Sorry I am coming to this a bit late but just wanted to add that plagiarism detection tools can be used as diagnostic tools, within the student's control to help them to see when they have failed to cite, or used (almost) someone else's words. However, this is a small part of the learning. Using sources as a process of synthesis where the author's creativity comes in the selection, critique, analysis and synthesis of ideas to form something 'new' is an apprenticeship of scholarship and takes time, patience, and a supportive community of scholars.
Students can collaborate through forums, glossary, database and wiki to my knowledge but I am not aware of any shared file system as you describe Others may have good examples of how such co-construction of knowledge can be supported.