I was trying to build ClojureCLR on Arch Linux but I was getting this error with both MonoDevelop and xbuild (following the directions here).
The attached patch fixes the problem and it works out of the box with MonoDevelop, but it requires an extra step to download the dependencies via NuGet when using xbuild:
I didn't have a chance to test it on Windows but I think it should work with a recent (>2.7) version of NuGet.
Arch Linux
mono 4.0.4.1-1
monodevelop 5.9.6.20-1
nuget 2.8.7-1
I just tested on Mac OSX, the same nuget/xbuild commands work fine. On Windows, Vistual Studio 2015 seems to be working fine as well.
With the move to Core (and all the work the .Net team has done to be become non-Windows-OS-friendly), this should not be an issue.
Microsoft has solved this problem with Core.