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I a using debian, and I have a custom apache.conf, so I was wondering how can I upgrade my phpmyadmin to 3.3.8 from 2.11 easily without overwriting my settings.

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You can upgrade apache in Debian with apt-get upgrade or just installing a newer Debian package with dpkg -i (though this will need to be from the same version of Debian unless you want to replace all Apache's dependents as well).

If Debian sees a modified configuration file where it would normally put a file from a package it will keep the modified file, see: http://www.debian.org/doc/debian-policy/ap-pkg-conffiles.html

Upgrading PHPMyAdmin is a slightly different issue as the latest packaged Debian version is version 2.11, I'd suggest the best way to do it would be to grab the source package from http://www.phpmyadmin.net and install it seperately, then move your settings by looking at the files in /etc/phpmyadmin (Debian PHPMyAdmin 2.11 conf file store) to the new version.

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