Manipulation of document collections

In a system for inputting and managing document collections, the order in which documents and cover or separator sheets are presented to the system dictates the organization and hierarchy for the electronically stored document collection. Users can add annotations to documents and collections by writing on a coversheet; the system scans the coversheet, reads the written material, and adds the material to the electronically stored document and/or collection. In addition, in one aspect the invention provides a mechanism for granting different levels of access to different individuals, by generating coversheets that point to the same collection but that provide different levels of access to the collection.