With the new .csproj format (as well as the old), it is possible to add files as linked outside of the project folder:
While this was previously possible using the %(RecursiveDir) metadata when using glob expansion ( Link="Resources\%(RecursiveDir)%(Filename)%(Extension)"), the 2.0.0 version of the .NET Core SDK allows the use of a new LinkBase metadata:
Note that you need to install the 2.0.0 in addition to the recently released VS 2017 15.3 (and ensure no global.json selects a lower version).
It was introduced with this pull request which is probably the best documentation at the moment.