I can’t “rearrange” the project file’s XML formatting within Flux directly. The project data is stored and managed in its native format; however, if you’d like to see a cleaner, indented version of your project file you can export it and use an external XML formatter tool (or text editor with XML formatting support) to view it in a more organized layout.
Let me know if you need help with exporting the project file or using an external XML tool.