Comment A Prof Using Drupal (Score 1) 122
As a member of the esteemed (please infer sarcasm) faculty of academia myself, I have been employing Drupal [drupal.org] to address this same issue. In my case, I have shifted toward converting my text-based content to plain text and simple HTML based, housed in the database as individual webpage posts. This affords better flexibility with what I can do with the content. Also, there are several file management options with Drupal for the media- and PDF-type of files. However, converting my text documents to web content resolves the issue you are referring to with download > edit > re-upload of each document. I realize it is essentially the same process when you edit an online post, but the process is a lot less cumbersome and can be done from a computer anywhere without downloading special document software to edit the document.
What I like best about using Drupal for this is the flexibility to manage permissions, structure topics, tag, and reorganize content among other things. I wouldn't rate it as user-friendly in this regard, but it definitely has some powerful capabilities that I am taking advantage of. Modules in Drupal allow for Wiki-style editing, revision history, discussions, etc. You can also build a referencing and bibliography system associated with the content. I am also beginning to adress a peer-review system too and modules have been developed to focus on a workflow review process.