You can totally do that in nextcloud. All your file structure is keeped in the directory of nextcloud. The database only keep metadatas about what is shared and such things. One soft that strip the file structure and store it only as metadata in a database is Seafile. For your usecase, you can drop your files in your nextcould directory at the right place and invoke the command occ files:scan. It doesn’t watch for file changes, but you could certainly setup a Cron or a script to invoke it remotely.