The Tree

The tree in your config is a Rojo project tree. Rogen adds your routed files to it and writes the result to default.project.json. Folder names place only the code in your source paths, so everything else goes in the tree: packages and the place's map.

Packages

Mount a package folder with $path where your code requires it from. Wally installs packages into Packages:

{
	"routes": {
		"Server": "ServerScriptService",
		"Shared": "ReplicatedStorage/Shared"
	},
	"tree": {
		"$className": "DataModel",
		"ReplicatedStorage": {
			"Packages": { "$path": { "optional": "Packages" } }
		}
	}
}

Your code requires a package by its path in the game, as in require(ReplicatedStorage.Packages.Promise). optional lets Rojo build before wally install has run.

rogen init mounts the package folders for you. It reads a wally.toml or a pesde.toml, so it mounts Packages in ReplicatedStorage and ServerPackages in ServerScriptService before you install anything. In a roblox-ts project, it mounts node_modules/@rbxts, as Using roblox-ts shows.

The Place

rogen init puts the starting map, a baseplate and Rojo's lighting, in a place folder and mounts it:

{
	"tree": {
		"$className": "DataModel",
		"Lighting": { "$path": "place/Lighting" },
		"SoundService": { "$path": "place/SoundService" },
		"Workspace": { "$path": "place/Workspace" }
	}
}

The place folder is outside the source paths, so Rogen doesn't route it. To start without it, run rogen init --no-sample. Anything else a Rojo project tree can hold, such as a service's $properties, goes here too.