The manual has been updated to reflect that GuineuIDE is now the preferred method to use Guineu. You can still use Guineu.EXE to directly run an FXP, if you wish. I think, though, that compiling a project with SCXes, VCXes and PRGs into a single EXE is closer to what most developers actually want to do. GuineuIDE only runs in Visual FoxPro 9.0 which is now checked when you start GuineuIDE. The Build menu itself remains enabled even if there's no project open.
Most changes in this build are internal stuff. For instance, I enhanced the way that variables are internally managed, fixed several issues that Code Analysis in VS.NET 2008 flagged, and the like.