returns OK
   • tools/list returns 7 tools

6. Open a Codex Desktop thread in the same workspace:
   C:\Users\QQ\Desktop\altin-starter

7. Ask Codex to check for the MCP tools:
   get_current_baseline, get_task_policy, get_forbidden_surfaces, get_validation_profile, search_project_sources, verify_hash_only, get_report_contract

8. Codex performs tool_search, but the result is an empty list:
   tools: []

9. The thread reports MCP_TOOLS_NOT_VISIBLE.

Session id from the failing run:
019e98f4-1731-79c2-a00d-62736bace39e

What is the expected behavior?

If a custom STDIO MCP server is enabled in Codex Desktop, visible in /mcp, and its local MCP protocol tools/list call succeeds, its tools should be exposed to the active Codex Desktop thread/tool registry.

Expected:

• tool_search should find the custom MCP tools.
• Codex should be able to call get_current_baseline and the other MCP tools.
• If tools are intentionally not exposed, Codex Desktop should show a clear reason or error, such as unsupported transport, invalid schema, disabled tool list, workspace restriction, approval issue, or thread type incompatibility.

Actual:

• The MCP server is enabled and protocol-valid.
• /mcp shows the server as enabled.
• Local tools/list returns 7 tools.
• The Codex Desktop thread tool_search returns tools: [].
• Codex reports MCP_TOOLS_NOT_VISIBLE.

Additional information

In Codex Desktop Settings → MCP servers, kuponcu-context-mcp appears under “Servers” and the toggle is enabled. Built-in/plugin MCP entries such as codex_apps and node_repl appear separately under plugins. Despite this, the active thread tool_search returns tools: [] for all custom MCP tool names.

No secrets, .env values, tokens, cookies, runtime_state contents, or private payloads are included in this report.

codex_mcp_issue_evidence_pack.zip

[github-actions]

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• Codex Desktop does not expose custom MCP tools although codex mcp list sees the server. #25843
• Remote MCP server installs incompletely or not at all, even though initialize and tools/list succeed #26094
• Streamable HTTP MCP server is shown as enabled/authenticated, but agent tool layer cannot use it #26072
• MCP disconnectiong #26347

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[ilkerfatih44]

Small correction to the reproduction section:

The command path should be:

C:\Users\QQ\Desktop\altin-starter\.venv\Scripts\python.exe

[ilkerfatih44]

Update: Streamable HTTP MCP works in the same Codex Desktop environment.

STDIO MCP result:

• local initialize/tools-list: PASS
• visible in /mcp: enabled
• Codex Desktop thread tool exposure: FAIL (tools: [] / MCP_TOOLS_NOT_VISIBLE)

Streamable HTTP MCP result:

• local HTTP initialize: PASS
• local HTTP tools/list: PASS, 7 tools
• visible in /mcp: enabled
• Codex Desktop thread tool exposure: PASS
• get_current_baseline was visible and callable from the thread
• bounded smoke test also passed using:
  • get_task_policy
  • get_forbidden_surfaces
  • get_report_contract
  • search_project_sources

HTTP MCP URL:

http://127.0.0.1:8765/mcp