What I needed to do was to first create a folder inside Godot by rightclicking res:// and choosing “New Folder…”, giving it the same name as the folder I want to import. This creates a folder by that name inside the project root folder.
Then I open the folder I want to import in the operating systems file explorer, copy/cutting all the content inside and then open the folder I created in the project root and pasting the content there.
After that, when focusing the Godot Window again, it starts an import operation.
Why not just drag the folders to project directory?
att | 2019-04-09 11:07
As I said in the question just putting the folder structure in the project folder doesn’t cause Godot to understand it is there (not even when restarting Godot and so on), I have to first create a subfolder using the Godot app, then put the files from the original folder in there. I’ve tried this several times, with both new and existing projects and this is the only way I can find as of now. Hopefully there will be better features for this implemented in the future (preferably drag and drop).
Karlsson | 2019-04-09 11:16
is there a fix to the FileSystem not showing the folder after restarting godot? it imports ok with the folder and all its assets showing after doing this, but not after restarting