MCP naming conflict: `/mcp` UI lists user-level entry but runtime uses repo-level settings

### Describe the bug

When the same MCP server name appears in both the user-level config (`$HOME/.copilot/mcp-config.json`) and a project-level config (`./.mcp.json` or `.github/mcp-config.json`), the CLI silently uses **different sources for the displayed metadata vs. the actually-launched process**:

- The `/mcp` UI shows the server under the **user-level** section (with the source path of the user config), strongly implying the user-level definition is in effect.
- But the **process that actually gets launched uses the project-level args/command** — the repo-level entry shadows the user-level one at runtime.

This is extremely confusing because you have no in-CLI indication that the displayed config isn't the one being used. In my case the user-level entry passed `--browser msedge` to `@playwright/mcp`, while the project's `.mcp.json` defined the same server with no `--browser` flag (defaulting to chrome). `/mcp` showed me the user-level entry with msedge, but the actually-running playwright process was looking for chrome and failing.

The naming conflict should at minimum be surfaced clearly (e.g., a warning in `/mcp` like "this server is also defined in `./.mcp.json` and the project definition is being used"), and ideally a documented precedence policy with an easy way to opt into whichever scope the user prefers.

### Affected version

1.0.49-6

### Steps to reproduce the behavior

1. Define an MCP server in `$HOME/.copilot/mcp-config.json` with distinct args, e.g.:
```json
"playwright": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@playwright/mcp@latest", "--browser", "msedge"]
}
```
2. In a separate repo, define the **same server name** in `./.mcp.json` with different args (e.g., no `--browser` flag, so it defaults to chrome).
3. Launch `copilot` from inside that repo.
4. Run `/mcp`. Observe that the playwright entry appears in the user-level section showing the user-level args.
5. Trigger any playwright tool call. Observe that the launched process uses the project-level args (looking for chrome instead of msedge).

### Expected behavior

Either:

1. The `/mcp` UI should display whichever config is **actually in effect**, with a clear annotation when there's a naming conflict ("shadowed by `./.mcp.json`" or similar), **OR**
2. A naming conflict should be surfaced as a warning/error at startup with guidance, **OR**
3. Configs should be merged with a documented precedence (and `/mcp` should display the merged result with provenance per field).

In all cases, the displayed metadata and the actually-launched process must match.

### Additional context

- OS: Windows 11 (PowerShell 7).
- This isn't just a UI bug; it actively breaks debugging. I spent significant time troubleshooting why playwright was looking for chrome when the only config I could see said msedge. The fix turned out to be "realise the project's `.mcp.json` is shadowing the user config you're looking at."
- Related: there's no easy way to ignore the project-level configs short of editing/deleting `.mcp.json` in the repo (which can't be committed because it's a shared file). See the related feature request for a `--disable-repo-mcps` flag.

Comienza con el comando /mcp y las fuentes de configuración de MCP mencionadas en el informe: $HOME/.copilot/mcp-config.json, ./.mcp.json y .github/mcp-config.json. Reproduce nombres de servidor duplicados con argumentos distintos y, a continuación, compara la fuente mostrada con el proceso iniciado. Se considera terminado cuando los conflictos se muestran y los metadatos de /mcp coinciden con el proceso efectivo, y el comportamiento de precedencia u opt-out está documentado.

Escrito por el modelo de indexación a partir del texto del issue.