Defragmentation is of all files, not just low level system files.
Files are continually being created/deleted on a webserver, lots of temporary files, clients adding deleting files - one server alone might be servicing a few hundred websites, with their owners changing files - or even writing entries on the PPRuNe forums
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I used this as an example of an instance where the HDD's are basically in constant use - these days the drives used are the same as the people use in their own home computers.
Oceanz.