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That's two OS X upgrades in a row (Yosemite, and now El Capitan) that the upgrade has moved the contents of my home directory /home/users/alphastorm/ into /home-preserved/. Luckily moving/copying everything back seems to fix almost everything.

Anyone else had this happen to them or know why it happens?

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Do you really mean /home or /Users? Only /Users is standard to OS X. I would put your home directory there.

They may create /home if it's required to exist for compatibility with other Unix standards. And since an OS upgrade probably has a checklist of things that must succeed (such as the ability to "create" /home), they feel forced to preserve whatever might have been there already before "creating" it again.

On my machine, /home exists but it is completely empty.

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