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Debian GNU/Linux FAQ
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10.7 How does the package management system deal with packages that contain configuration files for other packages?

Some users wish to create, for example, a new server by installing a group of Debian packages and a locally generated package consisting of configuration files. This is not generally a good idea, because dpkg will not know about those configuration files if they are in a different package, and may write conflicting configurations when one of the initial "group" of packages is upgraded.

Instead, create a local package that modifies the configuration files of the "group" of Debian packages of interest. Then dpkg and the rest of the package management system will see that the files have been modified by the local "sysadmin" and will not try to overwrite them when those packages are upgraded.

Debian GNU/Linux FAQ
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