While trying to publish the Ext.Net Examples to learn about an issue we were having in one of our applications while publishing we ran across a line that would help in the csproj file. Could you add:

<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" />
Following the line:

<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
We are running an autobuild after pushing a repository, via Mercurial, to the server.

See this article for a discussion:

MSBuild target PipelinePreDeployCopyAllFilesToOneFolder cannot be found when deploying