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I tried to add the Japanese input method and so I installed fcitx to do so as I read it was the best. It didn't work so I tried on ibus and also uninstalled the fcitx software after that and I don't know how but I ended up with every layout remapped to some weird layout as shown in the pictures. The first picture is from an English keyboard layout and the second one is from a Portuguese keyboard layout.

English layout remapped? Portuguese layout remapped?

My setxkbmap -print -verbose 10 can be seen below, showing that the configuration is locked to some weird options.

Setting verbose level to 10
locale is C
Trying to load rules file ./rules/evdev...
Trying to load rules file /usr/share/X11/xkb/rules/evdev...
Success.
Applied rules from evdev:
rules:      evdev
model:      pc105
layout:     br,us
variant:    ,
options:    grp:alt_shift_toggle,japan:hztg_escape,japan:nicola_f_bs,japan:kana_lock
Trying to build keymap using the following components:
keycodes:   evdev+aliases(qwerty)
types:      complete
compat:     complete+japan(kana_lock)
symbols:    pc+br+us:2+inet(evdev)+group(alt_shift_toggle)+jp(nicola_f_bs)+jp(hztg_escape)
geometry:   pc(pc105)
xkb_keymap {
    xkb_keycodes  { include "evdev+aliases(qwerty)" };
    xkb_types     { include "complete"  };
    xkb_compat    { include "complete+japan(kana_lock)" };
    xkb_symbols   { include "pc+br+us:2+inet(evdev)+group(alt_shift_toggle)+jp(nicola_f_bs)+jp(hztg_escape)"    };
    xkb_geometry  { include "pc(pc105)" };
};

How can I go back to the default?

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To simply reset the keyboard layout configurations you can use dconf. From the wiki:

dconf is a low-level configuration system and settings management tool. Its main purpose is to provide a back end to GSettings on platforms that don't already have configuration storage systems.

To reset the keyboard configuration you just reset the org/gnome/input-sources using the command dconf -reset /org/gnome/desktop/input-sources.

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