v1.0.81 broke compatibility with chroma-mcp

Describe the bug

The update from GitHub Copilot CLI v1.0.80 to v1.0.81 broke compatibility with https://github.com/chroma-core/chroma-mcp

Affected version

GitHub Copilot CLI 1.0.81

Steps to reproduce the behavior

Use an mcp-config.json as follows:

{
  "mcpServers": {
    "io.github.chroma-core/chroma-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "--index-url",
        "https://pypi.org/simple",
        "--with",
        "ollama",
        "chroma-mcp@0.2.6"
      ],
      "env": {
        "CHROMA_DATA_DIR": "C:\\Users\\REDACTED\\chroma-embeddings",
        "CHROMA_CLIENT_TYPE": "persistent"
      },
      "tools": [
        "*"
      ]
    }
  }
}

Observe the following warning in the log. The MCP server will not work.

2026-08-28T06:30:35.641Z [WARNING] [rust:copilot_runtime::mcp::native_connector] MCP server connection failed {"server_name":"io.github.chroma-core/chroma-mcp","raw_error":"MCP server process exited before completing the MCP initialize handshake (exit code 1) (underlying transport failure: failed to initialize MCP client: connection closed: initialize response)","stderr_detail":"      | CallToolRequest.method\n      |   Input should be 'tools/call' [type=literal_error, input_value='server/discover', input_type=str]\n      |     For further information visit https://errors.pydantic.dev/2.13/v/literal_error\n      | CallToolRequest.params.name\n      |   Field required [type=missing, input_value={'_meta': {'io.modelconte...form': {}, 'url': {}}}}}, input_type=dict]\n      |     For further information visit https://errors.pydantic.dev/2.13/v/missing\n      | ListToolsRequest.method\n      |   Input should be 'tools/list' [type=literal_error, input_value='server/discover', input_type=str]\n      |     For further information visit https://errors.pydantic.dev/2.13/v/literal_error\n      +------------------------------------"}

Expected behavior

The chroma-mcp server should connect and MCP tools should be available.

Additional context

No response

Start with the MCP connection path and the mcp-config.json reproduction shown in the issue, then compare the initialization behavior between GitHub Copilot CLI v1.0.80 and v1.0.81. Use the logged native_connector handshake failure and chroma-mcp@0.2.6 to verify the protocol mismatch. Done means the server connects successfully and its MCP tools are available.