I found the solution I was looking for after all these months here
In case the above link goes bad, here's the skinny of what it says:
Unload then edit your project file. Look for the line where it's importing Microsoft.WebApplication.targets. Will look like:
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" />
Beneath that line, paste in this XML:
<Target Name="PublishToFileSystem" DependsOnTargets="PipelinePreDeployCopyAllFilesToOneFolder">
<Error Condition="'$(PublishDestination)'==''" Text="The PublishDestination property must be set to the intended publishing destination." />
<MakeDir Condition="!Exists($(PublishDestination))" Directories="$(PublishDestination)" />
<ItemGroup>
<PublishFiles Include="$(_PackageTempDir)\**\*.*" />
</ItemGroup>
<Copy SourceFiles="@(PublishFiles)" DestinationFiles="@(PublishFiles->'$(PublishDestination)\%(RecursiveDir)%(Filename)%(Extension)')" SkipUnchangedFiles="True" />
</Target>
Now, run this in a command prompt within the same folder as your project file:
msbuild TestWebApp.csproj "/p:Platform=AnyCPU;Configuration=Debug;PublishDestination=C:\pub" /t:PublishToFileSystem
Remember to specify the path to MSBUILD in the command or add the path to your global path environmental variable (which is what I did). On my machine, it was here:
C:\Windows\Microsoft.NET\Framework\v4.0.30319
To test this, I put a config transform in my Web.Release.config to add an AppSetting key (if you do this, make sure the AppSettings node is present in your base config file or you will get an error). When I used the above command to build the debug configuration, the key was not present in the published config file as expected. However, when I used the release config, the key was successfully added to the file.
I really wish Microsoft hadn't obfuscated the heck out of this. At any rate, this is the simplest solution I have found anywhere on the internet. I hope it helps the rest of you.