AzureFunctionsAssemblyRepro

Reproduction steps:

1. Run the function.
2. Visit the endpoint.

To repro without cloning:

1. Create a new Azure Functions app (C#, .NET Core v3) with a single HTTP-triggered function (anonymous auth).
2. Update the Functions SDK version to 3.0.5.
3. Add the Microsoft.IdentityModel.Tokens package and reference a type from that package in your function.
4. Visit the endpoint.
5. Enjoy your System.Private.CoreLib: Exception while executing function: Function1. FunctionApp1: Could not load file or assembly 'Microsoft.IdentityModel.Tokens, Version=6.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35'. The system cannot find the file specified.
6. ???
7. Profit!

This likely happens with many other packages; I just happened to hit it with Microsoft.IdentityModel.Tokens.

Details

I suspect the problem is caused by the RemoveRuntimeDependencies task from the Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator package. MSBuild logs seem to implicate it.

Microsoft.NET.Sdk.Functions v3.0.5 (Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator v1.1.5)

Build succeeds, but most of the assemblies listed below are deleted from the output directory, causing runtime failure:

1>  Using "GenerateFunctions" task from assembly "C:\Users\steph\.nuget\packages\microsoft.net.sdk.functions\3.0.5\build\..\tools\netcoreapp3.0\\Microsoft.NET.Sdk.Functions.MSBuild.dll".
1>  Task "GenerateFunctions"
1>    Function generator path: 'dotnet'
1>    Microsoft.NET.Sdk.Functions.Generator.dll "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\FunctionApp1.dll " "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\ " "False "
1>  Done executing task "GenerateFunctions".
1>Target _GenerateFunctionsExtensionsMetadataPostBuild:
1>  Using "GenerateFunctionsExtensionsMetadata" task from assembly "C:\Users\steph\.nuget\packages\microsoft.azure.webjobs.script.extensionsmetadatagenerator\1.1.5\build\..\tools\net46\Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.dll".
1>  Task "GenerateFunctionsExtensionsMetadata"
1>    Extensions generator working directory: 'C:\Users\steph\.nuget\packages\microsoft.azure.webjobs.script.extensionsmetadatagenerator\1.1.5\tools\net46\..\netstandard2.0\generator'
1>    Extensions generator path: 'dotnet'
1>    Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.Console.dll "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin" "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\extensions.json"
1>    Found 52 assemblies to evaluate in 'C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin':
1>      FunctionApp1.dll
1>        Resolving assembly: 'System.Runtime, Version=4.2.2.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a'
1>        Assembly 'System.Runtime' loaded.
1>      Microsoft.AspNetCore.Authentication.Abstractions.dll
1>      Microsoft.AspNetCore.Authentication.Core.dll
1>      Microsoft.AspNetCore.Authorization.dll
1>      Microsoft.AspNetCore.Authorization.Policy.dll
1>      Microsoft.AspNetCore.Hosting.Abstractions.dll
1>      Microsoft.AspNetCore.Hosting.Server.Abstractions.dll
1>      Microsoft.AspNetCore.Http.Abstractions.dll
1>      Microsoft.AspNetCore.Http.dll
1>      Microsoft.AspNetCore.Http.Extensions.dll
