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

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: 👉 <this branch>

+ 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 ?