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I need to install a package in a script. This process needs to write over some already existing configuration files. Right now even though run with DEBIAN_FRONTEND=noninteractive and --force-yes -y, apt still asks for user input:

Configuration file `/etc/init.d/nginx'
 ==> File on system created by you or by a script.
 ==> File also in package provided by package maintainer.
   What would you like to do about it ?  Your options are:
    Y or I  : install the package maintainer's version
    N or O  : keep your currently-installed version
     D     : show the differences between the versions
      Z     : start a shell to examine the situation
 The default action is to keep your current version.
*** nginx (Y/I/N/O/D/Z) [default=N] ? 

How to make this completely uninteractive?

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You can try yes | program or dpkg-reconfigure debconf

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