Codex IDE extension fails GitHub MCP startup with "connection closed: initialize response" in PyCharm AI Chat

What version of the IDE extension are you using?

JetBrains AI Assistant / Codex integration bundled with PyCharm 2026.1 – v0.0.44

What subscription do you have?

ChatGPT subscription with Codex access

Which IDE are you using?

PyCharm 2026.1

What platform is your computer?

Darwin arm64 arm 25.4.0

What issue are you seeing?

n PyCharm AI Chat, Codex fails to start a custom GitHub MCP server configured via npx mcp-remote.

The startup error shown in chat is:

mcp__github__startup
[codex-acp forwarded startup error] MCP server github failed to start: MCP client for github failed to start: MCP startup failed: handshaking with MCP server failed: connection closed: initialize response

At the same time, /mcp still shows the server as configured:

Configured MCP servers:
• codex_apps: 90 tools, 0 resources, auth=bearerToken
• atlassian
• github

This happens in a new chat after restarting the IDE.

Important detail: the MCP backend itself appears to work. In github.log, the GitHub MCP process:

• receives initialize
• returns a valid initialize response
• receives tools/list
• returns a valid tools/list response

Example of a valid initialize response from github.log:

{
  "jsonrpc":"2.0",
  "id":"09c567a3be744276a0716fba3ce4b48e",
  "result":{
    "capabilities":{"completions":{},"prompts":{},"resources":{},"tools":{}},
    "protocolVersion":"2025-06-18",
    "serverInfo":{
      "name":"github-mcp-server",
      "version":"github-mcp-server/remote-b3a6334d17cb745035c4ef75d2d5ae76a67f655d"
    }
  }
}

Example of a minimal valid tools/list response from github.log:

{
  "jsonrpc":"2.0",
  "id":"627bed4c48204a839d0ea4a95bb68ca0",
  "result":{
    "tools":[
      {
        "name":"get_file_contents",
        "inputSchema":{
          "type":"object",
          "properties":{
            "owner":{"type":"string"},
            "path":{"type":"string","default":"/"},
            "ref":{"type":"string"},
            "repo":{"type":"string"},
            "sha":{"type":"string"}
          },
          "required":["owner","repo"]
        }
      },
      {
        "name":"get_me",
        "inputSchema":{
          "type":"object",
          "properties":{}
        }
      }
    ]
  }
}

So the failure seems to happen in the ACP / IDE extension layer, not in the GitHub MCP server itself.

What steps can reproduce the bug?

1. Open a project in PyCharm 2026.1.
2. Configure a project-level MCP server in .ai/mcp/mcp.json using npx mcp-remote, for example:

``json
{
"mcpServers": {
"github": {
"command": "npx",
"args": [
"-y",
"mcp-remote@latest",
"https://api.githubcopilot.com/mcp/",
"--header",
"Authorization:Bearer ${CODEX_GITHUB_PERSONAL_ACCESS_TOKEN}",
"--header",
"X-MCP-Readonly:true",
"--header",
"X-MCP-Tools:get_me,get_file_contents",
"--transport",
"http-only"
]
}
}
}
``

1. Ensure CODEX_GITHUB_PERSONAL_ACCESS_TOKEN is available in the IDE process environment.
2. Restart PyCharm.
3. Open a new AI Chat with Codex.
4. Run /mcp.
5. Observe the mcp__github__startup failure.
6. Inspect:

• idea.log
• ~/Library/Logs/JetBrains/PyCharm2026.1/mcp/github.log

Outside the IDE extension, the same MCP setup works. For example, this succeeds locally:

npx -y -p mcp-remote@latest mcp-remote-client \
  https://api.githubcopilot.com/mcp/ \
  --header "Authorization:Bearer ${CODEX_GITHUB_PERSONAL_ACCESS_TOKEN}" \
  --header "X-MCP-Readonly:true" \
  --header "X-MCP-Tools:get_me,get_file_contents" \
  --transport http-only

It connects and retrieves the tools list successfully.

What is the expected behavior?

The GitHub MCP server should start successfully in Codex AI Chat, and the configured GitHub tools should become available to the model.

If the MCP process returns valid initialize and tools/list responses, the IDE extension should not fail startup with connection closed: initialize response.

Additional information

Relevant observations from logs:

• idea.log shows the server being exposed as:

``text
Stdio(name=github, command=npx, args=[-y, mcp-remote@latest, https://api.githubcopilot.com/mcp/, --header, Authorization:Bearer ${CODEX_GITHUB_PERSONAL_ACCESS_TOKEN}, --header, X-MCP-Readonly:true, --header, X-MCP-Tools:get_me,get_file_contents, --transport, http-only], env=[])
``

• then the IDE extension reports:

``text
MCP server github failed to start: MCP client for github failed to start: MCP startup failed: handshaking with MCP server failed: connection closed: initialize response
``

• github.log shows that:
• initialize succeeds
• tools/list succeeds
• the tool payload is already reduced to only get_file_contents and get_me

So this does not appear to be:

• a PAT/auth problem
• a GitHub MCP server problem
• a full toolset size problem

It appears to be an IDE extension / ACP integration bug when handling GitHub MCP startup over npx mcp-remote.

I created a bug report for JetBrains too: https://youtrack.jetbrains.com/issue/IJPL-244795/Codex-ACP-fails-GitHub-MCP-startup-with-connection-closed-initialize-response-although-initialize-tools-list-succeed-via-npx-mcp