The built-in file management is adapted optimal to requirements of a content management system. Normally there is no more functionality neccessary.
You can create as many nested private folders as you want. You can cut and paste files and folders, edit file info, rename files and create thumbnails. There is also a simple search available. To use files in articles you have to mark its parent directory and the file as "active" and "public". Try it — it's simple.