I've just been bitten by this on stretch. So I dutifully looked up the current bug list before submitting a new one, and there was one there - 6 years old!
So then I thought "maybe a patch would help", but lo and behold someone already had. Then I noticed it was me - when I got bitten by the very same thing 4 years ago! /var/run has moved to /run in the mean time so I've attached a refreshed version of the patch. Would it be possible to apply it in time for stretch? Or if you are too busy, would an NMU be appropriate?
diff -Nur ntp-4.2.8p8+dfsg.orig/debian/apparmor-profile ntp-4.2.8p8+dfsg/debian/apparmor-profile --- ntp-4.2.8p8+dfsg.orig/debian/apparmor-profile 2016-10-09 03:32:52.000000000 +1000 +++ ntp-4.2.8p8+dfsg/debian/apparmor-profile 2016-11-21 16:28:12.592851918 +1000 @@ -45,7 +45,7 @@ /etc/ntp.conf.dhcp r, /etc/ntpd.conf r, /etc/ntpd.conf.tmp r, - /var/lib/ntp/ntp.conf.dhcp r, + /run/ntp.conf.dhcp r, /etc/ntp.keys r, /etc/ntp/** r, diff -Nur ntp-4.2.8p8+dfsg.orig/debian/ntpdate-debian ntp-4.2.8p8+dfsg/debian/ntpdate-debian --- ntp-4.2.8p8+dfsg.orig/debian/ntpdate-debian 2016-10-09 03:32:52.000000000 +1000 +++ ntp-4.2.8p8+dfsg/debian/ntpdate-debian 2016-11-21 16:28:24.000983662 +1000 @@ -7,7 +7,7 @@ fi if [ "$NTPDATE_USE_NTP_CONF" = yes ]; then - for f in /var/lib/ntp/ntp.conf.dhcp /etc/ntp.conf /etc/openntpd/ntpd.conf; do + for f in /run/ntp.conf.dhcp /etc/ntp.conf /etc/openntpd/ntpd.conf; do if [ -r "$f" ]; then file=$f break diff -Nur ntp-4.2.8p8+dfsg.orig/debian/ntp.dhcp ntp-4.2.8p8+dfsg/debian/ntp.dhcp --- ntp-4.2.8p8+dfsg.orig/debian/ntp.dhcp 2016-10-09 03:32:52.000000000 +1000 +++ ntp-4.2.8p8+dfsg/debian/ntp.dhcp 2016-11-21 16:28:28.497035584 +1000 @@ -1,5 +1,5 @@ NTP_CONF=/etc/ntp.conf -NTP_DHCP_CONF=/var/lib/ntp/ntp.conf.dhcp +NTP_DHCP_CONF=/run/ntp.conf.dhcp ntp_server_restart() { diff -Nur ntp-4.2.8p8+dfsg.orig/debian/ntp.init ntp-4.2.8p8+dfsg/debian/ntp.init --- ntp-4.2.8p8+dfsg.orig/debian/ntp.init 2016-10-09 03:32:52.000000000 +1000 +++ ntp-4.2.8p8+dfsg/debian/ntp.init 2016-11-21 16:28:05.380768632 +1000 @@ -22,8 +22,8 @@ . /etc/default/ntp fi -if [ -e /var/lib/ntp/ntp.conf.dhcp ]; then - NTPD_OPTS="$NTPD_OPTS -c /var/lib/ntp/ntp.conf.dhcp" +if [ -e /run/ntp.conf.dhcp ]; then + NTPD_OPTS="$NTPD_OPTS -c /run/ntp.conf.dhcp" fi diff -Nur ntp-4.2.8p8+dfsg.orig/debian/README.Debian ntp-4.2.8p8+dfsg/debian/README.Debian --- ntp-4.2.8p8+dfsg.orig/debian/README.Debian 2016-10-09 03:32:52.000000000 +1000 +++ ntp-4.2.8p8+dfsg/debian/README.Debian 2016-11-21 16:28:17.300906289 +1000 @@ -28,7 +28,7 @@ If DHCP is used to configure the host, and the DHCP server sends information about NTP servers, then this information will be used automatically. This is done by making a copy of /etc/ntp.conf at -/var/lib/ntp/ntp.conf.dhcp, replacing the server entries with the +/run/ntp.conf.dhcp, replacing the server entries with the information provided by the DHCP server, and restarting the NTP server.
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