1>      Microsoft.AspNetCore.Http.Features.dll
1>      Microsoft.AspNetCore.JsonPatch.dll
1>      Microsoft.AspNetCore.Mvc.Abstractions.dll
1>      Microsoft.AspNetCore.Mvc.Core.dll
1>      Microsoft.AspNetCore.Mvc.Formatters.Json.dll
1>      Microsoft.AspNetCore.Mvc.WebApiCompatShim.dll
1>      Microsoft.AspNetCore.ResponseCaching.Abstractions.dll
1>      Microsoft.AspNetCore.Routing.Abstractions.dll
1>      Microsoft.AspNetCore.Routing.dll
1>      Microsoft.AspNetCore.WebUtilities.dll
1>      Microsoft.Azure.WebJobs.dll
1>      Microsoft.Azure.WebJobs.Host.dll
1>      Microsoft.Azure.WebJobs.Host.Storage.dll
1>      Microsoft.DotNet.PlatformAbstractions.dll
1>      Microsoft.Extensions.Configuration.Abstractions.dll
1>      Microsoft.Extensions.Configuration.Binder.dll
1>      Microsoft.Extensions.Configuration.dll
1>      Microsoft.Extensions.Configuration.EnvironmentVariables.dll
1>      Microsoft.Extensions.Configuration.FileExtensions.dll
1>      Microsoft.Extensions.Configuration.Json.dll
1>      Microsoft.Extensions.DependencyInjection.Abstractions.dll
1>      Microsoft.Extensions.DependencyInjection.dll
1>      Microsoft.Extensions.DependencyModel.dll
1>      Microsoft.Extensions.FileProviders.Abstractions.dll
1>      Microsoft.Extensions.FileProviders.Physical.dll
1>      Microsoft.Extensions.FileSystemGlobbing.dll
1>      Microsoft.Extensions.Hosting.Abstractions.dll
1>      Microsoft.Extensions.Hosting.dll
1>      Microsoft.Extensions.Logging.Abstractions.dll
1>      Microsoft.Extensions.Logging.Configuration.dll
1>      Microsoft.Extensions.Logging.dll
1>      Microsoft.Extensions.ObjectPool.dll
1>      Microsoft.Extensions.Options.ConfigurationExtensions.dll
1>      Microsoft.Extensions.Options.dll
1>      Microsoft.Extensions.Primitives.dll
1>      Microsoft.IdentityModel.Logging.dll
1>      Microsoft.IdentityModel.Tokens.dll
1>      Microsoft.Net.Http.Headers.dll
1>      Microsoft.WindowsAzure.Storage.dll
1>      NCrontab.Signed.dll
1>      Newtonsoft.Json.Bson.dll
1>      Newtonsoft.Json.dll
1>    'C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\extensions.json' successfully written.
1>  Done executing task "GenerateFunctionsExtensionsMetadata".
1>  Task "Move" skipped, due to false condition; ($(_IsFunctionsSdkBuild) == 'true' AND Exists('$(TargetDir)extensions.json')) was evaluated as (true == 'true' AND Exists('C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\extensions.json')).
1>Target _FunctionsBuildCleanOutput:
1>  Using "RemoveRuntimeDependencies" task from assembly "C:\Users\steph\.nuget\packages\microsoft.azure.webjobs.script.extensionsmetadatagenerator\1.1.5\build\..\tools\net46\Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.dll".
1>  Task "RemoveRuntimeDependencies"
1>  Done executing task "RemoveRuntimeDependencies".
1>Target "DotNetPublish" skipped, due to false condition; ( '$(DeployOnBuild)' == 'true' ) was evaluated as ( '' == 'true' ).
1>Target "_PackAsBuildAfterTarget" skipped, due to false condition; ('$(GeneratePackageOnBuild)' == 'true' AND '$(IsInnerBuild)' != 'true') was evaluated as ('false' == 'true' AND '' != 'true').
1>
1>Done building project "FunctionApp1.csproj".
1>
1>Build succeeded.
1>    0 Warning(s)
1>    0 Error(s)
1>
1>Time Elapsed 00:00:01.94

