User submitted content in drupal (Drupal Noobie)
Have you taken a look at Open Atrium? It is not a Drupal module, rather a Drupal distribution pre-configured with a set of modules to help you manage projects. It includes functionality to upload files into projects, allows users to create new projects, etc.

Open Atrium has been around for a few years now, and it is pretty stable. Since it is Drupal (and hence, GPL'd), if the features that it brings does not satisfy your needs, as always, you can create your own modules to extend the existing functionality, or as a minimum, you could use Open Atrium to provide you ideas on how you might structure your project, which modules might help you out, etc.

There's also Storm, but it is currently available only for Drupal 6.x, and it's 7.x version is still not stable.