My /etc/hostname has:

name.domain.net

Previously, it was:

old.domain2.net

If I do hostame I get name.domain.net. But doing hostname -s returns old.

According to the man page:

   -s, --short
          Display the short host name. This is the host name cut at the first dot.

Which is not what I get. I have even rebooted the server.

Any ideas?

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