Eu tenho o projeto API do ASP.NET WEB com o arquivo Web.conig. Quando ele é compilado no VS2015, nenhum erro e nenhum aviso é relatado. No entanto, quando crio este projeto no TeamCity usando a etapa de compilação do MSBuild, recebo o aviso MSB3247:

[ResolveAssemblyReferences] ResolveAssemblyReference
[14:30:01] : [ResolveAssemblyReference] No way to resolve conflict between "protobuf-net, Version=2.0.0.602, Culture=neutral, PublicKeyToken=257b51d87d2e4d67" and "protobuf-net, Version=2.0.0.480, Culture=neutral, PublicKeyToken=257b51d87d2e4d67". Choosing "protobuf-net, Version=2.0.0.602, Culture=neutral, PublicKeyToken=257b51d87d2e4d67" arbitrarily.
[14:30:01] : [ResolveAssemblyReference] No way to resolve conflict between "Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed" and "Newtonsoft.Json, Version=4.5.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed". Choosing "Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed" arbitrarily.
[14:30:01] : [ResolveAssemblyReference] Consider app.config remapping of assembly "protobuf-net, Culture=neutral, PublicKeyToken=257b51d87d2e4d67" from Version "2.0.0.602" [] to Version "2.0.0.668" [D:\TeamCity\buildAgent\work\2772494ce0e0bbd7\branches\Stategic.Window.Release1\src\Strategic.Window\packages\protobuf-net.2.0.0.668\lib\net40\protobuf-net.dll] to solve conflict and get rid of warning.
[14:30:01] : [ResolveAssemblyReference] Consider app.config remapping of assembly "Newtonsoft.Json, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed" from Version "6.0.0.0" [] to Version "7.0.0.0" [D:\TeamCity\buildAgent\work\2772494ce0e0bbd7\branches\Stategic.Window.Release1\src\Strategic.Window\packages\Newtonsoft.Json.7.0.1\lib\net45\Newtonsoft.Json.dll] to solve conflict and get rid of warning.
[14:30:01] : [ResolveAssemblyReference] Consider app.config remapping of assembly "RazorEngine, Culture=neutral, PublicKeyToken=9ee697374c7e744a" from Version "3.0.8.0" [] to Version "3.7.4.0" [D:\TeamCity\buildAgent\work\2772494ce0e0bbd7\branches\Stategic.Window.Release1\src\Strategic.Window\packages\RazorEngine.3.7.4\lib\net45\RazorEngine.dll] to solve conflict and get rid of warning.
[14:30:01] : [ResolveAssemblyReference] Consider app.config remapping of assembly "WebGrease, Culture=neutral, PublicKeyToken=31bf3856ad364e35" from Version "1.5.1.25624" [] to Version "1.5.2.14234" [D:\TeamCity\buildAgent\work\2772494ce0e0bbd7\branches\Stategic.Window.Release1\src\Strategic.Window\packages\WebGrease.1.5.2\lib\WebGrease.dll] to solve conflict and get rid of warning.
[14:30:01]W: [ResolveAssemblyReference] C:\Program Files (x86)\MSBuild\14.0\bin\Microsoft.Common.CurrentVersion.targets(1819, 5): warning MSB3247: Found conflicts between different versions of the same dependent assembly. In Visual Studio, double-click this warning (or select it and press Enter) to fix the conflicts; otherwise, add the following binding redirects to the "runtime" node in the application configuration file: <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"><dependentAssembly><assemblyIdentity name="protobuf-net" culture="neutral" publicKeyToken="257b51d87d2e4d67" /><bindingRedirect oldVersion="0.0.0.0-2.0.0.668" newVersion="2.0.0.668" /></dependentAssembly></assemblyBinding><assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"><dependentAssembly><assemblyIdentity name="Newtonsoft.Json" culture="neutral" publicKeyToken="30ad4fe6b2a6aeed" /><bindingRedirect oldVersion="0.0.0.0-7.0.0.0" newVersion="7.0.0.0" /></dependentAssembly></assemblyBinding><assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"><dependentAssembly><assemblyIdentity name="RazorEngine" culture="neutral" publicKeyToken="9ee697374c7e744a" /><bindingRedirect oldVersion="0.0.0.0-3.7.4.0" newVersion="3.7.4.0" /></dependentAssembly></assemblyBinding><assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"><dependentAssembly><assemblyIdentity name="WebGrease" culture="neutral" publicKeyToken="31bf3856ad364e35" /><bindingRedirect oldVersion="0.0.0.0-1.5.2.14234" newVersion="1.5.2.14234" /></dependentAssembly></assemblyBinding>

Parece que o arquivo app.config está sendo considerado pelo MSBuild em vez do Web.config, porque propõe adicionar bindingRedirtect, que já está presente no meu arquivo Web.config. Eu verifiquei isso copiando e colando Web.config e renomeando-o para App.config. Isso removeu o aviso. Quando App.config é excluído - o aviso reaparece. Portanto, minhas perguntas são 1) por que, embora o MSBuild pareça estar usando o app.config não falha quando eu tenho apenas o Web.config no projeto; 2) Como posso dar uma dica ao MSBuild para usar o Web.config para redirecionamento de ligação? 3) por que construir exatamente o mesmo projeto no VS não gera um aviso?