I realize this in an old question, but I ran into it recently and here is how I solved it.
Background: I had an old project that I upgraded to VS studio 13. It looks like the project file wasn't upgraded properly.
There are references to VS v10.0, in the csproj file, but I am running VS 13 which is really "v12.0".
So I told the csproj file to use the "v12.0" folder, not a "v10.0" folder.
This is what I had:
<PropertyGroup>
<VisualStudioVersion Condition="'$(VisualStudioVersion)' == ''">10.0</VisualStudioVersion>
<VSToolsPath Condition="'$(VSToolsPath)' == ''">$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)</VSToolsPath>
</PropertyGroup>
<Import Project="$(MSBuildBinPath)\Microsoft.CSharp.targets" />
<Import Project="$(SolutionDir)\..\BuildTools\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" Condition="'$(VSToolsPath)' != ''" />
<Import Project="$(SolutionDir)\..\BuildTools\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" Condition="false" />
This is what I changed it into:
<PropertyGroup>
<VisualStudioVersion Condition="'$(VisualStudioVersion)' == ''">12.0</VisualStudioVersion>
<VSToolsPath Condition="'$(VSToolsPath)' == ''">$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)</VSToolsPath>
</PropertyGroup>
<Import Project="$(MSBuildBinPath)\Microsoft.CSharp.targets" />
<Import Project="$(VSToolsPath)\WebApplications\Microsoft.WebApplication.targets" Condition="'$(VSToolsPath)' != ''" />
Now my publishing to the filesystem works!