Implement Project-Level Directory Processing in download Module

[Aberdur]

Issue Description:

Currently, the download module in relecov-tools does not process directories at the project level. Instead, directory handling is managed at a base level, which can lead to inefficiencies and inconsistencies when organizing downloaded data.

Expected Behavior:

• Directory processing should be handled at the project level within the download module.
• Ensure that all relevant files are properly organized within their respective project directories.