For those of you that attended the Lightning Now Tour for Service in San Francisco, there was a question around how to organize the Documents that are converted to Files. Our suggestion is to use Libraries to represent folders (https://help.salesforce.com/articleView?id=000250175&language=en_US&type=1). You can use this tool which is open source as an example - https://github.com/douglascayers/sfdc-convert-documents-to-files - and can modify it based on your requirements. 

Please note this solution may not handle all use cases, so please use it as a reference and customize as needed.