Standardize Path objects in CytoSnake with pathlib.Path objects.

[axiomcura]

After looking how the cli handle file paths, it seems there's a large mixture of str and pathlib.Path objects.

I think it's best to standardize them into pathlib.Path objects, allowing easier development.

[axiomcura]

The init argument parser returns strings instead of pathlib.path objects. This is a good start for updating file paths objects. However, by changing this, this can trigger a domino effect and may result in a considerable amount of work. .