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@montengarde thank you for considering the WP Docs as a replacement.
The directory management structure of this plugin is slightly different from Memphis, we are not creating a lot of _posts table entries but using the existing one in RDBMS fashion with foreign and primary keys with metadata so we can avoid burdening the database.
All the media like videos, images, documents and other stuff are not mixed up by choice in this plugin, it is actually the default feature/style of the WordPress actually. Media library was designed like this since beginning.
About import from memphis to wp-docs plugin, at our best we tried to link/sync the items where they are instead of relocating everything from scratch but their entries in the database would be maintained differently when you click import. So whatever it would be, a good method to continue further. 1000+ of people are already using it and they are happy with it.
Please do not feel it as a messy mix, it is the default feature of the WordPress. Either you like it or not, by default WordPress uploads every new item to YEAR/MONTH directory with all of its possible thumbnails etc.
In case you need a separate directory for each file-types so you can use this plugin to create separate directories logically, which is already in action. Memphis was already mixing all of this stuff the _posts table with another post_type and staking-up the _meta table with huge information about each file, wp-docs is simply using the existing fields of library module.