I would also like to be able to customise permissions or create custom roles, as I would need a type of user who is able to upload files, comment on their files only, and not be able to neither delete their own files, nor others and not even their comments.

This would be for students.

We have added some user types now that might meet your needs. See Roles, Permissions and User Access Management for details.

Currently we have role based permissions, not user based permissions.

In the future however, we are planning to allow users to create custom roles with a customized set of permissions.