The Readme file gives you an introduction to the product and quick links to other relevant documentation. It also includes quick start guides to get you up and running with the GUI or the command line tool as soon as possible.
The User Guide gives a high-level introduction to the main principles of DITA Compare and describes how to perform topic and map-level comparison. It describes the various output format options and gives an overview of how to configure a comparison for your needs.
The DITA Compare reference document gives a more detailed description of the configuration options available and also lists all parameter settings with their accepted values.
The API documentation is a detailed programmer's guide to the Objects and methods available via either the Java or .NET APIs.
The release notes give a version by version breakdown of new features, updates and bug fixes. They will also notify you of any unavoidable API changes that may require you to update your own code.