Move to pathlib workflow instead of os

[SBeairsto]

Use pathlib.Path for consistent and portable file path handling

Much of the current filepath logic in the repository still uses os.path and string concatenation for constructing paths. For consistency and improved readability/portability, we should update all path-related code to use pathlib.Path.

Benefits:

• Cleaner syntax with / operator for joining paths
• Cross-platform compatibility
• Avoids manual string formatting for filepaths
• Makes downstream refactoring and testing easier

Suggested action:

• Identify all uses of os.path.join, os.makedirs, and string-based path handling
• Replace with equivalent pathlib.Path logic
• Ensure backwards compatibility where needed

This will help align with modern Python best practices and improve maintainability.