Mapping notes
Actually Godot uses sky panoramas instead of skyboxes. All skies should be placed in skies folder. In Hammer open Map -> Map Properties and set Skybox Texture Name field with a sky panorama texture name with extension. Also keep in mind that these textures should be imported/precached in the Godot otherwise they won't work.
The importer supports instances. If you have some geometry that you use repeatedly - select this geometry, Right Mouse Click -> Create Instance from Selection. All instances will be imported into res://instances folder.
Keep in mind that in case you changed some instance you need to reimport it in Godot.
