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Rough script for migrating common settings from your .deb Atom to user-specific flatpak Atom (Pop!_OS 22.04 tested)
#! /bin/bash
# global config
cp -f ~/.atom/config.cson ~/.var/app/io.atom.Atom/data/
# keybindings
cp -f ~/.atom/keymap.cson ~/.var/app/io.atom.Atom/data/
# init script (maybe you defined some custom function and then bound to a key combo?)
cp -f ~/.atom/init.coffee ~/.var/app/io.atom.Atom/data/
# packages
cp -rf ~/.atom/packages ~/.var/app/io.atom.Atom/data/
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