AI: Custom MCP Servers do not work, Timeout

[Askath]

Summary

When adding a custom MCP server, it times out and is not able to be activated.

Description

When adding a custom MCP server, it times out and is not able to be activated. Same MCP server works when running command + args in terminal and with other tools like opencode, crush or Claude Code.

I tried out 2 different servers to make sure it is not a problem with the individual server.

Steps to trigger the problem:

1. Open AI Panel or settings
2. Configure custom MCP server
3. Click "Configure Server" or save Settings.json
4. "Waiting for Contest Server" appears and times out eventually

Expected Behavior:
Server should be added and usable

Actual Behavior:
Server timed out.

Model Provider Details

My 2 MCP I tried.

"context_servers": {
    /// The name of your MCP server
    "some-mcp-server": {
      "source": "custom",
      /// The command which runs the MCP server
      "command": "npx",
      /// The arguments to pass to the MCP server
      "args": ["@benborla29/mcp-server-mysql"],
      /// The environment variables to set
      "env": {
        "MYSQL_HOST": "127.0.0.1",
        "MYSQL_PORT": "3306",
        "MYSQL_USER": "user",
        "MYSQL_PASSWORD": "password",
        "MYSQL_DATABASE": "phoenix-database",
        "ALLOW_INSERT_OPERATION": "true",
        "ALLOW_UPDATE_OPERATION": "true",
        "ALLOW_DELETE_OPERATION": "true"
      }
    }

{
  /// The name of your MCP server
  "some-mcp-server": {
    /// The command which runs the MCP server
    "command": "uv",
    /// The arguments to pass to the MCP server
    "args": ["run", "--directory", "/abs/path/to/serena", "serena", "start-mcp-server"],
    /// The environment variables to set
    "env": {}
  }
}

I ommited personal Details like DB connection and Folder names. But Even without, both servers work fine in other cli tools like crush,open Code and Claude Code

Log Entries when starting mysql mcp:

2025-08-05T09:13:49+02:00 INFO  [context_server::client] starting context server (executable="npx", args=["@benborla29/mcp-server-mysql"])
2025-08-05T09:13:49+02:00 INFO  [context_server] starting context server some-mcp-server
2025-08-05T09:14:49+02:00 ERROR [context_server::client] cancelled csp request task for "initialize" id 0 which took over 60s
2025-08-05T09:14:49+02:00 ERROR [project::context_server_store] some-mcp-server context server failed to start: Context server request timeout 

Zed Version and System Specs

Zed: v0.197.5 (Zed)
OS: macOS 15.5.0
Memory: 48 GiB
Architecture: aarch64

[notpeter]

Is there any hints in your Zed.log as to what might be happening?

I ommited personal Details like DB connection and Folder names. But Even without, both servers work fine in other cli tools like crush,open Code and Claude Code

Your instructions for mcp-server-mysql are incomplete -- I would expect you would need to specify all the necessary environment variables (if you are doing this, please include redacted versions in your details above). As-is this is insufficient to reproduce because I can't tell if you're just missing an env var / providing them incorrectly. Perhaps your zed log has more?

[Askath]

Is there any hints in your Zed.log as to what might be happening?

I ommited personal Details like DB connection and Folder names. But Even without, both servers work fine in other cli tools like crush,open Code and Claude Code

Your instructions for mcp-server-mysql are incomplete -- I would expect you would need to specify all the necessary environment variables (if you are doing this, please include redacted versions in your details above). As-is this is insufficient to reproduce because I can't tell if you're just missing an env var / providing them incorrectly. Perhaps your zed log has more?

I added the full config for the mcp-server-mysql and added the Logs. Again, same config works in other clients.
Since until yesterday I had a problem with using Zed and our corporate certificate, maybe that could have something to do with it?

I had to add the following fix to solve that issue so I could sign in. Did not fix the MCP issue though

#35580

[Askath]

I might have found the issue. Running npx as mcp command fails because for some reason the corporate certificate is not used that I set in

export NODE_EXTRA_CA_CERTS=
export SSL_CERT_FILE