Tengo un proyecto ASP.NET WEB API con el archivo Web.conig. Cuando se construye en VS2015, no se informan errores ni advertencias. Sin embargo, cuando construyo este proyecto en TeamCity usando el paso de compilación MSBuild, recibo la advertencia 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 MSBuild está considerando el archivo app.config en lugar de Web.config, porque propone agregar un enlaceRedirtect, que ya está presente en mi archivo Web.config. Verifiqué esto al copiar y pegar Web.config y renombrarlo a App.config. Esto eliminó la advertencia. Cuando se elimina App.config, vuelve a aparecer la advertencia. Entonces, mis preguntas son 1) por qué aunque MSBuild parece estar usando app.config no falla cuando solo tengo Web.config en el proyecto; 2) ¿Cómo puedo dar una pista a MSBuild para usar Web.config para la redirección de enlaces? 3) ¿por qué construir exactamente el mismo proyecto en VS no genera una advertencia?