My update.sh: apt, flatpak, uv tool, etc

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You can put flatpak, uv and npm update scripts in /etc/qubes/post-install.d in your templates. In this way, your alternative package managers will perform upgrades when updating through the Qubes Update GUI. Example script for Flatpak that I use (found somewhere on the forums):

#!/bin/sh

# abort if not in a template
if [ "$(qubesdb-read /type)" = "TemplateVM" ]
then
    echo "Upgrading flatpak apps..."
    export all_proxy=http://127.0.0.1:8082/
    flatpak upgrade -y --noninteractive
    echo "Done upgrading flatpak apps"
fi
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