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Rooting (with or without Magisk) allows you to remove some warts.
Onyx does goofy things with fonts, look at /system/etc/fonts.xml
You can add custom keylayouts where they belong, in /system/usr/keylayout
You can bypass the Onyx short/long keypress processing in /system/framework/framework.jar
You can customize sleep/shutdown images in /system/media
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