Using Gnome 3 on Manjaro I swapped Ctrl and Alt Keys, to use my OSX muscle memory. dconf settings:
/org/gnome/desktop/input-sources/xkb-options=['caps:ctrl_modifier', 'ctrl:nocaps', 'ctrl:swap_lalt_lctl']
Having this set up, Atom does not recognize any key commands involving Alt (the key that says ctrl on it). Ctrl commands (using the key that says alt on it) work fine though. Seems like Atom handles keystrokes at a lower layer than Gnome, bypassing the Gnome system settings.
Is there a way to fix this within Atom?