Why do modules get double folders?
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When creating a new module (right-click on the source folder and choose New > Ceylon Module), this folder structure is created:
source/moduleName/moduleName
The only content of the first moduleName folder is that second moduleName folder.
Why this double nested structure?
Well, that's not actually right. There is only one folder named moduleName on disk. But in the Project view, all packages are grouped under a node representing the module they belong to. That includes the package that has the same name as the module.
The first node is actually a fake node that shows the module name, it's not a directory. That node holds the actual folders, which can be presented by IntelliJ as a "flattened" structure (com.foo.mymodule) or a hierarchical structure (com/foo/mymodule).