When using the Eclipse plugin, I have the same problem has when using Maven import : all dependencies are flatten, ie compile, test runtime all become compile dependencies. Even worst, all transitive dependencies become direct (compile) dependencies.
The expected result would be to keep only direct compile dependencies, and to create a launcher with the runtime and transitive dependencies.
But this problem is so acute (in fact, it makes the whole thing totally unusable) that I feel I must be missing something. But what ?