Nautilus, Thunar et al. take their information from mimeapps.list files¹.
So the solution is to edit .config/mimeapps.list and/or .local/share/applications/mimeapps.list. Add entries in the [Removed Associations] section like so:
[Removed Associations]
application/xml=firefox.desktop;wine-extension-xml.desktop;
image/png=shutter.desktop;wine-extension-png.desktop;
image/jpeg=shutter.desktop;wine-extension-jpe.desktop;wine-extension-jfif.desktop;
image/svg+xml=shutter.desktop;wine-notepad.desktop;libreoffice-writer.desktop;gitkraken.desktop;gimp.desktop;wine-extension-xml.desktop;yed.desktop;
application/xml=yed.desktop;
Look here for some details.
You might have to do some digging to find the correct .desktop files; note, for instance, that multiple wine-*.desktop files declared the same application for image/jpeg.
- The different
mimeinfo.cache files are populated by update-desktop-database from the .desktop files you have around. I don't know how those relate to mimeapps.list; see here.