ASP.net core 1.0 web.config está sendo substituído, causando exceções de CGI

Eu tenho um web.config funcionando, como mostrado abaixo:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
  <!--
    Configure your application settings in appsettings.json. Learn more at http://go.microsoft.com/fwlink/?LinkId=786380
  -->
  <system.webServer>
    <handlers>
      <add name="aspNetCore" path="*" verb="*" modules="AspNetCoreModule" resourceType="Unspecified" />
    </handlers>
    <aspNetCore processPath="dotnet" arguments=".\Example.dll" stdoutLogEnabled="false" stdoutLogFile="\\?\%home%\LogFiles\stdout" forwardWindowsAuthToken="false" />
  </system.webServer>
</configuration>

Mas de alguma forma o Visual studio está atualizando meu web.config para:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
  <!--
    Configure your application settings in appsettings.json. Learn more at http://go.microsoft.com/fwlink/?LinkId=786380
  -->
  <system.webServer>
    <handlers>
      <add name="aspNetCore" path="*" verb="*" modules="AspNetCoreModule" resourceType="Unspecified" />
    </handlers>
    <aspNetCore processPath="%LAUNCHER_PATH%" arguments="%LAUNCHER_ARGS%" stdoutLogEnabled="false" stdoutLogFile="\\?\%home%\LogFiles\stdout" forwardWindowsAuthToken="false" />
  </system.webServer>
</configuration>

Isso funciona no Visual studio através dos menus de publicação (e funciona uma vez implantado em um aplicativo da web azul). No entanto, se eu usar a CLI do dotnet, como a publicação do dotnet, ele não funcionará, pois mantém esse web.config com as variáveis:% LAUNCHER_PATH% e% LAUNCHER_ARGS% em vez dos meus: dotnet e. \ Example.dll desejados.

Nota: Meu servidor de construção não polui o web.config ao usar o dotnet restore e o dotnet build via linha de comando. Nem ao usar o MSBuild para criar meu sln. Eu tenho o visual studio 2015 localmente e no meu servidor de compilação e verifiquei se minhas versões da linha de comando correspondem ao cli "dotnet".

Como não posso combater o Visual studio revertendo meu web.config antes de cada confirmação? Estou claramente fazendo algo errado que deve ser uma correção fácil de configuração?

Atualizar:

Startup.cs

public Startup(IHostingEnvironment env)
{
    var builder = new ConfigurationBuilder()
        .SetBasePath(env.ContentRootPath)
        .AddJsonFile("appsettings.json", optional: true, reloadOnChange: true)
        .AddJsonFile($"appsettings.{env.EnvironmentName}.json", optional: true)
        .AddEnvironmentVariables();
    Configuration = builder.Build();
}

Appsettings.json

{
  "Logging": {
    "IncludeScopes": false,
    "LogLevel": {
      "Default": "Debug",
      "System": "Information",
      "Microsoft": "Information"
    }
  }
}

Program.cs

public static void Main(string[] args)
{
    var host = new WebHostBuilder()
        .UseKestrel()
        .UseContentRoot(Directory.GetCurrentDirectory())
        .UseIISIntegration()
        .UseStartup<Startup>()
        .Build();

    host.Run();
}

Project.json

{
  "version": "1.0.0-*",
  "compilationOptions": {
    "emitEntryPoint": true,

    "exclude": [
      "wwwroot",
      "typings",
      "node_modules"
    ],
    "publishExclude": [
      "**.user",
      "**.vspscc"
    ]
  },

  "dependencies": {
    "Microsoft.NETCore.App": {
      "version": "1.0.0",
      "type": "platform"
    }
  },

  "tools": {
    "Microsoft.AspNetCore.Server.IISIntegration.Tools": {
      "version": "1.0.0-preview2-final",
      "imports": "portable-net45+win8+netstandard1.6"
    },

    "Microsoft.AspNetCore.Razor.Tools": {
      "version": "1.0.0-preview2-final",
      "imports": "portable-net45+win8+netstandard1.6"
    }
  },

  "frameworks": {
    "netcoreapp1.0": {
      "imports": [
        "netstandard1.4",
        "dnxcore50"
      ],
      "dependencies": {
        "Microsoft.AspNetCore.Diagnostics": "1.0.0",
        "Microsoft.AspNetCore.Mvc": "1.0.0",
        "Microsoft.AspNetCore.Server.IISIntegration": "1.0.0",
        "Microsoft.AspNetCore.Server.Kestrel": "1.0.0",
        "Microsoft.AspNetCore.StaticFiles": "1.0.0",
        "Microsoft.Extensions.Configuration.EnvironmentVariables": "1.0.0",
        "Microsoft.Extensions.Configuration.Json": "1.0.0",
        "Microsoft.Extensions.Logging": "1.0.0",
        "Microsoft.Extensions.Logging.Console": "1.0.0",
        "Microsoft.Extensions.Logging.Debug": "1.0.0",
        "Microsoft.VisualStudio.Web.BrowserLink.Loader": "14.0.0",
        "Microsoft.Extensions.Configuration.UserSecrets": "1.0.0",
        "Microsoft.AspNetCore.Mvc.TagHelpers": "1.0.0",
        "Microsoft.AspNetCore.Hosting": "1.0.0",
        "System.ServiceModel.Primitives": "4.1.0",
        "System.ServiceModel.Http": "4.1.0",
        "System.Private.ServiceModel": "4.1.0",
        "Presentation.Common": "*",
        "System.Runtime": "4.1.0",
        "System.Runtime.Numerics": "4.0.1",
        "SharedContract": "*"
      }
    }
  },

  "runtimes": {
    "win10-x64": {},
    "win10-x86": {},
    "win8-x64": {},
    "win8-x86": {}
  },

  "buildOptions": {
    "emitEntryPoint": true,
    "preserveCompilationContext": true
  },

  "publishOptions": {
    "include": [
      "wwwroot",
      "Views",
      "appsettings.json",
      "web.config"
    ]
  },

  "scripts": {
    "prepublish": [ "npm install", "gulp rebuild", "gulp min" ],
    "postpublish": [ "dotnet publish-iis --publish-folder %publish:OutputPath% --framework %publish:FullTargetFramework%" ]
  },

  "devDependencies": {
    "gulp": "^3.9.1",
    "gulp-clean": "^0.3.2",
    "gulp-concat": "^2.6.0",
    "gulp-less": "3.0.2",
    "gulp-tsc": "^1.1.5",
    "gulp-typescript": "^2.13.1",
    "lite-server": "^2.2.0",
    "path": "^0.12.7",
    "rimraf": "2.3.2",
    "typescript": "^1.8.10",
    "typings": "^0.8.1"
  }
}

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