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For iTunes, you can stop this happening by unchecking "Keep iTunes Media folder organized" (In Preferences/Advanced).

• FussyZeus 11y ago
  That eliminates some of the behavior, but for someone like me who operates in both Windows and Mac and uses other programs to keep my large collection of mp3's up to date on all my machines, it doesn't work because iTunes won't simply use a directory as the basis for it's library and leave it at that, it feels the need to move everything AND as a bonus deletes it from the original location. When I tried to set this up using BitTorrent Sync, iTunes kept removing the files BTS would copy. I had set it to read only so BTS would then copy the file over, and iTunes would add it a second time to the library. Then a third time. Then suddenly when I had 12 copies of everything and my half a terrabyte SSD was nearing capacity for no obvious reason, I finally figured out what the hell was going on and put a stop to it. Appreciate the attempt at help though. :)
• JadeNB 11y ago
  If I remember correctly, this option wasn't always there, but Apple eventually learned their lesson. What puzzles me is that the feature is missing in iBooks, which didn't even exist until well after iTunes got the feature; there is no way (that I can find) to convince it that you can manage your own ePUBs, leaving me still looking for a good reader on the Mac.