Steps to reproduce:
- Create new solution with new project in it
- add some dependency, i.e: via PM> Install-Package Nancy
- Project->Enable Nuget Package Restore 
- Commit your solution somewhere.
- Check out solution in a Linux machine with Mono 3.0.
- Build it with xbuild.
XBuild generates some warnings about not finding some nuget things 
The above warnings are "ignored", then when really trying to build the solution, it doesn't find the libraries (references) of the nuget packages installed.
 This step modifies the project in this way:
- Adds a ".nuget" folder.
- Adds 4 files inside the .nuget folder: NuGet.Config, NuGet.exe, NuGet.targets, packages.config
 One of the warnings is:
WebApplication1.csproj: warning : Could not find project file //.nuget/nuget.targets, to import. Ignoring.
Pull request coming.