This paper describes a novel approach to managing finegrained changes in software documents and logical relationships among them. The logical relationship management tool in the Software Concordance development environment is distinguished itself from existing ones by its ability to manage versions of complex document relationship networks, which are represented by hypermedia structures. Hypermedia structures are managed separately from document contents. Hyperlinks are also explicitly represented and versioned as first-class entities, allowing developers to browse, visualize, and systematically analyze logical relationships among software artifacts.