As you probably already know, Amazon's user accounts system allowed the attackers to first add a new credit card to Honan's account just by knowing his name, email and billing address (got by a simple whois search for his website), then to claim that he had forgotten the password to the account and convince Amazon employees to allow them to add an additional email address to the account, and finally to start a password reset process that delivered the new password into the newly added email account.
Having gotten access to the account, they now had in their hands the last four digit's of Honan's credit card, which along his billing address and his username was enough to trick Apple representatives into giving them a temporary password into Honanís Apple ID.
Immediately following they revelation of the hacking Wired journalists were able to replicate both social engineering attacks, but now it seems that both Apple and Amazon have changed the policies that were misused.
According to Wired, Amazon no longer allows people to call Amazon and change account settings such as email addresses and credit cards, and Apple has temporarily suspended the option of asking for an AppleID password reset over the phone.
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