Fix CS0006 errors when NuGet cache cleared during file-based app recompilation

[Copilot]

Clearing NuGet cache (dotnet nuget locals all -c) breaks recompilation of file-based apps when using cached CSC arguments. The optimized CSC path references DLLs from NuGet cache (e.g., ILLink.RoslynAnalyzer.dll) that no longer exist after cache clearing, causing CS0006 metadata file errors.

Changes

Reactive fallback on CS0006 errors

• Detect CS0006 errors in CSC compilation output
• Set fallbackToNormalBuild = true to trigger existing MSBuild fallback
• Report errors only to verbose output, not standard output
• Error code "CS0006" is language-independent; only the message text varies by locale

Test coverage

• Added CscOnly_AfterMSBuild_NuGetCacheCleared test following existing test patterns
• Includes proper XML doc comments with issue reference
• Documents testing limitations (MSBuild restore recreates deleted packages, making negative testing challenging)

Original prompt

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This section details on the original issue you should resolve

<issue_title>Clearing NuGet package local cache breaks re-compiling file-based apps</issue_title>
<issue_description>### Describe the bug
Clearing local NuGet package cache breaks re-compiling file-based apps.

To Reproduce

1. Add NuGet package source (at least until 10.0.1 packages exist on nuget.org):
   dotnet nuget add source https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet10/nuget/v3/index.json -n dotnet10
2. Create a whatever.cs file with execute (chmod +x whatever.cs) with below contents.
3. Execute it to compile and run the first time:
   ./whatever.cs
4. Clear NuGet package local cache:
   dotnet nuget locals all -c
5. At this point, executing ./whatever.cs still works fine (cached binary)
6. Make any slight tweak to the code, e.g. the string passed to WriteLine: Console.WriteLine("I broke it!");
7. Now, trying to rebuild / execute will fail:
   ./whatever.cs

Error:

error CS0006: Metadata file '/Users/bruck/.nuget/packages/microsoft.net.illink.tasks/10.0.0-rtm.25513.102/analyzers/dotnet/cs/ILLink.CodeFixProvider.dll' could not be found
error CS0006: Metadata file '/Users/bruck/.nuget/packages/microsoft.net.illink.tasks/10.0.0-rtm.25513.102/analyzers/dotnet/cs/ILLink.RoslynAnalyzer.dll' could not be found

The build failed. Fix the build errors and run again.

Code:

#!/usr/bin/env dotnet
#:property TargetFramework=net10.0
#:property RuntimeFrameworkVersion=10.0.0-rtm.25513.102
Console.WriteLine("Hello from a .NET script!");

Exceptions (if any)

Further technical details

.NET SDK:
Version: 10.0.101
Commit: e17b0d08de
Workload version: 10.0.100-manifests.c57ac48b
MSBuild version: 18.0.3+e17b0d08d

Runtime Environment:
OS Name: Mac OS X
OS Version: 15.7
OS Platform: Darwin
RID: osx-arm64
Base Path: /usr/local/share/dotnet/sdk/10.0.101/

.NET workloads installed:
There are no installed workloads to display.
Configured to use workload sets when installing new manifests.
No workload sets are installed. Run "dotnet workload restore" to install a workload set.

Host:
Version: 10.0.1
Architecture: arm64
Commit: e17b0d08de

.NET SDKs installed:
8.0.407 [/usr/local/share/dotnet/sdk]
8.0.411 [/usr/local/share/dotnet/sdk]
10.0.101 [/usr/local/share/dotnet/sdk]

.NET runtimes installed:
Microsoft.AspNetCore.App 8.0.14 [/usr/local/share/dotnet/shared/Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 8.0.17 [/usr/local/share/dotnet/shared/Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 10.0.1 [/usr/local/share/dotnet/shared/Microsoft.AspNetCore.App]
Microsoft.NETCore.App 8.0.14 [/usr/local/share/dotnet/shared/Microsoft.NETCore.App]
Microsoft.NETCore.App 8.0.17 [/usr/local/share/dotnet/shared/Microsoft.NETCore.App]
Microsoft.NETCore.App 10.0.1 [/usr/local/share/dotnet/shared/Microsoft.NETCore.App]

Other architectures found:
None

Environment variables:
Not set

global.json file:
Not found

Learn more:
https://aka.ms/dotnet/info

Download .NET:
https://aka.ms/dotnet/download
</issue_description>

<agent_instructions>If the optimized file-based app compilation fails with CS0006, let's fallback to full msbuild (and avoid reporting the original errors; just perhaps to the verbose reporter). Also add a test for this (running a simple app; clearing nuget cache; changing .cs file; rerunning again - should fail without the fix - the app in this test doesn't even need to reference packages because there are some referenced implicitly due to PublishAot=true being the default; but if that ever changes consider adding also a test where we specifically reference some package and it can have PublishAot=false).</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@jjonescz Thanks for reporting this. There is an optimization to recompile using C# compiler only (skipping MSBuild, so also restore) on subsequent re-runs of file-based apps. You can force full recompilation using `dotnet run app.cs --no-cache` (or `dotnet build app.cs`).

I don't think the NuGet command can reliably find and clear the file-based app cache. Instead, the optimization logic could check that the referenced DLLs still exist and fallback to full build if not (we could also do that only if the optimized compilation fails; to not slow down the fast path).</comment_new>

• Fixes Clearing NuGet package local cache breaks re-compiling file-based apps #51597

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[Copilot]

Pull Request Overview

This PR adds a fallback mechanism to handle CS0006 errors (missing metadata files) during fast CSC-only compilation, ensuring that the build falls back to full MSBuild when NuGet packages are missing. This addresses scenarios where the NuGet cache is cleared between builds.

Key Changes:

• Added CS0006 error detection in the fast compilation path that triggers a fallback to full MSBuild
• Relocated the binary logger warning message to display only after successful CSC compilation
• Added comprehensive test coverage for NuGet cache clearing scenarios

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
src/Cli/dotnet/Commands/Run/CSharpCompilerCommand.cs	Implements CS0006 error detection logic to trigger fallback to MSBuild when metadata files are missing
src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs	Moves binary logger warning to display only after successful CSC compilation, avoiding misleading messages when falling back to MSBuild
test/dotnet.Tests/CommandTests/Run/RunFileTests.cs	Adds test methods to verify correct behavior when NuGet cache is cleared, and extends the Build helper method to support custom command configuration