I've a solution with two pprojects mvc5 web app and tests. If I publish the web site as file system by right click and publish with a custom profile it's all good. Specifying that custom profile from command line leads to all folders/source code in the solution being published. There's something I'm missing but I don't know where to look anymore.
msbuild C:\eqsnet452\Eqs.sln /p:DeployOnBuild=true /p:PublishProfile=IntegrationPublish /p:VisualStudioVersion=12.0
The IntegrationPublish profile is set to File System but all files get copied in the pusblished.