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Is storing the private key and public keys in same directory on server recommended?

Is this recommended or a good/normal practice? I think not.
Because I saw that OwnCloud stores all encryption keys in one directory on the server. One directory contains the private key(s) and one all public keys.

But their documentation says about their encryption: "But you should make sure to never lose this password, because that’s the only way to recover users’ files."
doc.owncloud.org/server/6.0/admin_manual/configuration/configuration_encryption.html

This seems totally wrong and unprofessional to me.
Or is there any good reason why both are stored there?

user6090