Storing files and applications on your drive isn't performed with any logistical manner. Files should be stored in one continuous block, which means that they can be located and loaded in to memory without your drive having to skim over the entire surface. The problem is, fragmentation quickly occurs which means that it takes longer to boot your computer and launch applications.
Diskeeper 2008 has been around for a while and is commercial defragmentation software. The latest version contains a number of tasks that will attempt to keep your drive defragmented whilst you use your computer. This means that you shouldn't have to spend hours defragmenting your drive, at the end of every month.
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