I have the same issue. As discussed in bug 663597, setting
/etc/domainname doesn't work for me; hostname -f still reports the wrong
result.

I now worked around this by putting the FQDN into /etc/hostname (rather
than just the plain hostname), and so far I've had no problem with this.
However, according to "man hostname", setting /etc/hostname to the FQDN
is wrong:

     /etc/hostname  This  file  should only contain the hostname and not the
       full FQDN.

but it's the only way I could get hostname -f to work.

(BTW, If someone could have a look at bug 663597 and change its status
from "opinion" to something else or at least give a reason why that
status makes sense, that would be appreciated.)

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https://bugs.launchpad.net/bugs/645648

Title:
  network-manager updates /etc/hosts, breaks hostname -f

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