func pack errors in custom handler project because 'functions.metadata' not found

### Version

4.3.0

### Description

Running `func pack` in a custom handler errors because `'functions.metadata' not found in deployment structure`. The custom handler is an mcp server, and has FWR set to `dotnet-isolated`. Running `dotnet publish` as suggested doesn't help -

```
local.settings.json found in root directory (/Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet).
Resolving worker runtime to 'dotnet-isolated'.
local.settings.json found in root directory (/Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet).
Resolving worker runtime to 'dotnet-isolated'.

Validating project...

Validate host.json: PASSED

Building .NET project...
Determining projects to restore...
All projects are up-to-date for restore.
QuickstartWeatherServer -> /Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet/bin/Release/net8.0/QuickstartWeatherServer.dll
QuickstartWeatherServer -> /Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet/output/


Validating published output...
Validate Published Structure: FAILED
Required file 'functions.metadata' not found in deployment structure. Ensure 'dotnet publish' has been run.
Published output validation failed: Required file 'functions.metadata' not found in deployment structure. Ensure 'dotnet publish' has been run.
```

### Running command inside output directory

I tried running `func pack` inside the `output` directory instead of the root. Ran into a different error -

```
lily@MacBookPro output % func pack
local.settings.json found in root directory (/Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet/output).
Resolving worker runtime to 'dotnet-isolated'.
local.settings.json found in root directory (/Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet/output).
Resolving worker runtime to 'dotnet-isolated'.

Validating project...

Validate host.json: PASSED

Building .NET project...
MSBUILD : error MSB1003: Specify a project or solution file. The current working directory does not contain a project or solution file.

Error publishing .NET project
```
Here's what's inside that directory
```
/Users/lily/Desktop/Functions/mcp/functions-hosting/test/mcp-sdk-functions-hosting-dotnet/output
lily@MacBookPro output % ls -la
total 3304
drwxr-xr-x 22 lily staff 704 Oct 23 19:22 .
drwxr-xr-x@ 24 lily staff 768 Oct 27 10:50 ..
-rw-r--r-- 1 lily staff 361 Oct 23 19:09 host.json
drwxr-xr-x 5 lily staff 160 Oct 23 19:22 infra
-rw-r--r-- 1 lily staff 175 Oct 14 12:42 local.settings.json
-rwxr--r-- 1 lily staff 332856 Jun 10 13:55 Microsoft.Extensions.AI.Abstractions.dll
-rwxr--r-- 1 lily staff 63768 Sep 16 2024 Microsoft.Extensions.DependencyInjection.Abstractions.dll
-rwxr--r-- 1 lily staff 30480 Sep 16 2024 Microsoft.Extensions.Diagnostics.Abstractions.dll
-rwxr--r-- 1 lily staff 51472 Sep 16 2024 Microsoft.Extensions.Hosting.Abstractions.dll
-rwxr--r-- 1 lily staff 65288 Jan 16 2025 Microsoft.Extensions.Logging.Abstractions.dll
-rwxr--r-- 1 lily staff 64776 Jan 17 2024 Microsoft.Extensions.Options.dll
-rwxr--r-- 1 lily staff 60416 Jun 20 12:25 ModelContextProtocol.AspNetCore.dll
-rwxr--r-- 1 lily staff 729600 Jun 20 12:25 ModelContextProtocol.Core.dll
-rwxr--r-- 1 lily staff 32256 Jun 20 12:25 ModelContextProtocol.dll
-rwxr-xr-x 1 lily staff 124448 Oct 23 19:18 QuickstartWeatherServer
-rw-r--r-- 1 lily staff 10072 Oct 23 19:18 QuickstartWeatherServer.deps.json
-rw-r--r-- 1 lily staff 16384 Oct 23 19:18 QuickstartWeatherServer.dll
-rw-r--r-- 1 lily staff 23452 Oct 23 19:18 QuickstartWeatherServer.pdb
-rw-r--r-- 1 lily staff 469 Oct 23 19:18 QuickstartWeatherServer.runtimeconfig.json
-rw-r--r-- 1 lily staff 53 Oct 15 17:30 QuickstartWeatherServer.staticwebassets.endpoints.json
-rwxr--r-- 1 lily staff 41752 May 8 19:55 System.Net.ServerSentEvents.dll
-rw-r--r-- 1 lily staff 499 Oct 23 19:22 web.config
```

FYI @im-samz

### Steps to reproduce

1. Clone this repo: https://github.com/Azure-Samples/mcp-sdk-functions-hosting-dotnet
2. Run `func pack` in the root

Reproduce with the mcp-sdk-functions-hosting-dotnet sample and run `func pack` from its root, then compare the published `output` directory with the required `functions.metadata` validation. Trace the `func pack` project discovery and published-output validation paths, including handling of `host.json` and the project root. Done means the sample packs successfully without the missing-metadata or MSBuild errors.

Written by the indexing model from the issue text.