Have you identified a performance issue? If not, do nothing.
Are you sure that the physical distribution of files on disk is the cause of this performance problem? If not, then measure where the time is spent in your application, and try to improve the algorithms, if necessary, enter caches.
If you have done all this and are confident in the physical distribution of files on the disk that cause performance problems, have you considered buying a faster disk or using several? Hardware is often much cheaper than development time.
I highly doubt that the physical distribution of files on disk has a significant impact on the performance of your application. First, I would search elsewhere.
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