After publishing a .Net Core RC1 application, commands specified in the project.json had corresponding .cmd files created for them which could be executed after deployment (e.g.
For EF Core 3.1 I succeeded with the following line ran in the release files folder. Of course the path to MyUser can be tweaked with
dotnet exec --depsfile ProjectName.deps.json --runtimeconfig ProjectName.runtimeconfig.json C:\Users\MyUser.nuget\packages\dotnet-ef\3.1.9\tools\netcoreapp3.1\any\tools\netcoreapp2.0\any\ef.dll database update --context MyContext --assembly Project.dll --verbose