A software development environment exposes a GUI with visual markings for differentiating developer modifications to software files. The differentiation techniques can be provided as defaults with embodiments of the invention, or can be customizable to allow for useful grouping of modifications. The software development environment may also provide a selection tool for accepting, rejecting, or further modifying previous file modifications. A history of modifications may be maintained in the event that a developer needs to re-implement modifications that have been removed or distorted. A navigation tool facilitates analysis of modifications.