We are also interessting in Subfolder/Subdirectory-Support.
For Input:
The Bulk Import Supports “all Files in one Folder” – “foldermode”.
For Output:
You can bypass it by using categories as folder but only one layer deep might be possible.
(https://www.wpdownloadmanager.com/support/topic/display-category-as-a-list-with-file-list-download-buttons/)
Deeper categories you have to create wordpress pages to put your files on a tree like you want.
But maybe there will be a module supporting it in the future?