Fix relative hint paths added to project file.

Relative paths are incorrect when packages folder is one level up from the project.

Workaround Mono issue with Uri.MakeRelativeUri not returning "../" in relative uri.
MakeRelativeUri method taken from latest Mono Uri class and added to UriUtility
   https://github.com/mono/mono/blob/master/mcs/class/System/System/Uri.cs
   Commit: 8c7c1ff5f325ad34d38341c93e80b81ce9c553ae
Fix files not being returned in unzipped jQuery package.

Directory.EnumerateFiles() when using SearchOptions.AllDirectories under Mono 2.10.9
does not seem to return all files inside subdirectories.
Switched to Directory.GetFiles() which works.
Change NuGet.Core to target .NET 4.0