What lies behind the problem being discussed here is the simple fact
that there exists no single adequate network configuration utility for
GNU/Linux.  I am most familiar with Debian.  From Debian we inherit
ifupdown which was designed for static configuration.  Debian developers
have known for more than ten years that ifupdown needed to be replaced,
but have never managed to come up with a replacement.  From RedHat we
get NetworkManager which was never intended to be a general network
configurer but in the absence of any alternative continues to be
enhanced with new features.  Considerable effort has obviously been
spent in Ubuntu just to get NM to coexist with other networking
packages. It still doesn't fully cooperate with them (see #47379 for
another example) and will probably never be well integrated with them.

So we are still forced to choose between two network configuration
approaches, NM-oriented in the desktop version and ifupdown-oriented in
the server version.  Each one has its limitations.  If you try to
combine the two, as you (Alkis) want to do, then you are confronted with
these limitations.  You are lucky that all you have to do is comment out
one line in a configuration file to get things to work!

We can continue playing around with the existing tools so that they work
better in particular use cases but what we really need is a properly
designed network configuration utility to supersede both ifupdown and
NM.

I am vaguely aware of the Wicd project.  Must go read up on that.

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https://bugs.launchpad.net/bugs/959037

Title:
  Local resolver prohibits DNS servers from running

Status in “dnsmasq” package in Ubuntu:
  Confirmed
Status in “network-manager” package in Ubuntu:
  Triaged

Bug description:
  As described in
  https://blueprints.launchpad.net/ubuntu/+spec/foundations-p-dns-
  resolving, network manager now starts a dnsmasq instance for local DNS
  resolving.

  That breaks the default bind9 and dnsmasq installations, for people that 
actually want to install a DNS server.
  Having to manually comment out "#dns=dnsmasq" in 
/etc/NetworkManager/NetworkManager.conf doesn't sound good, and if it stays 
that way, it should be moved to the bind9 and dnsmasq postinst scripts.

  Please make network-manager smarter so that it checks if bind9 or
  dnsmasq are installed, so that it doesn't start the local resolver in
  that case.

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