I know that PGP provides an hybrid scheme of encryption which can ensure both the encryption of a message and the authentication, but how it stores the secondary data, such as the object, the sender, the receiver, time, etc. on the server? Are they encrypted or stored in plaintext?
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The secondary data or metadata are stored in plaintext.
Should you receive an encrypted mail by pgp, you will notice that you have 2 files attached:
encrypted.asc. Thus the content of the message is hidden but not the metadata.
Why don't we also encrypt the metadata? Well how would we know who to give the mail to then? If you give your mailman a letter and don't tell him who the receiver is, how do you expect him to give it to the right person?
By the same principle, your receiver should be able to at least know what the message is about. Should you not want anyone to know, you could also leave the field blank.
Hence no, only the content is encrypted the meta data are still in clear text.