I have a project that uses some dynamically compiled code and I am upgrading from .net framework to .net core 3.1.
I can't get a simple test case to include newtonsoft.json.dll and get the error "Type or namespace name 'Newtonsoft' could not be found. I had a similar problem when I first tried add the library, but got past it by using the currently loaded assemblies (Can't include Newtonsoft JSON in CSharpCodeProvider script). With "Core" I don't get errors about a library, but it doesn't know the type, like it didn't get loaded.
I tried both using the project libraries (commented out) and specifying them directly, but have the same issue. To recreate, make a new .netCore 3.1 console application called "TestScript" and install nuget packages "Microsoft.CodeAnalysis.CSharp.Scripting" v 3.7.0, "Newtonsoft.Json" v12.0.3 and use the following code.
using System;
using System.IO;
using System.Linq;
using System.Collections.Generic;
using System.Reflection;
using Microsoft.CodeAnalysis;
using Microsoft.CodeAnalysis.CSharp;
using System.Diagnostics;
using Newtonsoft.Json.Linq;
namespace TestScript
{  
  class Program
  {
    public static void Example1()
    {
      var assemblyName = "UserScript";
      var code = @"namespace UserScript
                { 
                  using System;
                  using System.IO;
                  using System.Collections.Generic;
                  using Newtonsoft.Json.Linq;
                  public class RunScript
                  {
                    private const int x = 99;
                    public int Eval()
                    {
                      JObject j = new JObject();
                      return x; 
                    }
                  }
                }";
      SyntaxTree syntaxTree = CSharpSyntaxTree.ParseText(code);
      var references = new List<MetadataReference>();
      //Load project libraries
      //var assemblies = AppDomain.CurrentDomain
      //                .GetAssemblies()
      //                .Where(a => !a.IsDynamic)
      //                .Select(a => a.Location);
      //foreach (var item in assemblies)
      //{
      //  if (!item.Contains("xunit"))
      //    references.Add(MetadataReference.CreateFromFile(item));
      //}
      //or specify the libraries to load.
      var coreDir = Directory.GetParent(typeof(Enumerable).GetTypeInfo().Assembly.Location);
      var exeDir = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName);
      references.Add(MetadataReference.CreateFromFile(typeof(Object).GetTypeInfo().Assembly.Location));
      references.Add(MetadataReference.CreateFromFile(typeof(Uri).GetTypeInfo().Assembly.Location));
      references.Add(MetadataReference.CreateFromFile(coreDir.FullName + Path.DirectorySeparatorChar + "mscorlib.dll"));
      references.Add(MetadataReference.CreateFromFile(coreDir.FullName + Path.DirectorySeparatorChar + "System.Runtime.dll"));
      if (File.Exists(exeDir + "\\Newtonsoft.Json.dll"))
        references.Add(MetadataReference.CreateFromFile(exeDir + "\\Newtonsoft.Json.dll"));
      else
        throw new Exception("Missing newtonsoft DLL");
      CSharpCompilation compilation = CSharpCompilation.Create(
          assemblyName,
          new[] { syntaxTree },
          new MetadataReference[]
          {
        MetadataReference.CreateFromFile(typeof(object).Assembly.Location)
          },
          new CSharpCompilationOptions(OutputKind.DynamicallyLinkedLibrary));
      using (var memoryStream = new MemoryStream())
      {
        var result = compilation.Emit(memoryStream);
        if (result.Success)
        {
          memoryStream.Seek(0, SeekOrigin.Begin);
          Assembly assembly = Assembly.Load(memoryStream.ToArray());
          Type testClassType = assembly.GetType("TestNamespace.TestClass");
          var addResult = (int)testClassType.GetMethod("Add").Invoke(null, new object[] { 3, 4 });
          Console.WriteLine(addResult);
        }
        else
        {
          Console.WriteLine("Failed to compile");
          for (var i = 0; i < result.Diagnostics.Length; i++)
          {
            Console.WriteLine(result.Diagnostics[i].ToString());
          }
        }
      }
    }
    static void Main(string[] args)
    {
      JObject j = null; //to make sure newtonsoft is included if loading current projects libraries
      Example1();
    }
  }
}