> Please, do post your dnsmasq configuration so we can try to figure out
the right way to integrate this with the current setup.

Just assume the default dnsmasq configuration, any other settings we have there 
are completely unrelated to this problem.
When one installs dnsmasq, it's supposed to start listening on 0.0.0.0:53, 
without manually editing any configuration files at all, i.e. with the stock 
/etc/dnsmasq.conf.
Now with the local resolver listening on 127.0.0.1:53, dnsmasq complains that 
the port is in use and fails to start.

> Now any system that runs NetworkManager will also be running a local
dnsmasq

Let's step back a bit and talk about that. You're launching a DNS server 
without using a sysvinit or upstart job. So you're bypassing update-rc.d, 
policy-rc.d, upstart .override files, package Conflicts:, Provides: etc, all 
the standard framework for managing services.
Why wouldn't it be more reasonable to start the local resolver service normally 
like all the other daemons?
Even make a package out of it, and declare that it Conflicts: bind9, dnsmasq, 
so that people installing those automatically get rid of the local resolver and 
its conflicting configuration?
If you assume that "network-manager contains a hardcoded DNS server", then the 
network-manager package itself should conflict with other DNS servers... But 
that shouldn't be the case, people should be allowed to install any DNS  server 
they want alongside network-manager, and that could be done seamlessly and 
without editing any configuration files at all if:
network-manager recommented the local-resolver package,
and the local-resolver package conflicted with the other dns server packages.

Then, when I install dnsmasq over the desktop installation, the local-
resolver package would be automatically uninstalled, and I wouldn't have
to edit any configuration file at all to resolve the conflict, it would
be resolved by the package manager.

> I don't understand how your systems are setup, and I think that's
where the confusion come from. What I'm expecting is that the LTSP
server also runs a dnsmasq daemon to provide resolving to all the LTSP
clients; with none of the clients running dnsmasq "locally".

The problem isn't LTSP specific, it applies to anyone that wants to use dnsmasq 
as a DNS server for his local network.
But yes, for LTSP labs that use dnsmasq, it is exactly as you described it. 
Now, LTSP clients are all diskless and netbooted, but of two kinds: thin and 
fat clients. Imagine thin clients like XDMCP clients, i.e. many users working 
remotely on the same server. So those would be using the local resolver, and 
miss the caching feature and the speed up that it offers.
Imagine fat clients like regular machines that have nameserver=the LTSP server 
in their resolv.conf. In the solution you proposed above, those would be using 
the real dnsmasq instance, with caching and everything.

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

Title:
  Don't start local resolver if a DNS server is installed

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