In more detail
The layout file is not part of the coding template and is never filled in by hand. Themescape writes it as a .json file when you have placed bubbles with Custom placement, reordered the hierarchy or file tree, or built a figure in Build mode.
It holds those arrangements as names and positions only. Since nothing about a project is kept in the browser, the layout file is the only way to keep an arrangement between sessions.
In Themescape
The layout file is saved with your progress files. Load it in the Layout slot of Start a project, or with Open layout in Build mode, to bring the arrangement back. A file that is not a Themescape layout file is turned away with a short note.