retain package structure in generated stubs

[worstell]

we should consider retaining the package structure in generated stubs. because we flatten everything into a single module stub at the moment, we introduce a lot of unnecessary naming constraints that otherwise aren't required by the compiler (two types can't have the same name even across different packages, if they are in the same module).

proposal:
include namespace in the ref, e.g.
foo.Type
foo.subpackage.Type

and generate stubs with directory structure correspondingly