Internal structures of software artifacts, especially program source code, are very important to software engineers in developing and maintaining a high-quality software. However, existing version control and configuration management systems often treat a software system as a set of files in directories on a file system. They usually disregard the logical structures of documentations and program source code and treat them as a set of lines for version control. Therefore, it creates burdensome for ordinary developers because the implementation domain (logical level) and the version control domain (file level) require different mental models. This paper describes the fine-grained version control tool of the Software Concordance environment that is flexible to manage the evolution of many different structural levels in a software document.