The module layout doesn't package dependencies with a custom scope

[wilkinsona]

If you configure a custom configuration for the bootRepackage task and use the module layout, the resulting jar will be empty. When a custom configuration is used all of the libraries have a scope of LibraryScope.CUSTOM and the Module layout only provides a destination for compile and runtime scoped dependencies.

[wilkinsona]

War layout has the same problem with custom-scoped dependencies. I'll open a separate issue for that as the war problem applies to 1.1 and 1.2.