Yes, there is a new folder (in the common directory), and you can now create your own 01_ file so that when Paradox makes future changes you don't have to copy paste your changes to and from your document to their document. Its a bit of a pain at first because they still have a 'dummy' file in place, but once you have your own file full of modifiers, all you should need to do is rename it. I wish they would also do this to the defines.lua file - as if anything is going to break your game, I've found that 90% of the time its that file. It would be nice to have a file which you could have in your mod that overrides the default, but if the game engine requires new ones, the developers can ensure their file is correct, and you don't need to perform surgery on your file to get the game to run with your mod every time.
As a precaution, I also renamed my localisation file to 999999998 just in case Paradox has 999999990 more patches in store. (it was 8 before).