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I need to use

sudo apt-get -y --purge remove $manypackages

where $manypackages includes dependencies of a package that I don't want removed.

Is it possible to prevent apt-get from removing those dependencies instead of me having to determine them and remove them from the $manypackages list beforehand?

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There is no way to prevent explicitly removing packages, which is what the command you want to issue will do. A workaround is to mark the packages as auto, then let apt autoremove the ones that are no longer needed.

sudo apt-mark auto $many_packages
sudo apt-mark manual $keep_packages
sudo apt autoremove
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