Use 'apt-get dist-upgrade'.
Use 'apt-get dist-upgrade'. Even this will not necessarily be successful on the first pass and you may have to run it up to 3 times.
'ntp' is a special case; ntp has been extensively revised fairly recently and you'll have to spend (a lot of) time reading through the documentation to see what's changed. The upgrade should still work though.
apt-cache search 'ntp-refclock'
ntp-refclock - transition package
What happened (in a very brief and somewhat incorrect summary) is that the functions of various utilities have now been incorporated into NTP itself in the NTPv4. So now 'refclock', 'ntpdate', 'ntpd' are really all in the same program.