Please provide any extra information you can to reproduce and debug this
issue. I can't reproduce it. If both IPv4 and IPv6 are set to not take
the default route, things are behaving correctly here; just like the DNS
settings are correctly configured when no split-tunnelling is in use at
all.

Also note that this will not work if dns=dnsmasq isn't set; this is
important as some versions of NetworkManager have disabled that feature.

>From my logs; calling on to kill -USR1 dnsmasq before doing any tests (5
sent to local (192.168.0.1), 0 to the VPN (10.x.x.1) DNS):

ug 19 14:04:30 demeter NetworkManager[2922]: <debug> [1471629870.6888] 
dnsmasq[0x5580dd157040]: dnsmasq update successful
Aug 19 14:05:16 demeter dnsmasq[5238]: horodatage 1471629916
Aug 19 14:05:16 demeter dnsmasq[5238]: taille de cache 0, 0/0 insertions dans 
le cache entrées non-expirées réutilisées
Aug 19 14:05:16 demeter dnsmasq[5238]: requêtes transmises 40322, requêtes 
résolues localement 448
Aug 19 14:05:16 demeter dnsmasq[5238]: queries for authoritative zones 0
Aug 19 14:05:16 demeter dnsmasq[5238]: serveur 192.168.0.1#53: requêtes 
envoyées 5, requêtes réessayées ou échouées 0
Aug 19 14:05:16 demeter dnsmasq[5238]: serveur 10.x.x.1#53: requêtes envoyées 
0, requêtes réessayées ou échouées 0
Aug 19 14:05:49 demeter dnsmasq[5238]: horodatage 1471629949
Aug 19 14:05:49 demeter dnsmasq[5238]: taille de cache 0, 0/0 insertions dans 
le cache entrées non-expirées réutilisées
Aug 19 14:05:49 demeter dnsmasq[5238]: requêtes transmises 40324, requêtes 
résolues localement 448
Aug 19 14:05:49 demeter dnsmasq[5238]: queries for authoritative zones 0
Aug 19 14:05:49 demeter dnsmasq[5238]: serveur 192.168.0.1#53: requêtes 
envoyées 7, requêtes réessayées ou échouées 0
Aug 19 14:05:49 demeter dnsmasq[5238]: serveur 10.x.x.1#53: requêtes envoyées 
0, requêtes réessayées ou échouées 0
Aug 19 14:06:06 demeter dnsmasq[5238]: horodatage 1471629966
Aug 19 14:06:06 demeter dnsmasq[5238]: taille de cache 0, 0/0 insertions dans 
le cache entrées non-expirées réutilisées
Aug 19 14:06:06 demeter dnsmasq[5238]: requêtes transmises 40325, requêtes 
résolues localement 448
Aug 19 14:06:06 demeter dnsmasq[5238]: queries for authoritative zones 0
Aug 19 14:06:06 demeter dnsmasq[5238]: serveur 192.168.0.1#53: requêtes 
envoyées 7, requêtes réessayées ou échouées 0
Aug 19 14:06:06 demeter dnsmasq[5238]: serveur 10.x.x.1#53: requêtes envoyées 
1, requêtes réessayées ou échouées 0

Followed by tries to resolve www.google.com (local), www.canonical.com
(local), at which point you reached 7/0; then lcy01.buildd (intended for
the VPN), which brings the status up to 7/1. The only one that went to
the VPN was the request for lcy01.buildd; and it was rejected NXDOMAIN
(and didn't go to the local DNS at all). Everything happened as
intended.

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https://bugs.launchpad.net/bugs/1603898

Title:
  DNS resolution fails when using VPN and routing all traffic over it

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