v11.0\WebApplications\Microsoft.WebApplication.targets was not found when file actually references v10

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I ran into the same issue with Visual Studio 2013. It turns out that I was using the old version of MSBuild–the one that ships with the .NET Framework–from the command line. Microsoft is now releasing MSBuild as part of Visual Studio itself and also as a separate installer (http://blogs.msdn.com/b/visualstudio/archive/2013/07/24/msbuild-is-now-part-of-visual-studio.aspx).

The solution was to use the new version of MSBuild.exe located in C:\Program Files (x86)\MSBuild\12.0\Bin. Once I did that, all the targets errors disappeared.

EDIT 1

As mentioned in the comments, each new version of MSBuild brings with it a new directory. For Visual Studio 2015, use C:\Program Files (x86)\MSBuild\14.0\Bin.

EDIT 2

As mentioned in the comments, for Visual Studio 2017, use C:\Program Files (x86)\Microsoft Visual Studio\2017\<Edition>\MSBuild\15.0\Bin\MSBuild.exe.

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