fix: Missing subdirectories top-level submodules

[sizmailov]

The handling of submodules as the CLI argument was never perfect, but it got utterly broken in 1.0.

Compare tree structure in different versions

```text VERSION: 👉 0.16 + pybind11-stubgen module1.module2.module3 stubs └── module1 └── module2 └── module3-stubs ├── __init__.pyi └── setup.py 3 directories, 2 files + pybind11-stubgen module1.module2.module3 --root-module-suffix= stubs └── module1 └── module2 └── module3 ├── __init__.pyi └── setup.py 3 directories, 2 files + pybind11-stubgen module1.module2.module3 --root-module-suffix=-stubs stubs └── module1 └── module2 └── module3-stubs ├── __init__.pyi └── setup.py 3 directories, 2 files VERSION: 👉 pybind11-stubgen~=1.0 + pybind11-stubgen module1.module2.module3 stubs └── module3.pyi 0 directories, 1 file + pybind11-stubgen module1.module2.module3 --root-suffix= stubs └── module1.module2.module3 └── __init__.pyi 1 directory, 1 file + pybind11-stubgen module1.module2.module3 --root-suffix=-stubs stubs └── module1.module2.module3-stubs └── __init__.pyi 1 directory, 1 file VERSION: 👉 + pybind11-stubgen module1.module2.module3 stubs └── module1 └── module2 └── module3.pyi 2 directories, 1 file + pybind11-stubgen module1.module2.module3 --root-suffix= stubs └── module1 └── module2 └── module3.pyi 2 directories, 1 file + pybind11-stubgen module1.module2.module3 --root-suffix=-stubs stubs └── module1-stubs └── module2 └── module3.pyi ```

Fixes #135

[sasq64]

I still get submodules as submodule.pyi instead of submodule/__init__.pyi with the latest version ?