VS Code extension starts the same MCP stdio server twice from one config entry #19338

[mcp_servers.serena]
command = "uvx"
args = [
  "--from",
  "git+https://github.com/oraios/serena",
  "serena",
  "start-mcp-server",
  "--context",
  "codex"
]

### What steps can reproduce the bug?

1. Start VS Code with the OpenAI ChatGPT/Codex extension installed.
2. Open a workspace that has Codex MCP configured in ~/.codex/config.toml.
3. Configure one Serena MCP server only:

[mcp_servers.serena]
command = "uvx"
args = [
  "--from",
  "git+https://github.com/oraios/serena",
  "serena",
  "start-mcp-server",
  "--context",
  "codex"
]

4. Start/open the Codex Agent session from the VS Code extension.
5. Trigger/use the Serena MCP tools from Codex.
6. Inspect the process tree.

Expected result:
Only one Serena MCP server process should be started.

Actual result:
Two identical Serena MCP server process trees are started by the same codex.exe app-server process.

Observed process tree:

codex.exe app-server --analytics-default-enabled
  -> uvx.exe --from git+https://github.com/oraios/serena serena start-mcp-server --context codex
     -> uv.exe tool uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context codex
        -> serena.exe start-mcp-server --context codex

codex.exe app-server --analytics-default-enabled
  -> uvx.exe --from git+https://github.com/oraios/serena serena start-mcp-server --context codex
     -> uv.exe tool uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context codex
        -> serena.exe start-mcp-server --context codex

Both uvx.exe processes had the same parent process:
codex.exe app-server --analytics-default-enabled

There was only one [mcp_servers.serena] entry in ~/.codex/config.toml.
VS Code settings did not contain a separate Serena/MCP configuration.


### What is the expected behavior?

When a single MCP server is configured once in ~/.codex/config.toml, the Codex VS Code extension should start exactly one MCP server process for that entry.

For the Serena MCP config below, I expect one process tree only:

codex.exe app-server
  -> uvx.exe --from git+https://github.com/oraios/serena serena start-mcp-server --context codex
     -> uv.exe tool uvx ...
        -> serena.exe start-mcp-server --context codex

The extension should not start two identical uvx/serena MCP process trees from the same codex.exe app-server parent unless there are two distinct configured MCP entries or two separate Codex Agent sessions that intentionally require separate MCP servers.


### Additional information

This does not appear to be VS Code itself launching Serena directly. The duplicate launch appears under the OpenAI/Codex extension's codex.exe app-server process.

In the same process snapshot, another MCP server (xcodebuildmcp) also appeared to be started twice under the same codex.exe parent, so this may be a duplicate MCP initialization issue rather than Serena-specific behavior.