There is a hack-ish workaround, yet it reminds me of the good ol' days of Linux 
when you could actually control things from simple text files:
    See Method 1 at https://gist.github.com/magnetikonline/6236150

Between NetworkManager, resolvconf, Bonjour, mDNS, dnsmasq (and I think
even dbus)... things seem to be quite hard to understand, control and
fix these days.

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https://bugs.launchpad.net/bugs/993298

Title:
  Please make NetworkManager-controlled dnsmasq respect /etc/hosts

Status in network-manager package in Ubuntu:
  Confirmed

Bug description:
  Since 12.04 NetworkManager uses the dnsmasq plugin by default to
  resolve DNS requests. Unfortunately the dnsmasq plug-in has --no-
  hosts, etc. hard coded [1] which means (among other things) that after
  the upgrade to 12.04 /etc/hosts will no longer be used to resolve DNS
  requests. This changes the prior behavior of NetworkManager without
  any visible warning to the end user. AFAICS there's no other way to
  work around this problem as to manually revert the change and disable
  the dnsmasq plug-in in the NetworkManager config, see [2,3]:

  "To turn off dnsmasq in Network Manager, you need to edit
  /etc/NetworkManager/NetworkManager.conf and comment the 'dns=dnsmasq'
  line then do a 'sudo restart network-manager'."

  This is of course not a bug in the NetworkManager which just behaves
  as intended. The problem is in the change of the configuration of the
  Ubuntu packaging which will probably leave many wondering why their
  /etc/hosts suddenly no longer works. This cost me considerable time to
  debug and probably is a usability problem for others, too.

  Maybe you could provide a more visible documentation than that in [3]?
  E.g., *including a comment in /etc/hosts that explains the change* and
  how to work around it would have saved me a lot of time. It would have
  automatically alerted me on upgrade as manual changes to /etc/hosts
  would then have triggered a prompt while leaving those users with
  standard /etc/hosts in peace.

  Probably similar problems arise with other disabled config files and
  could be alerted to the users? Thinking of resolv.conf, etc.

  [1] 
http://cgit.freedesktop.org/NetworkManager/NetworkManager/tree/src/dnsmasq-manager/nm-dnsmasq-manager.c,
 line 285
  [2] i.e. http://ubuntuforums.org/showthread.php?t=1968061
  [3] http://www.stgraber.org/2012/02/24/dns-in-ubuntu-12-04/

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