The File Order plugin allows users to customize the order of files and folders in their Obsidian vault using number-prefixes in file names. Users can drag and drop items within the file explorer to reorder them, and the plugin updates all references to affected files automatically. Options include customizing prefix length, delimiter, and starting index. The plugin stores order information directly in file names, ensuring compatibility even after uninstalling the plugin. Users can clear custom ordering to revert to default arrangements, and default settings can be defined for consistent usage.