Microsoft.NET.Sdk.Functions v3.0.3 (Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator v1.1.3)

If you roll back to v3.0.3, your build will succeed, the assemblies are present in the output directory, and the function succeeds at runtime. The 3.0.3 build does not use the RemoveRuntimeDependencies task:

1>  Using "GenerateFunctions" task from assembly "C:\Users\steph\.nuget\packages\microsoft.net.sdk.functions\3.0.3\build\..\tools\netcoreapp3.0\\Microsoft.NET.Sdk.Functions.MSBuild.dll".
1>  Task "GenerateFunctions"
1>    Function generator path: 'dotnet'
1>    Microsoft.NET.Sdk.Functions.Generator.dll "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\FunctionApp1.dll " "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\ " "False "
1>  Done executing task "GenerateFunctions".
1>Target "DotNetPublish" skipped, due to false condition; ( '$(DeployOnBuild)' == 'true' ) was evaluated as ( '' == 'true' ).
1>Target _GenerateFunctionsExtensionsMetadataPostBuild:
1>  Using "GenerateFunctionsExtensionsMetadata" task from assembly "C:\Users\steph\.nuget\packages\microsoft.azure.webjobs.script.extensionsmetadatagenerator\1.1.3\build\..\tools\net46\Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.dll".
1>  Task "GenerateFunctionsExtensionsMetadata"
1>    Extensions generator working directory: 'C:\Users\steph\.nuget\packages\microsoft.azure.webjobs.script.extensionsmetadatagenerator\1.1.3\tools\net46\..\netstandard2.0\generator'
1>    Extensions generator path: 'dotnet'
1>    Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.Console.dll "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin" "C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\extensions.json"
1>    Found 54 assemblies to evaluate in 'C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin':
1>      FunctionApp1.dll
1>        Resolving assembly: 'System.Runtime, Version=4.2.2.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a'
1>        Assembly 'System.Runtime' loaded.
1>      Microsoft.AspNetCore.Authentication.Abstractions.dll
1>      Microsoft.AspNetCore.Authentication.Core.dll
1>      Microsoft.AspNetCore.Authorization.dll
1>      Microsoft.AspNetCore.Authorization.Policy.dll
1>      Microsoft.AspNetCore.Hosting.Abstractions.dll
1>      Microsoft.AspNetCore.Hosting.Server.Abstractions.dll
1>      Microsoft.AspNetCore.Http.Abstractions.dll
1>      Microsoft.AspNetCore.Http.dll
1>      Microsoft.AspNetCore.Http.Extensions.dll
1>      Microsoft.AspNetCore.Http.Features.dll
1>      Microsoft.AspNetCore.JsonPatch.dll
1>      Microsoft.AspNetCore.Mvc.Abstractions.dll
1>      Microsoft.AspNetCore.Mvc.Core.dll
1>      Microsoft.AspNetCore.Mvc.Formatters.Json.dll
1>      Microsoft.AspNetCore.Mvc.WebApiCompatShim.dll
1>      Microsoft.AspNetCore.ResponseCaching.Abstractions.dll
1>      Microsoft.AspNetCore.Routing.Abstractions.dll
1>      Microsoft.AspNetCore.Routing.dll
1>      Microsoft.AspNetCore.WebUtilities.dll
1>      Microsoft.Azure.WebJobs.dll
1>      Microsoft.Azure.WebJobs.Host.dll
1>      Microsoft.Azure.WebJobs.Host.Storage.dll
1>      Microsoft.Build.Framework.dll
1>      Microsoft.Build.Utilities.Core.dll
1>      Microsoft.DotNet.PlatformAbstractions.dll
1>      Microsoft.Extensions.Configuration.Abstractions.dll
1>      Microsoft.Extensions.Configuration.Binder.dll
1>      Microsoft.Extensions.Configuration.dll
1>      Microsoft.Extensions.Configuration.EnvironmentVariables.dll
1>      Microsoft.Extensions.Configuration.FileExtensions.dll
1>      Microsoft.Extensions.Configuration.Json.dll
1>      Microsoft.Extensions.DependencyInjection.Abstractions.dll
1>      Microsoft.Extensions.DependencyInjection.dll
1>      Microsoft.Extensions.DependencyModel.dll
1>      Microsoft.Extensions.FileProviders.Abstractions.dll
1>      Microsoft.Extensions.FileProviders.Physical.dll
1>      Microsoft.Extensions.FileSystemGlobbing.dll
1>      Microsoft.Extensions.Hosting.Abstractions.dll
1>      Microsoft.Extensions.Hosting.dll
1>      Microsoft.Extensions.Logging.Abstractions.dll
1>      Microsoft.Extensions.Logging.Configuration.dll
1>      Microsoft.Extensions.Logging.dll
1>      Microsoft.Extensions.ObjectPool.dll
1>      Microsoft.Extensions.Options.ConfigurationExtensions.dll
1>      Microsoft.Extensions.Options.dll
1>      Microsoft.Extensions.Primitives.dll
1>      Microsoft.IdentityModel.Logging.dll
1>      Microsoft.IdentityModel.Tokens.dll
1>      Microsoft.Net.Http.Headers.dll
1>      Microsoft.WindowsAzure.Storage.dll
1>      NCrontab.Signed.dll
1>      Newtonsoft.Json.Bson.dll
1>      Newtonsoft.Json.dll
1>    'C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\bin\extensions.json' successfully written.
1>  Done executing task "GenerateFunctionsExtensionsMetadata".
1>  Task "Move" skipped, due to false condition; ($(_IsFunctionsSdkBuild) == 'true' AND Exists('$(TargetDir)extensions.json')) was evaluated as (true == 'true' AND Exists('C:\Work\AzureFunctionsAssemblyRepro\FunctionApp1\FunctionApp1\bin\Debug\netcoreapp3.1\extensions.json')).
1>Target "_PackAsBuildAfterTarget" skipped, due to false condition; ('$(GeneratePackageOnBuild)' == 'true' AND '$(IsInnerBuild)' != 'true') was evaluated as ('false' == 'true' AND '' != 'true').
1>
1>Done building project "FunctionApp1.csproj".
1>
1>Build succeeded.
1>    0 Warning(s)
1>    0 Error(s)
1>
1>Time Elapsed 00:00:02.10