Update download Module to Process Data by Laboratory COD and Project Subfolder

[Aberdur]

PR Description

This PR modifies the download module to ensure that downloads and folder cleanup for the options download_only, download_clean, and delete_only are now performed at the project folder level.

Changes:

• Updated the logic for downloading, cleaning, and deleting files to operate at the project directory level instead of broader directory structures.
• Ensured that all three options (download_only, download_clean, and delete_only) consistently follow this new behavior.
• Improved handling of project-specific data organization to enhance clarity and prevent unintended data modifications.