Submodules that are `using`'d  in parent module not detected

```
$ cat src/Foobar.jl
module Foobar

include("SubModule.jl")
using .SubModule

f(x::SubType) = 123

end # module Foobar

$ cat src/SubModule.jl
module SubModule

export SubType
const SubType = Int

end
```
There is no flag for the usage of `SubType` in `src/Foobar.jl` here.

Maybe a duplicate of #80 but that is related to extensions specifically (or maybe not?).