I have this bug since a few fedora version. In some applications, the shortcuts obeys the localized ibus keymap, but other keeps the default keymap when pressing CTRL. Typical example includes gimp (follows keymap) and inkscape (ignore keymap). I'm personally using both the us and dvorak keymap, and this behaviour is pernicious as the key locations are very dissimilar.
Using "setxkbmap" is hard erasure of the keymap, and after that _all_ applications follows the keymap when using the shortcuts. But then ibus doesn't really work anymore, and it's inconvenient.
Thus a solution could either be that:
*ibus is resilient to "setxkbmap"
*All software are presented with the same keymap, which can be configured to be the current map.
GNOME Shell 3.16.3
Could you explain your problem with the reproducing steps with detail?
I tried gimp Text Tool and Ctrl+A works fine.
I'm not on my linux computer often lately, so I didn't upadet the issue yet. But it might get long before I get the time, so I did reproduce the exact same bug on a fedora VM on Virtual Box.
By the way, qwerty and dvorak happens to have the key at the same place, so CTRL+A won't help to detect the bug.
Steps to reproduce
1. Install a new fedora distribution. Select US/Dvorak whenever possible.
2. On you fresh fedora, install Gimp and Inkscape
3. On the gnome settings "Regions&Languages", add a new keyboard : "English(US)"
4. Make sure you have the dvorak keyboard selected in gnome.
5. Launch Gimp and Inkscape
6. In gimp press the dvorak CTRL+N. It correspond on CTRL+L on you keyboard if it's print with the qwerty layout. As expected, a new document is (asked to be) created.
7. Do the same step in inkscape, pressing the dvorak CTRL+N. Again, as expected a new document is created.
8. Switch you layout to qwerty using the ibus icon on top right.
9. In gimp, press the qwerty CTRL+N. So I'm speakingt of the keys actually labelled CTRL and N on a qwerty keyboard. As expected, a new document is created.
10. Repeat the same step in inkscape. The scrollbars of the current document appears/disappears, as if we pressed CTRL+B. If the layout was set to dvorak, we would actually press CTRL+B by pressing CTRL and the key labelled N on a keyboard printed with a qwerty keymap.
Note. We already see a chang. of behavior here. Gimp treats CTRL+Key as the current keymap while Inkscape keeps treating them as the original Dvorak keymap.
11. In gimp, press the qwerty CTRL+L, (which correspond to the CTRL+N in dvorak). As expected, the "layers" dialog is selected.
12. Press the same keys in inkscape. Now, a new document is created as if we did press CTRL+N in dvorak.
12. open a terminal and enter `setxkbmap us`.
13. Repeat step 9. Gimp should behaves the same
14. Repeat setp 10. Now inkscape creates a new document, which is the exact same behavior as gimp.
15. Repeat step 11. Gimp should behaves the same.
16. Repeat step 12. Inscape should notify you have to select a path. If you create one and select it, and then doing this step, the path is simplified as if we pressed CTRL+L. The behavior is the same as in gimp.
17. Switch you layout to dvorak using the ibus icon on top right.
18. Type in a terminal. Your input is still qwerty. Ibus is basically not working anymore.
I can reproduce this bug with comment #3.
This problem happens in GNOME only because ibus-ui-gtk3 runs setxkbmap.
gnome-shell -> meta_backend_x11_lock_layout_group() -> XkbLockGroup() seems not to work.
FYI. ibus does not use the xkb group layouts but ibus uses joint layout for non-ascii layout. e.g. "ara,us" , "ru,us" to work Ctrl+C so ibus switches "us" and "ru,us".
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This bug still here (i18n test day)