Today, I was following multiple tutorial to run a C# application on Linux but always got stuck at the command
Yes. They are introducing new command line toolchain, ASP.NET 5 will transition to the new tools for RC2. This is already in progress. There will be a smooth transition from DNX to these new .NET Core components.
dnxcommands completely replaced?
No. You can use
dnx, if you follow this instruction Installing .NET Core on Linux.
Is there some documentation somewhere about the dotnet commands?