I'm unable to edit https://git.kolab.org/diffusion/D/browse/master/source/upgrade-guide/kolab-16.rst in phabricator, so here are some notes from my upgrade:
I'm running Debian and used the following repository:

$ cat /etc/apt/sources.list.d/kolab.list 
deb http://obs.kolabsys.com:82/Kolab:/16/Debian_8.0/ ./
$ sudo aptitude update

Replace php-mysql with php-mysqlnd:

$ sudo aptitude install php5-mysqlnd

Update all:

$ sudo aptitude full-upgrade

Drop the policy_result table from MySQL database kolab.

$ mysql -D kolab
mysql> drop table policy_result;

or maybe

mysql> rename table policy_result to policy_result_backup;

Configure the new module "Manticore":
​This is missing for debian.

After the upgrade I got in /var/log/roundcube/errors:
[24-Jan-2017 19:43:03,041751 +0100]: <2atk0meh> DB Error: [1146] Table 'roundcube.chwala_sessions' doesn't exist

Created the table roundcube.chwala_sessions with /usr/share/doc/chwala/SQL/mysql.initial.sql.
Also table chwala_invitations. Shouldn't we create the tables with the installation?
Updated system table:
mysql> update system set value = '2016101700' where name = 'chwala-version';