Here is how to do that.
Log in to your SSH, as root.
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apt-get update
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apt-get -y --with-new-pkgs upgrade
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apt-get -y dist-upgrade
Please select No (or select "keep the local version currently installed").
Those options are actually default options.
Why not to override conf files?
Here is an example.
If you override php.ini with new version - you'll override disable_functions option (that we put as best security setup) and that way you will actually downgrade security of your web system.
Other example is /etc/exim4/exim4.conf.template - we modified that file a lot, and if you install default Debian version of that file, you will completly mess up exim4 service.
During updates, it is very often that apt will also ask to overwrite /etc/clamav/clamd.conf or /etc/roundcube/config.inc.php.
Just don't do it.
Actually, there are very rare situations where you should override config files during apt upgrades... almost never.
In general, most likely you will mess up services if you install config files that comes via apt updates.