EDIT: Is there a web based file manager / Workspace similar to EyeOS but uses Unix authentication and allows them to edit their files? If that makes sense? Thanks. It'd be awesome if something like this existed if it doesn't...(?)
Webmin includes that java based file manager, which does in fact allow you to edit/view files (so long as they can be edited or viewed in plain text) and does Unix auth.
Can you provide some more specifics in regards to what you're looking for because it sounds like the latest version of webmin already includes these features?