You will use most of the remaining modules in the second list if you want to let users upload files attached to new content and/or comments. The list of modules is long, but you won't need all of them for a simple system that allows sharing. If your site limits file access to group members or to users in particular roles, the setup becomes more complex.

For example, if your site uses a public file system, but you make some files available to an organization's leaders, you may already be using the Private Uploads module to put some files out of reach of other users and visitors. If so, you'll need the Private Download module as well.

You probably will need Mail Mime, Mime Detect and/or Mime Decode, Filefield Paths, etc., to separate attachements from emails and put them in appropriate directories in you files path. Check the modules listed and their dependencies. Some are helpers that do nothing visible. Others give you a great deal of flexibility in setting up and keeping track of content and files.

Most of the modules that allow settings choices are documented. Because there are many ways to set them up, it is pointless to set out all the permutations.