1. A computer-implemented method for arranging files on a computer system storage device, comprising: determining commonly used files based on an analysis of a type of computer system utilizing the storage device, including determining a type of operating system; determining commonly used files, and any related files, by monitoring system operation; determining a specific physical order to store the files on the storage device based on the determinations of commonly used files and related files; analyzing available fee space on the storage device; re-arranging pre-determining files and placing the predetermined files in a pre-determined location before re-arranging any remaining files; and re-arranging any remaining files on the storage device according to the determined specific order by placing the files in sequential and contiguous locations on the storage device in a directory structure of a file system; wherein the analyzing of available free space and the re-arranging of the files are performed dynamically during system operation.