Using `WithReference` on a resource that depends on another resource annoated `ExcludeFromManifest` fails

### Is there an existing issue for this?

- [x] I have searched the existing issues

### Describe the bug

When a resource is marked `ExcludeFromManifest`, it should be excluded from the publish step.

However, if you reference that resource from another resource using `WithReference`, it appears to be considered a dependency in the pipeline graph during `aspire deploy` or `aspire do`.

Example:

```c#
var mcpInspector = builder.AddMcpInspector("mcp-inspector", options =>
{
options.InspectorVersion = "0.18.0";
})
.WithMcpServer(mcp, path: "/");

mcp.WithReference(mcpInspector);
```

The `McpInspectorResource` is marked excluded from manifest in the toolkit.

Since `mcp` references `mcpInspector`, you will get an error during deployment:

```
❯ aspire deploy
13:26:27 (pipeline-execution) → Starting pipeline-execution...
13:26:27 (pipeline-execution) ✗ [ERR] Container app context not found for resource mcp-inspector.
13:26:27 (pipeline-execution) ✗ Failed
```

See https://github.com/CommunityToolkit/Aspire/issues/1093

### Expected Behavior

It should be safe to reference an excluded resource, and should be a no-op (no reference is created/maintained).

Otherwise, the error should be more clear. I thought initially it was an ACA deployment error.

### Steps To Reproduce

It should be trivial to reproduce but there's an example AppHost I have here:

https://github.com/kamranayub/pluralsight-course-mcp-in-practice/blob/ba0c08baf11817c7ae8d0b757935e6d8c25566cc/everything-demo/Globomantics.Demo.AppHost/AppHost.cs#L126-L136

### Exceptions (if any)

_No response_

### .NET Version info

_No response_

### Anything else?

**Workaround**

Add a conditional for `IsRunMode` before adding the reference:

```c#
var mcpInspector = builder.AddMcpInspector("mcp-inspector", options =>
{
options.InspectorVersion = "0.18.0";
})
.WithMcpServer(mcp, path: "/");

if (builder.ExecutionContext.IsRunMode) {
mcp.WithReference(mcpInspector);
}
```

Start with the linked AppHost.cs reproduction around lines 126-136 and run aspire deploy or aspire do with the WithReference and ExcludeFromManifest combination. Trace how the dependency graph handles the excluded mcp-inspector resource. Done means referencing an excluded resource is a no-op or produces a clear error instead of failing with a missing container app context.

Written by the indexing model from the issue text.