fix: improve s3 indexing with source_dir and target_dir

[msm-cert]

Your checklist for this pull request

• I've read the contributing guideline.
• I've tested my changes by building and running mquery, and testing changed functionality (if applicable)
• I've added automated tests for my change (if applicable, optional)
• I've updated documentation to reflect my change (if applicable)

What is the current behaviour?
Previous PR was buggy (despite being tested in a local environment, the setup was a bit too simplistic)

What is the new behaviour?
Fixed the code (hopefully), split download_dir into source and target dirs.